U.S. patent application number 10/973919 was filed with the patent office on 2005-10-27 for method for amplifying nucleic acid sequence.
This patent application is currently assigned to TAKARA BIO INC.. Invention is credited to Asada, Kiyozo, Enoki, Tatsuji, Hagiya, Michio, Kato, Ikunoshin, Kobayashi, Eiji, Miyake, Kazue, Moriyama, Mariko, Mukai, Hiroyuki, Sagawa, Hiroaki, Sato, Yoshimi, Sawaragi, Haruhisa, Takeda, Osamu, Tomono, Jun, Uemori, Takashi, Yamamoto, Junko.
Application Number | 20050239100 10/973919 |
Document ID | / |
Family ID | 27551369 |
Filed Date | 2005-10-27 |
United States Patent
Application |
20050239100 |
Kind Code |
A1 |
Mukai, Hiroyuki ; et
al. |
October 27, 2005 |
Method for amplifying nucleic acid sequence
Abstract
A convenient and effective method for amplifying a nucleic acid
sequence characterized by effecting a DNA synthesis reaction in the
presence of chimeric oligonucleotide primers; a method for
supplying a large amount of DNA amplification fragments; an
effective method for amplifying a nucleic acid sequence by
combining the above method with another nucleic acid sequence
amplification method; a method for detecting a nucleic acid
sequence for detecting or quantitating a microorganism such as a
virus, a bacterium, a fungus or a yeast; and a method for detecting
a DNA amplification fragment obtained by the above method in
situ.
Inventors: |
Mukai, Hiroyuki; (Shiga,
JP) ; Sagawa, Hiroaki; (Shiga, JP) ; Uemori,
Takashi; (Shiga, JP) ; Yamamoto, Junko;
(Shiga, JP) ; Tomono, Jun; (Shiga, JP) ;
Kobayashi, Eiji; (Shiga, JP) ; Enoki, Tatsuji;
(Shiga, JP) ; Takeda, Osamu; (Shiga, JP) ;
Miyake, Kazue; (Kyoto, JP) ; Sato, Yoshimi;
(Shiga, JP) ; Moriyama, Mariko; (Kyoto, JP)
; Sawaragi, Haruhisa; (Shiga, JP) ; Hagiya,
Michio; (Shiga, JP) ; Asada, Kiyozo; (Shiga,
JP) ; Kato, Ikunoshin; (Kyoto, JP) |
Correspondence
Address: |
BROWDY AND NEIMARK, P.L.L.C.
624 NINTH STREET, NW
SUITE 300
WASHINGTON
DC
20001-5303
US
|
Assignee: |
TAKARA BIO INC.
Shiga
JP
|
Family ID: |
27551369 |
Appl. No.: |
10/973919 |
Filed: |
October 27, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10973919 |
Oct 27, 2004 |
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09935338 |
Aug 23, 2001 |
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09935338 |
Aug 23, 2001 |
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PCT/JP00/01534 |
Mar 14, 2000 |
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Current U.S.
Class: |
435/6.12 ;
435/91.2 |
Current CPC
Class: |
C12P 19/34 20130101;
C12Q 2525/121 20130101; C12Q 2531/119 20130101; C12Q 2521/301
20130101; C12N 9/1252 20130101; C12Q 1/6853 20130101; C12Q 1/6853
20130101 |
Class at
Publication: |
435/006 ;
435/091.2 |
International
Class: |
C12Q 001/68; C12P
019/34 |
Foreign Application Data
Date |
Code |
Application Number |
Mar 19, 1999 |
JP |
11/076966 |
Dec 27, 1999 |
JP |
11/370035 |
Aug 23, 2000 |
JP |
2000-251981 |
Sep 19, 2000 |
JP |
2000-284419 |
Sep 22, 2000 |
JP |
2000-288750 |
Apr 3, 2001 |
JP |
2001-104191 |
Claims
What is claimed is:
1. A method for amplifying a nucleic acid, characterized in that
the method comprises: (a) preparing a reaction mixture by mixing a
nucleic acid as a template, a deoxyribonucleotide triphosphate, a
DNA polymerase having a strand displacement activity, at least one
primer and an endonuclease that cleaves an extended strand
generated from the primer, wherein the primer is a chimeric
oligonucleotide primer that is substantially complementary to the
nucleotide sequence of the nucleic acid as the template and
contains a ribonucleotide as well as at least one selected from the
group consisting of a deoxyribonucleotide and a nucleotide analog,
the ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer; and (b) incubating the reaction
mixture for a sufficient time to generate a reaction product under
conditions where specific annealing of the primer to the nucleic
acid as the template, an extended strand synthesis reaction and a
strand displacement reaction by the DNA polymerase, and a reaction
of cleaving the extended strand by the endonuclease take place.
2. The method according to claim 1, wherein the reaction mixture is
incubated isothermally.
3. The method according to claim 1, wherein the reaction mixture
further contains another chimeric oligonucleotide primer having a
sequence substantially homologous to the nucleotide sequence of the
nucleic acid as the template.
4. The method according to claim 1, wherein the DNA polymerase is
selected from the group consisting of Klenow fragment of DNA
polymerase I from Escherichia coli, Bst DNA polymerase lacking
5'.fwdarw.3' exonuclease from Bacillus stearothermophilus and Bca
DNA polymerase lacking 5'.fwdarw.3' exonuclease from Bacillus
caldotenax.
5. The method according to claim 1, wherein the endonuclease is an
endoribonuclease.
6. The method according to claim 5, wherein the endoribonuclease is
RNase H.
7. The method according to claim 6, wherein the RNase H is selected
from the group consisting of an RNase H from Escherichia coli, an
RNase H from a bacterium of genus Thermotoga, an RNase H from a
bacterium of genus Thermus, an RNase H from a bacterium of genus
Pyrococcus, an RNase H from a bacterium of genus Archaeoglobus and
an RNase H from a bacterium of genus Bacillus.
8. The method according to claim 1, wherein the DNA polymerase
having a strand displacement activity is Bca DNA polymerase lacking
5'.fwdarw.3' exonuclease from Bacillus caldotenax and the RNase H
as an endonuclease is selected from the group consisting of an
RNase H from Escherichia coli, an RNase H from a bacterium of genus
Pyrococcus and an RNase H from a bacterium of genus
Archaeoglobus.
9. The method according to claim 8, wherein the RNase H is type I
RNase H from Escherichia coli, or type II RNase H from a bacterium
of genus Pyrococcus or a bacterium of genus Archaeoglobus.
10. The method according to claim 1, wherein a DNA polymerase
having an endonuclease activity is used.
11. The method according to claim 10, wherein the DNA polymerase is
Bca DNA polymerase lacking 5'.fwdarw.3' exonuclease from Bacillus
caldotenax and the Bca DNA polymerase is used in the presence of a
substance that allows the endonuclease activity of the Bca DNA
polymerase to express.
12. The method according to claim 11, wherein the substance that
allows the endonuclease activity of the DNA polymerase to express
is a manganese ion.
13. The method according to claim 1, wherein the amplification
reaction is conducted in the presence of a substance that inhibits
the reverse transcription activity of the DNA polymerase.
14. The method according to claim 13, wherein the substance that
inhibits the reverse transcription activity of the DNA polymerase
is phosphonoformic acid.
15. The method according to claim 1, wherein the chimeric
oligonucleotide primer contains two or more successive
ribonucleotide residues.
16. The method according to claim 1, wherein the chimeric
oligonucleotide primer contains one or more modified
ribonucleotide.
17. The method according to claim 16, wherein the chimeric
oligonucleotide primer contains an (.alpha.-S) ribonucleotide in
which the oxygen atom bound to the phosphorous atom at the
.alpha.-position of the ribonucleotide is replaced by a sulfur
atom.
18. The method according to claim 1, wherein a chimeric
oligonucleotide primer represented by general formula below is
used: 5'-dNa-Nb-dNc-3' General formula wherein a is an integer of
11 or more; b is an integer of 1 or more; c is 0 or an integer of 1
or more; dN is an deoxyribonucleotide and/or nucleotide analog; N
is an unmodified ribonucleotide and/or modified ribonucleotide,
wherein some of dNs in dNa may be replaced by Ns, and the
nucleotide at the 3'-terminus may be modified such that extension
from the 3'-terminus by the action of the DNA polymerase does not
take place.
19. The method according to claim 18, wherein c is 0.
20. The method according to claim 18, wherein the nucleotide analog
is deoxyriboinosine nucleotide or deoxyribouracil nucleotide, and
the modified ribonucleotide is (.alpha.-S) ribonucleotide.
21. The method according to claim 18, wherein the nucleic acid
amplification reaction is conducted at a temperature suitable for
the chimeric oligonucleotide primer as defined in claim 18.
22. The method according to claim 1, wherein the chimeric
oligonucleotide primer is at least one chimeric oligonucleotide
primer selected from the group consisting of: a) a chimeric
oligonucleotide primer for detecting enterohemorrhagic Escherichia
coli having a nucleotide sequence selected from the group
consisting of SEQ ID NOS: 43 to 46, 136, 137, 140-142, 153-161,
173, 174, 202, 203, 219 and 220; b) a chimeric oligonucleotide
primer for detecting a viroid having a nucleotide sequence selected
from the group consisting of SEQ ID NOS: 148, 149, 208, 209, 211,
212; c) a chimeric oligonucleotide primer for detecting Clostridium
botulinum having a nucleotide sequence represented by SEQ ID NO:
205 or 206; d) a chimeric oligonucleotide primer for detecting
papilloma virus having a nucleotide sequence represented by SEQ ID
NO: 185 or 186; e) a chimeric oligonucleotide primer for detecting
hepatitis C virus having a nucleotide sequence selected from the
group consisting of SEQ ID NOS: 190, 191, 227, 228, 289 and 290; f)
a chimeric oligonucleotide primer for detecting Staphylococcus
aureus having a nucleotide sequence represented by SEQ ID NO: 225
or 226; g) a chimeric oligonucleotide primer for detecting
Mycobacterium tuberculosis having a nucleotide sequence selected
from the group consisting of SEQ ID NOS: 244, 245, 248 to 251, 283,
284; and h) a chimeric oligonucleotide primer for detecting
Chlamydia having a nucleotide sequence selected from the group
consisting of SEQ ID NOS: 246 and 247.
23. The method according to claim 1, which is conducted in a buffer
that contains a buffering component selected from the group
consisting of Tricine, a phosphate, tris, Bicine and HEPES.
24. The method according claim 1, wherein the nucleic acid as the
template is a single-stranded DNA or a double-stranded DNA.
25. The method according to claim 24, which is conducted after
converting a double-stranded DNA as the template into
single-stranded DNAs.
26. The method according to claim 24, wherein the nucleic acid as
the template is a cDNA obtained from an RNA by a reverse
transcription reaction.
27. The method according to claim 26, which is conducted after
synthesizing a cDNA by a reverse transcription reaction using an
RNA as a template.
28. The method according to claim 27, wherein a primer selected
from the group consisting of an oligo-dT primer, a random primer
and a specific primer is used as a primer for the reverse
transcription reaction.
29. The method according to claim 27, wherein a chimeric
oligonucleotide primer is used as a primer for the reverse
transcription reaction.
30. The method according to claim 27, wherein a DNA polymerase
having a reverse transcriptase activity is used as a reverse
transcriptase.
31. The method according to claim 27, wherein the reverse
transcription reaction and the nucleic acid amplification reaction
are conducted using one DNA polymerase having a reverse
transcriptase activity and a strand displacement activity.
32. The method according to claim 31, wherein the DNA polymerase is
Bst DNA polymerase lacking 5'.fwdarw.3' exonuclease from Bacillus
stearothermophilus or Bca DNA polymerase lacking 5'.fwdarw.3'
exonuclease from Bacillus caldotenax.
33. The method according to claim 26, wherein the RNA as the
template in the reverse transcription reaction is an RNA amplified
by an additional nucleic acid amplification reaction.
34. The method according to claim 33, which is conducted after
synthesizing an amplified RNA fragment by an additional nucleic
acid amplification reaction using an RNA as a template.
35. The method according to claim 33, wherein the additional
nucleic acid amplification reaction is selected from the group
consisting of the transcription-based amplification system (TAS)
method, the self-sustained sequence replication (3SR) method, the
nucleic acid sequence-based amplification (NASBA) method, the
transcription-mediated amplification (TMA) method and the Q.beta.
replicase method.
36. The method according to claim 24, wherein the nucleic acid as
the template is a DNA obtained by an additional nucleic acid
amplification reaction.
37. The method according to claim 36, which is conducted after
synthesizing an amplified DNA fragment by an additional nucleic
acid amplification reaction using an DNA as a template.
38. The method according to claim 36, wherein the additional
nucleic acid amplification reaction is selected from the group
consisting of the polymerase chain reaction (PCR) method, the
ligase chain reaction (LCR) method and the strand displacement
amplification (SDA) method.
39. The method according to claim 33, wherein a random primer or a
degenerate primer is used for the additional nucleic acid
amplification reaction.
40. The method according to claim 39, wherein the random primer or
the degenerate primer is a primer having a random sequence or a
degenerate sequence at least at the 3'-terminus or on the
3'-terminal side.
41. The method according to claim 36, wherein a random primer or a
degenerate primer is used for the additional nucleic acid
amplification reaction.
42. The method according to claim 41, wherein the random primer or
the degenerate primer is a primer having a random sequence or a
degenerate sequence at least at the 3'-terminus or on the
3'-terminal side.
43. The method according to claim 1, wherein the length of the
region of the nucleic acid to be amplified is 200 bp or
shorter.
44. The method according to claim 1, which comprises annealing the
nucleic acid as the template to the chimeric oligonucleotide primer
that is substantially complementary to the nucleotide sequence of
the nucleic acid in an annealing solution containing a substance
that enhances the annealing of the nucleic acid to the primer.
45. The method according to claim 44, wherein the annealing
solution contains spermidine and/or propylenediamine.
46. The method according to claim 44, wherein the annealing is
conducted by incubating the annealing solution containing the
nucleic acid as the template and the chimeric oligonucleotide
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid at 90.degree. C. or above and then
cooling the solution to a temperature at which the amplification
reaction is conducted or below.
47. The method according to claim 1, wherein the nucleic acid
amplification reaction is conducted in the presence of a
deoxyribonucleotide triphosphate analog.
48. The method according to claim 47, wherein the
deoxyribonucleotide triphosphate analog is deoxyuridine
triphosphate or a derivative thereof.
49. The method according to claim 1, wherein a template switching
reaction is effected.
50. The method according to claim 1, which further comprises a step
of duplicating a DNA or an RNA containing a sequence to be
amplified to prepare a nucleic acid as a template prior to step
(a), wherein the duplicated nucleic acid is used in step (a) as a
nucleic acid as a template.
51. A method for producing a nucleic acid in large quantities,
characterized in that the method comprises: (a) amplifying a
nucleic acid by the method defined by claim 1; and (b) collecting
the nucleic acid amplified in step (a).
52. A method for detecting a target nucleic acid in a sample,
characterized in that the method comprises: (a) amplifying a target
nucleic acid by the method defined by claim 1; and (b) detecting
the target nucleic acid amplified in step (a).
53. The method according to claim 52, which comprises detecting the
amplified nucleic acid using a probe for detection.
54. The method according to claim 53, wherein the probe for
detection is a probe that has been labeled with a labeling
substance.
55. The method according to claim 54, wherein the probe is an RNA
probe labeled with two or more fluorescent substances positioned at
a distance that results in a quenching state.
56. The method according to claim 53, wherein the probe is a probe
which hybridizes to a region amplified using at least one chimeric
oligonucleotide primer selected from the group consisting of: a) a
chimeric oligonucleotide primer for detecting enterohemorrhagic
Escherichia coli having a nucleotide sequence selected from the
group consisting of SEQ ID NOS: 43 to 46, 136, 137, 140-142,
153-161, 173, 174, 202, 203, 219 and 220; b) a chimeric
oligonucleotide primer for detecting a viroid having a nucleotide
sequence selected from the group consisting of SEQ ID NOS: 148,
149, 208, 209, 211 and 212; c) a chimeric oligonucleotide primer
for detecting Clostridium botulinum having a nucleotide sequence
represented by SEQ ID NO: 205 or 206; d) a chimeric oligonucleotide
primer for detecting papilloma virus having a nucleotide sequence
represented by SEQ ID NO: 185 or 186; e) a chimeric oligonucleotide
primer for detecting hepatitis C virus having a nucleotide sequence
selected from the group consisting of SEQ ID NOS: 190, 191, 227,
228, 289 and 290; f) a chimeric oligonucleotide primer for
detecting Staphylococcus aureus having a nucleotide sequence
represented by SEQ ID NO: 225 or 226; g) a chimeric oligonucleotide
primer for detecting Mycobacterium tuberculosis having a nucleotide
sequence selected from the group consisting of SEQ ID NOS: 244,
245, 248 to 251, 283, 284; and h) a chimeric oligonucleotide primer
for detecting Chlamydia having a nucleotide sequence selected from
the group consisting of SEQ ID NOS: 246 or 247.
57. A method for determining a nucleotide sequence of a nucleic
acid, characterized in that the method comprises: (a) amplifying a
nucleic acid by the method defined by claim 1; and (b) determining
the nucleotide sequence of the nucleic acid amplified in step
(a).
58. A method for preparing a single-stranded nucleic acid, the
method comprising generating a single-stranded nucleic acid using
the method defined by claim 1.
59. The method according to claim 58, wherein at least two primers
at different concentrations are used.
60. A method for amplifying a nucleotide sequence, characterized in
that the method comprises: (a) treating a nucleic acid as a
template with at least one primer that is substantially
complementary to the nucleotide sequence of the nucleic acid and a
DNA polymerase to synthesize a primer-extended strand that is
complementary to the template, wherein the primer is a chimeric
oligonucleotide primer containing a deoxyribonucleotide and a
ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer; (b) cleaving
the primer-extended strand of a double-stranded nucleic acid
obtained in step (a) with an endonuclease at a site that contains
the ribonucleotide; and (c) extending a nucleotide sequence that is
complementary to the template using a DNA polymerase having a
strand displacement activity from the 3'-terminus of the primer
portion of the double-stranded nucleic acid in which the
primer-extended strand is cleaved obtained in step (b) to effect a
strand displacement.
61. A method for amplifying a nucleotide sequence using at least
two primers, characterized in that the method comprises: (a)
treating a nucleic acid as a template with at least one primer that
is substantially complementary to the nucleotide sequence of the
nucleic acid and a DNA polymerase to synthesize a primer-extended
strand that is complementary to the template, wherein the primer is
a chimeric oligonucleotide primer containing a deoxyribonucleotide
and a ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer; (b) cleaving
the primer-extended strand of a double-stranded nucleic acid
obtained in step (a) with an endonuclease at a site that contains
the ribonucleotide; (c) extending a nucleotide sequence that is
complementary to the template using a DNA polymerase having a
strand displacement activity from the 3'-terminus of the primer
portion of the double-stranded nucleic acid in which the
primer-extended strand is cleaved obtained in step (b) to effect a
strand displacement, wherein a double-stranded nucleic acid
containing a regenerated primer-extended strand is reused in step
(b); (d) treating a released displaced strand obtained in step (c)
as a template with at least one primer that is different from that
used in step (a) and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the displaced
strand, wherein the primer that is different from that used in step
(a) is a chimeric oligonucleotide primer that is substantially
complementary to the nucleotide sequence of the displaced strand
and contains a deoxyribonucleotide and a ribonucleotide, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer; (e) cleaving the primer-extended
strand of a double-stranded nucleic acid obtained in step (d) with
an endonuclease at a site that contains the ribonucleotide; and (f)
extending a nucleotide sequence that is complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (e) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (e).
62. A method for amplifying a nucleic acid, characterized in that
the method comprises: (a) treating a nucleic acid as a template
with at least one primer that is substantially complementary to the
nucleotide sequence of the nucleic acid and a DNA polymerase to
synthesize a primer-extended strand that is complementary to the
template and synthesize a double-stranded nucleic acid, wherein the
primer is a chimeric oligonucleotide primer containing a
ribonucleotide as well as at least one selected from the group
consisting of a deoxyribonucleotide and a nucleotide analog, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer; (b) extending a nucleic acid that
is complementary to the double-stranded nucleic acid as a template
obtained in the previous step using a DNA polymerase having a
strand displacement activity in the presence of an RNase H to
effect a strand displacement and synthesize a displaced strand and
a double-stranded nucleic acid; and (c) reusing in step (b) the
double-stranded nucleic acid obtained in step (b) as a
template.
63. The method according to claim 62, wherein the DNA polymerase in
step (a) is different from the DNA polymerase having a strand
displacement activity in step (b).
64. A method for amplifying a nucleic acid using at least two
primers, characterized in that the method comprises: (a) treating a
nucleic acid as a template with at least one primer that is
substantially complementary to the nucleotide sequence of the
nucleic acid and a DNA polymerase to synthesize a primer-extended
strand that is complementary to the template, wherein the primer is
a chimeric oligonucleotide primer containing a ribonucleotide as
well as at least one selected from the group consisting of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer; (b) extending a nucleic acid that is complementary to
the double-stranded nucleic acid as a template obtained in the
previous step using a DNA polymerase having a strand displacement
activity in the presence of an RNase H to effect a strand
displacement and synthesize a displaced strand and a
double-stranded nucleic acid; (c) reusing in step (b) the
double-stranded nucleic acid obtained in step (b) as a template;
(d) treating a displaced strand obtained in step (b) as a template
with at least one primer that is different from that used in step
(a) and a DNA polymerase to synthesize a primer-extended strand
that is complementary to the displaced strand, wherein the primer
that is different from that used in step (a) is a chimeric
oligonucleotide primer that is substantially complementary to the
nucleotide sequence of the displaced strand and contains a
ribonucleotide as well as at least one selected from the group
consisting of a deoxyribonucleotide and a nucleotide analog, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer; (e) extending a nucleic acid that
is complementary to the double-stranded nucleic acid as a template
obtained in the previous step using a DNA polymerase having a
strand displacement activity in the presence of an RNase H to
effect a strand displacement and synthesize a displaced strand and
a double-stranded nucleic acid; and (f) reusing in step (e) the
double-stranded nucleic acid obtained in step (e) as a
template.
65. The method according to claim 64, wherein the DNA polymerase in
steps (a) and (d) is different from the DNA polymerase having a
strand displacement activity in steps (b) and (f).
66. A method for amplifying a nucleic acid, characterized in that
the method comprises: (a) treating a double-stranded nucleic acid
as a template with two primers that are substantially complementary
to the nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisting of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer; (b) cleaving the sites that contain the ribonucleotide
of the double-stranded nucleic acid consisting of the
primer-extended strands obtained in step (a) with the endonuclease;
and (c) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid in which the primer-extended
strands are cleaved obtained in step (b) to effect strand
displacements and obtain a double-stranded nucleic acid consisting
of the template and the primer-extended strand.
67. A method for amplifying a nucleic acid, characterized in that
the method comprises: (a) treating a double-stranded nucleic acid
as a template with two primers that are substantially complementary
to the nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisting of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer; (b) cleaving the sites that contain the ribonucleotide
of the double-stranded nucleic acid consisting of the
primer-extended strands obtained in step (a) with the endonuclease;
and (c) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid in which the primer-extended
strands are cleaved obtained in step (b) to effect strand
displacements and obtain a double-stranded nucleic acid consisting
of the primer-extended strands being annealed each other.
68. A method for amplifying a nucleic acid, characterized in that
the method comprises: (a) treating a double-stranded nucleic acid
as a template with two primers that are substantially complementary
to the nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisting of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer; (b) cleaving the sites that contain the ribonucleotide
of the double-stranded nucleic acid consisting of the
primer-extended strands obtained in step (a) with the endonuclease;
(c) extending nucleic acids that are complementary to the template
using a DNA polymerase having a strand displacement activity from
the 3'-termini of the respective primer portions of the
double-stranded nucleic acid in which the primer-extended strands
are cleaved obtained in step (b) to effect strand displacements and
obtain a double-stranded nucleic acid consisting of the
primer-extended strands being annealed each other and a
double-stranded nucleic acid consisting of the templates being
annealed each other to which the two primers in step (a) are
annealed; (d) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid to which the two primers are
annealed obtained in step (c) to effect strand displacements and
obtain a double-stranded nucleic acid consisting of the
primer-extended strands being annealed each other and a
double-stranded nucleic acid consisting of the templates being
annealed each other to which the two primers in step (a) are
annealed; and (e) reusing in step (d) the double-stranded nucleic
acid to which the two primers are annealed obtained in step
(d).
69. A method for amplifying a nucleic acid, characterized in that
the method comprises: (a) treating a double-stranded nucleic acid
as a template with two primers that are substantially complementary
to the nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisting of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer; (b) cleaving the sites that contain the ribonucleotide
of the double-stranded nucleic acid consisting of the
primer-extended strands obtained in step (a) with the endonuclease;
(c) extending nucleic acids that are complementary to the template
using a DNA polymerase having a strand displacement activity from
the 3'-termini of the respective primer portions of the
double-stranded nucleic acid in which the primer-extended strands
are cleaved obtained in step (b) to effect strand displacements and
obtain a double-stranded nucleic acid consisting of the
primer-extended strands being annealed each other and a
double-stranded nucleic acid consisting of the templates being
annealed each other to which the two primers in step (a) are
annealed; (d) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid to which the two primers are
annealed obtained in step (c) to effect strand displacements and
obtain a double-stranded nucleic acid consisting of the template
and the primer-extended strand; (e) cleaving the sites that contain
the ribonucleotide of the double-stranded nucleic acid consisting
of the template and the primer-extended strand obtained in step (d)
with the endonuclease; and (f) extending a nucleic acid that is
complementary to the template using a DNA polymerase having a
strand displacement activity from the 3'-terminus of the primer
portion of the double-stranded nucleic acid in which the
primer-extended strand is cleaved obtained in step (e) to
synthesize a displaced strand.
70. The method according to claim 60, wherein step (b) and step (c)
are sequentially repeated.
71. The method according to claim 60, wherein the DNA polymerase in
step (a) is different from the DNA polymerase having a strand
displacement activity in step (c).
72. The method according to claim 61, wherein one DNA polymerase
having a strand displacement activity is used.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This is continuation of co-pending application Ser. No.
09/935,338, filed Aug. 23, 2001, which itself is a
continuation-in-part application of PCT international application
No. PCT/JP00/01534 filed Mar. 14, 2000, which designated the United
States, the entire contents of which are incorporated by
reference.
BACKGROUND OF THE INVENTION
[0002] 1. Field of the Invention
[0003] The present invention relates to a method for detecting a
target nucleic acid which is useful in a field of clinical medicine
and a method for synthesizing a DNA which is useful in a field of
genetic engineering. It relates to a method for amplifying a
nucleic acid as a template and a method for detecting a target
nucleic acid amplified by said method.
[0004] 2. Description of Related Art
[0005] DNA synthesis is used for various purposes in studies in a
field of genetic engineering. Most of the DNA synthesis with the
exception of that of a short-chain DNA such as an oligonucleotide
is carried out by enzymatic methods in which a DNA polymerase is
utilized. An example of the methods is the polymerase chain
reaction (PCR) method as described in U.S. Pat. Nos. 4,683,195,
4,683,202 and 4,800,159 in detail. Another example is the reverse
transcription-PCR (RT-PCR) method, which is a combination of the
PCR and a reverse transcriptase reaction, as described in Trends in
Biotechnology, 10:146-152 (1992). The development of the
above-mentioned methods has enabled the amplification of a region
of interest from a DNA or an RNA.
[0006] The above-mentioned DNA synthesis methods are conducted, for
example, using a reaction that consists of three steps. The three
steps are a step of dissociating (denaturing) a double-stranded DNA
into single-stranded DNAs, a step of annealing a primer to the
single-stranded DNA and a step of synthesizing (extending) a
complementary strand from the primer in order to amplify a region
of a DNA of interest. Alternatively, they are conducted using a
reaction designated as "the shuttle PCR" ("PCR no saizensen"
(Recent advances in PCR methodology: Basic methodology and it's
application), Tanpakushitsu Kakusan Kouso, Bessatsu, (Protein,
Nucleic Acid and Enzyme, Supplement), 41(5):425-428 (1996)) in
which two of the three steps, that is, the step of annealing the
primer and the step of extending are carried out at the same
temperature.
[0007] Alternatively, the ligase chain reaction (LCR) method as
described in EP 320,308 published on Jun. 14, 1989 or the
transcription-based amplification system (TAS) method as described
in PCR Protocols, Academic Press Inc., 1990, pp. 245-252 may be
used. The four methods as mentioned above require repeating a
reaction at a high temperature and that at a low temperature
several times in order to regenerate a single-stranded target
molecule for the next amplification cycle. The reaction system
should be conducted using discontinuous phases or cycles because
the reaction is restricted by temperature as described above.
[0008] Thus, the methods require the use of an expensive thermal
cycler that can strictly adjust a wide range of temperature over
time. Furthermore, the reaction requires time for adjusting the
temperature to the two or three predetermined ones. The loss of
time increases in proportion to the cycle number.
[0009] Nucleic acid amplification methods that can be carried out
isothermally have been developed in order to solve the problems.
Examples thereof include the strand displacement amplification
(SDA) method as described in JP-B 7-114718, the self-sustained
sequence replication (3SR) method, the nucleic acid sequence based
amplification (NASBA) method as described in Japanese Patent No.
2650159, the transcription-mediated amplification (TMA) method, the
Q.beta. replicase method as described in Japanese Patent No.
2710159 and the various modified SDA methods as described in U.S.
Pat. No. 5,824,517, WO 99/09211, WO 95/25180 and WO 99/49081. A
method of isothermal enzymatic synthesis of an oligonucleotide is
described in U.S. Pat. No. 5,916,777. Extension from a primer
and/or annealing of a primer to a single-stranded extension product
(or to an original target sequence) followed by extension from the
primer take place in parallel in a reaction mixture incubated at a
constant temperature in the reaction of these methods of isothermal
nucleic acid amplification or synthesis of an oligonucleotide.
[0010] Among the isothermal nucleic acid amplification methods, the
SDA method is an example of systems in which a DNA is finally
amplified. The SDA method is a method for amplifying a target
nucleic acid sequence (and a complementary strand thereof) in a
sample by displacement of double strands using a DNA polymerase and
a restriction endonuclease. The method requires four primers used
for the amplification, two of which should be designed to contain a
recognition site for the restriction endonuclease. The method
requires the use of a modified deoxyribonucleotide triphosphate as
a substrate for DNA synthesis in large quantities. An example of
the modified deoxyribonucleotide triphosphates is an (.alpha.-S)
deoxyribonucleotide triphosphate in which the oxygen atom of the
phosphate group at the .alpha.-position is replaced by a sulfur
atom (S). The problem of running cost associated with the use of
the modified deoxyribonucleotide triphosphate becomes serious if
the reaction is routinely conducted, for example, for genetic test.
Furthermore, the incorporation of the modified nucleotide such as
the (.alpha.-S) deoxyribonucleotide into the amplified DNA fragment
in the method may abolish the cleavability of the amplified DNA
fragment with a restriction enzyme, for example, when it is
subjected to a restriction enzyme fragment length polymorphism
(RFLP) analysis.
[0011] The modified SDA method as described in U.S. Pat. No.
5,824,517 is a DNA amplification method that uses a chimeric primer
that is composed of an RNA and a DNA and has as an essential
element a structure in which DNA is positioned at least at the
3'-terminus. The modified SDA method as described in WO 99/09211
requires the use of a restriction enzyme that generates a
3'-protruding end. The modified SDA method as described in WO
95/25180 requires the use of at least two pairs of primers. The
modified SDA method as described in WO 99/49081 requires the use of
at least two pairs of primers and at least one modified
deoxyribonucleotide triphosphate. On the other hand, the method for
synthesizing an oligonucleotide as described in U.S. Pat. No.
5,916,777 comprises synthesizing a DNA using a primer having a
ribonucleotide at the 3'-terminus, completing a reaction using the
primer, introducing a nick between the primer and an extended
strand in an primer-extended strand with an endonuclease to
separate them, digesting a template and recovering the primer to
reuse it. It is required to isolate the primer from the reaction
system and then anneal it to the template again in order to reuse
the primer in the method. Additionally, the LAMP (Loop-mediated
Isothermal Amplification) method as described in WO 00/28082
requires four primers for amplification and the products amplified
using the method are DNAs having varying size in which the target
regions for the amplification are repeated.
[0012] As described above, the conventional isothermal nucleic acid
amplification methods still have various problems. Thus, a method
for amplifying a nucleic acid at low running cost by which a DNA
fragment that can be further genetically engineered is obtained has
been desired.
[0013] The main object of the present invention is to provide a
method for amplifying a target nucleic acid which specifically
amplifies with high sensitivity a target nucleic acid in a sample
by DNA synthesis reaction using a chimeric oligonucleotide primer,
a method for detecting a amplified fragment obtained by said
method, a method for producing a target nucleic acid using said
amplification method and a chimeric oligonucleotide primer used for
these methods.
SUMMARY OF THE INVENTION
[0014] As a result of intensive studies, the present inventors have
constructed an excellent system for gene amplification reaction.
The construction was accomplished by developing a method in which a
region of a DNA of interest is amplified in the presence of a
chimeric oligonucleotide primer having a ribonucleotide positioned
at the 3'-terminus or on the 3'-terminal side, an endonuclease and
a DNA polymerase. Thus, the present invention has been completed.
The method is a method for amplifying a nucleic acid in which a
chimeric oligonucleotide primer is used and herein referred to as
ICAN (Isothermal and Chimeric primer-initiated Amplification of
Nucleic acids) method.
[0015] The first invention of the present invention relates to a
method for amplifying a nucleotide sequence, characterized in that
the method comprises:
[0016] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer for cleavage with an endonuclease;
[0017] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with the endonuclease at a site
that contains the ribonucleotide; and
[0018] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement.
[0019] The second invention of the present invention relates to a
method for amplifying a nucleotide sequence using at least two
primers, characterized in that the method comprises:
[0020] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer for cleavage with an endonuclease;
[0021] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with the endonuclease at a site
that contains the ribonucleotide;
[0022] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (b);
[0023] (d) treating a released displaced strand obtained in step
(c) as a template with at least one primer that is different from
that used in step (a) and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the displaced
strand, wherein the primer that is different from that used in step
(a) is a chimeric oligonucleotide primer that is substantially
complementary to the nucleotide sequence of the displaced strand
and contains a deoxyribonucleotide and a ribonucleotide, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer for cleavage with an
endonuclease;
[0024] (e) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (d) with the endonuclease at a site
that contains the ribonucleotide; and
[0025] (f) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (e) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (e).
[0026] The method of the first and second inventions of the present
invention may be conducted isothermally. The nucleotide sequence as
the template may be a DNA sequence. A step of preparing a
single-stranded cDNA by a reverse transcription reaction using
reverse transcriptase and an RNA as a template may be comprised
prior to step (a) of the first and second inventions. The
single-stranded cDNA may be used as the nucleotide sequence as the
template. Both of a single-stranded DNA and a double-stranded DNA
can be preferably used as the DNA as the template in the first and
second inventions of the present inventions. If a double-stranded
DNA is used as the template, the method of the present invention
may be conducted after a pretreatment step of denaturing the
double-stranded DNA into single-stranded DNAs.
[0027] In the above-mentioned inventions, the extension from the
primer is conducted using a DNA polymerase having a strand
displacement activity. A DNA polymerase selected from the group
consisting of Klenow fragment of DNA polymerase I from Escherichia
coli, Bst DNA polymerase lacking 5'3' exonuclease from Bacillus
stearothermophilus and Bca DNA polymerase lacking 5'3' exonuclease
from Bacillus caldotenax can be preferably used in the present
invention. Additionally, an endoribonuclease can be preferably used
as the endonuclease. The endoribonuclease that can be used include,
but are not limited to, RNase H, for example.
[0028] The third invention of the present invention relates to a
method for amplifying a nucleotide sequence, characterized in that
the method comprises:
[0029] (a) preparing a reaction mixture by mixing a nucleic acid as
a template, a deoxyribonucleotide triphosphate, a DNA polymerase
having a strand displacement activity, at least one primer and an
endonuclease that cleaves an extended strand generated from the
primer, wherein the primer is a chimeric oligonucleotide primer
that is substantially complementary to the nucleotide sequence of
the nucleic acid as the template and contains a deoxyribonucleotide
and a ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer for cleavage
with the endonuclease; and
[0030] (b) incubating the reaction mixture for a sufficient time to
generate a reaction product.
[0031] Examples of the nucleotide sequences as the templates that
can be used in the third invention include a nucleotide sequence
selected from the group consisting of a single-stranded DNA, a
double-stranded DNA denatured into single-stranded DNAs and a cDNA
obtained by a reverse transcription reaction from an RNA. Two or
more chimeric oligonucleotide primers may be contained in the
reaction mixture. The DNA polymerase having a strand displacement
activity and the endonuclease used in the first and second
inventions can be preferably used in this invention.
[0032] The primer used in the first to third inventions of the
present invention is a chimeric oligonucleotide primer. For
example, a chimeric oligonucleotide having a structure in which at
least one, preferably two or more successive ribonucleotide
residues are attached at the 3'-terminus or on the 3'-terminal side
of the primer can be used.
[0033] The template used in the first to third inventions of the
present invention may be a nucleic acid that is amplified
beforehand by a nucleic acid amplification method. For example, the
TAS method, the 3SR method, the NASBA method, the TMA method, the
Q.beta. replicase method, the PCR method, the LCR method and the
SDA method can be utilized as the nucleic acid amplification method
although any methods for amplifying a nucleic acid can be used
without limitation. The method of the present invention can be used
in combination with these nucleic acid amplification methods.
[0034] A random primer or a degenerate primer can be used in the
nucleic acid amplification reaction. For example, without
limitation, a primer having a random sequence or a degenerate
sequence at least at the 3'-terminus or on the 3'-terminal side can
be preferably used.
[0035] The fourth invention of the present invention relates to a
chimeric oligonucleotide primer that can be used for the first to
third inventions. The primer is characterized in that it contains a
deoxyribonucleotide and a ribonucleotide and has a structure in
which the ribonucleotide is position at the 3'-terminus or on the
3'-terminal side of the primer. For example, a chimeric
oligonucleotide primer that contains at least one, preferably two
or more successive ribonucleotide residues and enables the
extension of a DNA strand from the 3'-terminus thereof may be used.
Such a primer is designed such that it is cleaved by the action of
a ribonuclease such as RNase H at the 3'-terminus of the
ribonucleotide residue.
[0036] The fifth invention of the present invention relates to a
DNA polymerase having a strand displacement activity, an
endonuclease, and a kit that contains them used for the first to
third inventions.
[0037] The sixth invention of the present invention relates to a
method for detecting a target nucleic acid, characterized in that
the method comprises amplifying a target nucleic acid by the method
for amplifying a nucleotide sequence of the first to third
inventions of the present invention and then detecting the nucleic
acid. The methods of detection include a method in which the target
nucleic acid is detected using a ribonucleotide (RNA) probe labeled
with two or more fluorescent dyes positioned at a distance that
results in a quenching state.
[0038] The seventh invention of the present invention relates to a
DNA polymerase having a strand displacement activity, an
endonuclease and a kit that contains them used for the method for
detecting a target nucleic acid of the sixth invention of the
present invention.
[0039] The eighth invention of the present invention relates to a
method for producing a material having an immobilized nucleic acid
in which the nucleic acid is arrayed in a predefined region,
characterized in that the method comprises arraying and
immobilizing the nucleic acid amplified by the method for
amplifying a nucleotide sequence of the first to third inventions
of the present invention in a predefined region on a substrate. A
method in which a single-stranded nucleic acid substantially free
of a complementary strand thereto is amplified, and arrayed and
immobilized in the predefined region is particularly
preferable.
[0040] The ninth invention of the present invention relates to a
material having an immobilized nucleic acid in which the nucleic
acid is arrayed in a predefined region produced by the method of
the eighth invention of the present invention. A material having an
immobilized nucleic acid in which a single-stranded nucleic acid
substantially free of a complementary strand thereto is arrayed and
immobilized in the predefined region is particularly
preferable.
[0041] The tenth invention of the present invention relates to a
method for detecting a target nucleic acid in a sample,
characterized in that the method uses the material having an
immobilized nucleic acid in which the nucleic acid is arrayed in a
predefined region of the ninth invention of the present invention
to detect a nucleic acid that hybridizes with the nucleic acid
arrayed and immobilized in the predefined region on the
material.
[0042] The eleventh invention of the present invention relates to a
method for producing a nucleic acid in large quantities,
characterized in that the method comprises:
[0043] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer for cleavage with an endonuclease;
[0044] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with the endonuclease at a site
that contains the ribonucleotide; and
[0045] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement.
[0046] The twelfth invention of the present invention relates to a
method for producing a nucleic acid in large quantities using at
least two primers, characterized in that the method comprises:
[0047] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer for cleavage with an endonuclease;
[0048] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with the endonuclease at a site
that contains the ribonucleotide;
[0049] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (b);
[0050] (d) treating a released displaced strand obtained in step
(c) as a template with at least one primer that is different from
that used in step (a) and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the displaced
strand, wherein the primer that is different from that used in step
(a) is a chimeric oligonucleotide primer that is substantially
complementary to the nucleotide sequence of the displaced strand
and contains a deoxyribonucleotide and a ribonucleotide, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer for cleavage with an
endonuclease;
[0051] (e) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (d) with the endonuclease at a site
that contains the ribonucleotide; and
[0052] (f) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (e) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (e).
[0053] The thirteenth invention of the present invention relates to
a method for producing a nucleic acid in large quantities,
characterized in that the method comprises:
[0054] (a) preparing a reaction mixture by mixing a nucleic acid as
a template, a deoxyribonucleotide triphosphate, a DNA polymerase
having a strand displacement activity, at least one primer and an
endonuclease that cleaves an extended strand generated from the
primer, wherein the primer is a chimeric oligonucleotide primer
that is substantially complementary to the nucleotide sequence of
the nucleic acid as the template and contains a deoxyribonucleotide
and a ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer for cleavage
with the endonuclease; and
[0055] (b) incubating the reaction mixture for a sufficient time to
generate a reaction product.
[0056] The fourteenth invention of the present invention relates to
a method for amplifying a nucleotide sequence, characterized in
that the method comprises:
[0057] (a) amplifying a nucleic acid containing a sequence to be
amplified by a nucleic acid amplification reaction to prepare a
nucleic acid as a template;
[0058] (b) treating the nucleic acid as the template obtained in
step (a) with at least one primer that is substantially
complementary to the nucleotide sequence of the nucleic acid and a
DNA polymerase to synthesize a primer-extended strand that is
complementary to the template, wherein the primer is a chimeric
oligonucleotide primer containing a deoxyribonucleotide and a
ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer for cleavage
with an endonuclease;
[0059] (c) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (b) with the endonuclease at a site
that contains the ribonucleotide; and
[0060] (d) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (c) to effect a strand displacement.
[0061] The fifteenth invention of the present invention relates to
a method for amplifying a nucleotide sequence using at least two
primers, characterized in that the method comprises:
[0062] (a) amplifying a nucleic acid containing a sequence to be
amplified by a nucleic acid amplification reaction to prepare a
nucleic acid as a template;
[0063] (b) treating the nucleic acid as the template obtained in
step (a) with at least one primer that is substantially
complementary to the nucleotide sequence of the nucleic acid and a
DNA polymerase to synthesize a primer-extended strand that is
complementary to the template, wherein the primer is a chimeric
oligonucleotide primer containing a deoxyribonucleotide and a
ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer for cleavage
with an endonuclease;
[0064] (c) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (b) with the endonuclease at a site
that contains the ribonucleotide;
[0065] (d) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (c) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (c);
[0066] (e) treating a released displaced strand obtained in step
(d) as a template with at least one primer that is different from
that used in step (b) and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the displaced
strand, wherein the primer that is different from that used in step
(b) is a chimeric oligonucleotide primer that is substantially
complementary to the nucleotide sequence of the displaced strand
and contains a deoxyribonucleotide and a ribonucleotide, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer for cleavage with an
endonuclease;
[0067] (f) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (e) with the endonuclease at a site
that contains the ribonucleotide; and
[0068] (g) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (f) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (f).
[0069] The sixteenth invention of the present invention relates to
a method for amplifying a nucleotide sequence, characterized in
that the method comprises:
[0070] (a) amplifying a nucleic acid containing a sequence to be
amplified by a nucleic acid amplification reaction to prepare a
nucleic acid as a template;
[0071] (b) preparing a reaction mixture by mixing the nucleic acid
as the template obtained in step (a), a deoxyribonucleotide
triphosphate, a DNA polymerase having a strand displacement
activity, at least one primer and an endonuclease that cleaves an
extended strand generated from the primer, wherein the primer is a
chimeric oligonucleotide primer that is substantially complementary
to the nucleotide sequence of the nucleic acid as the template and
contains a deoxyribonucleotide and a ribonucleotide, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer for cleavage with the endonuclease;
and
[0072] (c) incubating the reaction mixture for a sufficient time to
generate a reaction product.
[0073] In the fourteenth to sixteenth inventions of the present
invention, a nucleic acid containing a sequence to be amplified is
amplified beforehand by a nucleic acid amplification reaction. The
amplification product is then used as a nucleic acid as a template
in the method of the first to third inventions of the present
invention. For example, the TAS method, the 3SR method, the NASBA
method, the TMA method, the Q.beta. replicase method, the PCR
method, the LCR method and the SDA method can be used as the
nucleic acid amplification method used in the fourteenth to
sixteenth inventions although any methods for amplifying a nucleic
acid can be used without limitation.
[0074] A random primer or a degenerate primer can be used in the
nucleic acid amplification reaction. For example, without
limitation, a primer having a random sequence or a degenerate
sequence at least at the 3'-terminus or on the 3'-terminal side can
be preferably used.
[0075] The seventeenth invention of the present invention relates
to a method for amplifying a nucleotide sequence, characterized in
that the method comprises:
[0076] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0077] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with an endonuclease at a site
that contains the ribonucleotide; and
[0078] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement.
[0079] The eighteenth invention of the present invention relates to
a method for amplifying a nucleotide sequence using at least two
primers, characterized in that the method comprises:
[0080] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0081] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with an endonuclease at a site
that contains the ribonucleotide;
[0082] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (b);
[0083] (d) treating a released displaced strand obtained in step
(c) as a template with at least one primer that is different from
that used in step (a) and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the displaced
strand, wherein the primer that is different from that used in step
(a) is a chimeric oligonucleotide primer that is substantially
complementary to the nucleotide sequence of the displaced strand
and contains a deoxyribonucleotide and a ribonucleotide, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer;
[0084] (e) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (d) with an endonuclease at a site
that contains the ribonucleotide; and
[0085] (f) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (e) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (e).
[0086] The nineteenth invention of the present invention relates to
a method for amplifying a nucleotide sequence, characterized in
that the method comprises:
[0087] (a) preparing a reaction mixture by mixing a nucleic acid as
a template, a deoxyribonucleotide triphosphate, a DNA polymerase
having a strand displacement activity, at least one primer and an
endonuclease that cleaves an extended strand generated from the
primer, wherein the primer is a chimeric oligonucleotide primer
that is substantially complementary to the nucleotide sequence of
the nucleic acid as the template and contains a deoxyribonucleotide
and a ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer; and
[0088] (b) incubating the reaction mixture for a sufficient time to
generate a reaction product.
[0089] The twentieth invention of the present invention relates to
a method for amplifying a nucleotide sequence, characterized in
that the method comprises:
[0090] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer, wherein an endonuclease cleaves at a site that contains
the ribonucleotide;
[0091] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with the endonuclease at the site
that contains the ribonucleotide; and
[0092] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement.
[0093] The twenty-first invention of the present invention relates
to a method for amplifying a nucleotide sequence using at least two
primers, characterized in that the method comprises:
[0094] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a deoxyribonucleotide and a ribonucleotide, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer, wherein an endonuclease cleaves at a site that contains
the ribonucleotide;
[0095] (b) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (a) with the endonuclease at the site
that contains the ribonucleotide;
[0096] (c) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (b) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (b);
[0097] (d) treating a released displaced strand obtained in step
(c) as a template with at least one primer that is different from
that used in step (a) and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the displaced
strand, wherein the primer that is different from that used in step
(a) is a chimeric oligonucleotide primer that is substantially
complementary to the nucleotide sequence of the displaced strand
and contains a deoxyribonucleotide and a ribonucleotide, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer, wherein an endonuclease cleaves at
a site that contains the ribonucleotide;
[0098] (e) cleaving the primer-extended strand of a double-stranded
nucleic acid obtained in step (d) with the endonuclease at the site
that contains the ribonucleotide; and
[0099] (f) extending a nucleotide sequence that is complementary to
the template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (e) to effect a strand displacement,
wherein a double-stranded nucleic acid containing a regenerated
primer-extended strand is reused in step (e).
[0100] The twenty-second invention of the present invention relates
to a method for amplifying a nucleotide sequence, characterized in
that the method comprises:
[0101] (a) preparing a reaction mixture by mixing a nucleic acid as
a template, a deoxyribonucleotide triphosphate, a DNA polymerase
having a strand displacement activity, at least one primer and an
endonuclease that cleaves an extended strand generated from the
primer, wherein the primer is a chimeric oligonucleotide primer
that is substantially complementary to the nucleotide sequence of
the nucleic acid as the template and contains a deoxyribonucleotide
and a ribonucleotide, the ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the primer, wherein the
endonuclease cleaves at a site that contains the ribonucleotide;
and
[0102] (b) incubating the reaction mixture for a sufficient time to
generate a reaction product.
[0103] The twenty-third invention of the present invention relates
to a method for determining a nucleotide sequence of a nucleic
acid, characterized in that the method comprises amplifying a
nucleotide sequence according to the method of any one of the first
to third and fourteenth to twenty-second inventions.
[0104] The twenty-fourth invention of the present invention relates
to a method for amplifying a target nucleic acid, characterized in
that the method comprises:
[0105] (a) preparing a reaction mixture by mixing a nucleic acid as
a template, a deoxyribonucleotide triphosphate, a DNA polymerase
having a strand displacement activity, at least one primer and an
RNase H, wherein the primer is a chimeric oligonucleotide primer
that is substantially complementary to the nucleotide sequence of
the nucleic acid as the template and contains a ribonucleotide as
well as at least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer; and
[0106] (b) incubating the reaction mixture for a sufficient time to
generate a reaction product.
[0107] In the twenty-fourth invention of the present invention, a
reaction mixture that further contains a chimeric oligonucleotide
primer having a sequence that is substantially homologous to the
nucleotide sequence of the nucleic acid as the template can be
used.
[0108] The twenty-fifth invention of the present invention relates
to a method for amplifying a nucleic acid, characterized in that
the method comprises:
[0109] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template and
synthesize a double-stranded nucleic acid, wherein the primer is a
chimeric oligonucleotide primer containing a ribonucleotide as well
as at least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0110] (b) extending a nucleic acid that is complementary to the
double-stranded nucleic acid as a template obtained in the previous
step using a DNA polymerase having a strand displacement activity
in the presence of an RNase H to effect a strand displacement and
synthesize a displaced strand and a double-stranded nucleic acid;
and
[0111] (c) reusing in step (b) the double-stranded nucleic acid
obtained in step (b) as a template.
[0112] The twenty-sixth invention of the present invention relates
to a method for amplifying a nucleic acid using at least two
primers, characterized in that the method comprises:
[0113] (a) treating a nucleic acid as a template with at least one
primer that is substantially complementary to the nucleotide
sequence of the nucleic acid and a DNA polymerase to synthesize a
primer-extended strand that is complementary to the template,
wherein the primer is a chimeric oligonucleotide primer containing
a ribonucleotide as well as at least one selected from the group
consisitng of a deoxyribonucleotide and a nucleotide analog, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer;
[0114] (b) extending a nucleic acid that is complementary to the
double-stranded nucleic acid as a template obtained in the previous
step using a DNA polymerase having a strand displacement activity
in the presence of an RNase H to effect a strand displacement and
synthesize a displaced strand and a double-stranded nucleic
acid;
[0115] (c) reusing in step (b) the double-stranded nucleic acid
obtained in step (b) as a template;
[0116] (d) treating a displaced strand obtained in step (b) as a
template with at least one primer that is different from that used
in step (a) and a DNA polymerase to synthesize a primer-extended
strand that is complementary to the displaced strand, wherein the
primer that is different from that used in step (a) is a chimeric
oligonucleotide primer that is substantially complementary to the
nucleotide sequence of the displaced strand and contains a
ribonucleotide as well as at least one selected from the group
consisitng of a deoxyribonucleotide and a nucleotide analog, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer;
[0117] (e) extending a nucleic acid that is complementary to the
double-stranded nucleic acid as a template obtained in the previous
step using a DNA polymerase having a strand displacement activity
in the presence of an RNase H to effect a strand displacement and
synthesize a displaced strand and a double-stranded nucleic acid;
and
[0118] (f) reusing in step (e) the double-stranded nucleic acid
obtained in step (e) as a template.
[0119] In the twenty-fifth or twenty-sixth invention of the present
invention, a DNA polymerase having a strand displacement activity
can be used as the DNA polymerase.
[0120] The twenty-seventh invention of the present invention
relates to method for amplifying a nucleic acid, characterized in
that the method comprises:
[0121] (a) treating a double-stranded nucleic acid as a template
with two primers that are substantially complementary to the
nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0122] (b) cleaving the double-stranded nucleic acid consisting of
the primer-extended strands obtained in step (a) with the
endonuclease at sites that contain the ribonucleotides; and
[0123] (c) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid in which the primer-extended
strands are cleaved obtained in step (b) to effect strand
displacements and obtain a double-stranded nucleic acid consisting
of the template and the primer-extended strand.
[0124] The twenty-eighth invention of the present invention relates
to a method for amplifying a nucleic acid, characterized in that
the method comprises:
[0125] (a) treating a double-stranded nucleic acid as a template
with two primers that are substantially complementary to the
nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0126] (b) cleaving the double-stranded nucleic acid consisting of
the primer-extended strands obtained in step (a) with the
endonuclease at sites that contain the ribonucleotides; and
[0127] (c) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid in which the primer-extended
strands are cleaved obtained in step (b) to effect strand
displacements and obtain a double-stranded nucleic acid consisting
of the primer-extended strands being annealed each other.
[0128] The twenty-ninth invention of the present invention relates
to a method for amplifying a nucleic acid, characterized in that
the method comprises:
[0129] (a) treating a double-stranded nucleic acid as a template
with two primers that are substantially complementary to the
nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0130] (b) cleaving the double-stranded nucleic acid consisting of
the primer-extended strands obtained in step (a) with the
endonuclease at sites that contain the ribonucleotides;
[0131] (c) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid in which the primer-extended
strands are cleaved obtained in step (b) to effect strand
displacements and obtain a double-stranded nucleic acid consisting
of the primer-extended strands being annealed each other and a
double-stranded nucleic acid consisting of the templates being
annealed each other to which the two primers in step (a) are
annealed;
[0132] (d) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid to which the two primers are
annealed obtained in step (c) to effect strand displacements and
obtain a double-stranded nucleic acid consisting of the
primer-extended strands being annealed each other and a
double-stranded nucleic acid consisting of the templates being
annealed each other to which the two primers in step (a) are
annealed; and
[0133] (e) reusing in step (d) the double-stranded nucleic acid to
which the two primers are annealed obtained in step (d).
[0134] The thirtieth invention of the present invention relates to
a method for amplifying a nucleic acid, characterized in that the
method comprises:
[0135] (a) treating a double-stranded nucleic acid as a template
with two primers that are substantially complementary to the
nucleotide sequences of the respective strands of the
double-stranded nucleic acid and a DNA polymerase having a strand
displacement activity to synthesize primer-extended strands that
are complementary to the template and obtain a double-stranded
nucleic acid consisting of the synthesized primer-extended strands
being annealed each other, wherein each primer is a chimeric
oligonucleotide primer containing a ribonucleotide as well as at
least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0136] (b) cleaving the double-stranded nucleic acid consisting of
the primer-extended strands obtained in step (a) with the
endonuclease at sites that contain the ribonucleotides;
[0137] (c) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid in which the primer-extended
strands are cleaved obtained in step (b) to effect strand
displacements and obtain a double-stranded nucleic acid consisting
of the primer-extended strands being annealed each other and a
double-stranded nucleic acid consisting of the templates being
annealed each other to which the two primers in step (a) are
annealed;
[0138] (d) extending nucleic acids that are complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid to which the two primers are
annealed obtained in step (c) to effect a strand displacement and
obtain a double-stranded nucleic acid consisting of the template
and the primer-extended strand;
[0139] (e) cleaving the double-stranded nucleic acid consisting of
the template and the primer-extended strand obtained in step (d)
with the endonuclease at a site that contains the ribonucleotide;
and
[0140] (f) extending a nucleic acid that is complementary to the
template using a DNA polymerase having a strand displacement
activity from the 3'-terminus of the primer portion of the
double-stranded nucleic acid in which the primer-extended strand is
cleaved obtained in step (e) to synthesize a displaced strand.
[0141] In the twenty-seventh to thirtieth invention, an
endoribonuclease such as an RNase H can be used as the
endonuclease.
[0142] In the twenty-fourth to thirtieth invention wherein an RNase
H is used, an RNase H from Escherichia coli, a bacterium of genus
Thermotoga, a bacterium of genus Thermus, a bacterium of genus
Pyrococcus, a bacterium of genus Archaeoglobus, a bacterium of
genus Bacillus or the like can be used.
[0143] In the twenty-fourth to thirtieth invention, an example of
the suitable length of the region to be specifically amplified in
the nucleotide sequence of the target nucleic acid is 200 bp or
shorter.
[0144] For the twenty-fourth to thirtieth invention of the present
invention, a chimeric oligonucleotide primer represented by general
formula below can be used:
5'-dNa-Nb-dNc-3' General formula
[0145] (a: an integer of 11 or more; b: an integer of 1 or more; c:
0 or an integer of 1 or more; dN: deoxyribonucleotide and/or
nucleotide analog; N: unmodified ribonucleotide and/or modified
ribonucleotide, wherein some of dNs in dNa may be replaced by Ns,
and the nucleotide at the 3'-terminus may be modified such that
extension from the 3'-terminus by the action of the DNA polymerase
does not take place).
[0146] Such chimeric oligonucleotide primers are exemplified by a
primer in which c is 0 and a primer in which the nucleotide analog
is deoxyriboinosine nucleotide or deoxyribouracil nucleotide, and
the modified ribonucleotide is (.alpha.-S) ribonucleotide.
Furthermore, when such a chimeric oligonucleotide primer is used,
the DNA extension reaction is conducted at a DNA extension reaction
temperature suitable for the primer.
[0147] The amplification method of the twenty-fourth to thirtieth
invention can comprise annealing the nucleic acid as the template
to the chimeric oligonucleotide primer that is substantially
complementary to the nucleotide sequence of the nucleic acid in an
annealing solution containing a substance that enhances the
annealing of the nucleic acid to the primer. For example, the
annealing solution may contain spermidine and/or propylenediamine.
The annealing can be conducted by incubating the annealing solution
containing the nucleic acid as the template and the chimeric
oligonucleotide primer that is substantially complementary to the
nucleotide sequence of the nucleic acid at 90 C or above and then
cooling the solution to a temperature at which the amplification
reaction is conducted or below.
[0148] The amplification reaction of the twenty-fourth to thirtieth
invention can be conducted in a buffer containing a buffering
component selected from the group consisting of Bicine and
HEPES.
[0149] In the twenty-fourth to thirtieth invention, for example, a
DNA polymerase selected from the group consisting of Klenow
fragment of DNA polymerase I from Escherichia coli, Bst DNA
polymerase lacking 5'3' exonuclease from Bacillus
stearothermophilus and Bca DNA polymerase lacking 5'3' exonuclease
from Bacillus caldotenax can be used as the DNA polymerase having a
strand displacement activity.
[0150] In one aspect of the twenty-fourth to thirtieth invention,
Bca DNA polymerase lacking 5'3' exonuclease from Bacillus
caldotenax is used as the DNA polymerase having a strand
displacement activity and an RNase H from Escherichia coli, a
bacterium of genus Pyrococcus or a bacterium of genus Archaeoglobus
is used as the endonuclease. The RNase H is exemplified by type I
RNase H from Escherichia coli, or type II RNase H from a bacterium
of genus Pyrococcus or a bacterium of genus Archaeoglobus.
[0151] In the twenty-fourth to thirtieth invention, a DNA
polymerase having an endonuclease activity can be used. Bca DNA
polymerase lacking 5'3' exonuclease from Bacillus caldotenax can be
used as such a DNA polymerase and the amplification reaction can be
conducted in the presence of a substance that allows the
endonuclease activity of the DNA polymerase to express. The
substance that allows the endonuclease activity of the Bca DNA
polymerase to express is exemplified by a manganese ion.
[0152] The method for amplifying a target nucleic acid of the
twenty-fourth to thirtieth invention can be conducted in the
presence of a substance that inhibits the reverse transcription
activity of the DNA polymerase. The substance that inhibits the
reverse transcription activity of the DNA polymerase is exemplified
by phosphonoformic acid.
[0153] The twenty-fourth to thirtieth invention of the present
invention can be conducted using a single-stranded DNA or a
double-stranded DNA as the template. If the nucleic acid as the
template is a double-stranded DNA, the amplification reaction can
be conducted after converting it into single-stranded DNAs.
[0154] The nucleic acid as the template may be a cDNA obtained by a
reverse transcription reaction using an RNA as a template. In one
aspect, the amplification reaction is conducted after synthesizing
a cDNA by a reverse transcription reaction using an RNA as a
template. A DNA polymerase having a reverse transcriptase activity
can be used for the reverse transcription reaction. For example,
the reverse transcription reaction and the synthesis of the
extended strand that is complementary to the template can be
conducted using one DNA polymerase having a reverse transcriptase
activity and a strand displacement activity. Such a DNA polymerase
is exemplified by Bst DNA polymerase lacking 5'3' exonuclease from
Bacillus stearothermophilus or Bca DNA polymerase lacking 5'3'
exonuclease from Bacillus caldotenax.
[0155] In the twenty-fourth to thirtieth invention, the
amplification reaction can be conducted under isothermal
conditions. In addition, it can be conducted in the presence of a
deoxynucleotide triphosphate analog such as deoxyuridine
triphosphate or a derivative thereof.
[0156] The thirty-first invention of the present invention relates
to a composition for amplifying a nucleic acid which contains:
[0157] (a) at least one primer that is substantially complementary
to a nucleotide sequence of a nucleic acid as a template, wherein
the primer is a chimeric oligonucleotide primer that contains a
ribonucleotide as well as at least one selected from the group
consisitng of a deoxyribonucleotide and a nucleotide analog, the
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer;
[0158] (b) an endonuclease; and
[0159] (c) a DNA polymerase having a strand displacement
activity.
[0160] The thirty-second invention of the present invention relates
to a composition for amplifying a nucleic acid which contains:
[0161] (a) at least two primers that are substantially
complementary to nucleotide sequences of respective strands of a
double-stranded nucleic acid as a template, wherein each primer is
a chimeric oligonucleotide primer that contains a ribonucleotide as
well as at least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer;
[0162] (b) an endonuclease; and
[0163] (c) a DNA polymerase having a strand displacement
activity.
[0164] The thirty-third invention of the present invention relates
to a composition for amplifying a nucleic acid obtained by mixing a
nucleic acid as a template, a deoxyribonucleotide triphosphate, a
DNA polymerase having a strand displacement activity, at least one
primer and an endonuclease, wherein the primer is a chimeric
oligonucleotide primer that is substantially complementary to the
nucleotide sequence of the nucleic acid as the template and
contains a ribonucleotide as well as at least one selected from the
group consisitng of a deoxyribonucleotide and a nucleotide analog,
the ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer.
[0165] The thirty-fourth invention of the present invention relates
to composition for amplifying a nucleic acid obtained by mixing a
nucleic acid as a template, a deoxyribonucleotide triphosphate, a
DNA polymerase having a strand displacement activity, at least two
primers and an endonuclease, wherein each primer is a chimeric
oligonucleotide primer that is substantially complementary to the
nucleotide sequence of each strand of the double-stranded nucleic
acid as the template and contains a ribonucleotide as well as at
least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog, the ribonucleotide
being positioned at the 3'-terminus or on the 3'-terminal side of
the primer.
[0166] The primer contained in the composition of the thirty-first
to thirty-fourth invention of the present invention is exemplified
by a chimeric oligonucleotide primer represented by general formula
below:
5'-dNa-Nb-dNc-3' General formula
[0167] (a: an integer of 11 or more; b: an integer of 1 or more; c:
0 or an integer of 1 or more; dN: deoxyribonucleotide and/or
nucleotide analog; N: unmodified ribonucleotide and/or modified
ribonucleotide, wherein some of dNs in dNa may be replaced by Ns,
and the nucleotide at the 3'-terminus may be modified such that
extension from the 3'-terminus by the action of the DNA polymerase
does not take place).
[0168] Such chimeric oligonucleotide primers are exemplified by a
primer in which c is 0 and a primer in which the nucleotide analog
is deoxyriboinosine nucleotide or deoxyribouracil nucleotide, and
the modified ribonucleotide is (.alpha.-S) ribonucleotide.
[0169] The composition of the thirty-first to thirty-fourth
invention can contain a buffering component suitable for a nucleic
acid amplification reaction. For example, it can contain a
buffering component selected from the group consisting of Bicine
and HEPES.
[0170] The thirty-first to thirty-fourth invention is exemplified
by a composition containing a DNA polymerase selected from the
group consisting of Klenow fragment of DNA polymerase I from
Escherichia coli, Bst DNA polymerase lacking 5'3' exonuclease from
Bacillus stearothermophilus and Bca DNA polymerase lacking 5'3'
exonuclease from Bacillus caldotenax as the DNA polymerase having a
strand displacement activity. An endoribonuclease such as an RNase
H can be used as the endonuclease. The RNase H is exemplified by an
RNase H from Escherichia coli, a bacterium of genus Thermotoga, a
bacterium of genus Thermus, a bacterium of genus Pyrococcus, a
bacterium of genus Archaeoglobus, a bacterium of genus Bacillus or
the like.
[0171] In one aspect, the composition of the thirty-first to
thirty-fourth invention contains Bca DNA polymerase lacking 5'3'
exonuclease from Bacillus caldotenax as the DNA polymerase having a
strand displacement activity and an RNase H from Escherichia coli,
a bacterium of genus Pyrococcus or a bacterium of genus
Archaeoglobus as the endonuclease. The RNase H is exemplified by
type I RNase H from Escherichia coli, or type II RNase H from a
bacterium of genus Pyrococcus or a bacterium of genus
Archaeoglobus.
[0172] The composition of the thirty-first to thirty-fourth
invention may contain a DNA polymerase having an endonuclease
activity. Bca DNA polymerase lacking 5'3' exonuclease from Bacillus
caldotenax can be used as such a DNA polymerase, which can be used
in the presence of a substance that allows the endonuclease
activity of the DNA polymerase to express. The substance that
allows the endonuclease activity of the Bca DNA polymerase to
express is exemplified by a manganese ion.
[0173] The composition of the thirty-first to thirty-fourth
invention can contain a substance that inhibits the reverse
transcription activity of the DNA polymerase. The substance that
inhibits the reverse transcription activity of the DNA polymerase
is exemplified by phosphonoformic acid. Furthermore, the
composition may contain a deoxynucleotide triphosphate analog such
as deoxyuridine triphosphate or a derivative thereof.
[0174] The thirty-fifth invention of the present invention relates
to a composition for amplifying a nucleic acid used for the method
for amplifying a nucleic acid of the twenty-fourth to twenty-sixth
invention, which contains:
[0175] (a) an RNase H; and
[0176] (b) a DNA polymerase having a strand displacement
activity.
[0177] The thirty-sixth invention of the present invention relates
to a composition for amplifying a nucleic acid used for the method
for amplifying a nucleic acid of the twenty-seventh to thirtieth
invention, which contains:
[0178] (a) an endonuclease; and
[0179] (b) a DNA polymerase having a strand displacement
activity.
[0180] An endoribonuclease such as an RNase H can be used as the
endonuclease for the composition of the thirty-sixth invention.
[0181] An RNase H selected from the group consisting of an RNase H
from Escherichia coli, an RNase H from a bacterium of genus
Thermotoga, an RNase H from a bacterium of genus Thermus, an RNase
H from a bacterium of genus Pyrococcus, an RNase H from a bacterium
of genus Archaeoglobus and an RNase H from a bacterium of genus
Bacillus can be used as the RNase H for the composition of the
thirty-fifth or thirty-sixth invention which contains an RNase
H.
[0182] The composition of the thirty-fifth or thirty-sixth
invention can further contain a buffering component suitable for a
nucleic acid amplification reaction. For example, the composition
may contain a buffering component selected from the group
consisting of Bicine and HEPES.
[0183] The thirty-fifth or thirty-sixth invention is exemplified by
a composition that contains a DNA polymerase selected from the
group consisting of Klenow fragment of DNA polymerase I from
Escherichia coli, Bst DNA polymerase lacking 5'3' exonuclease from
Bacillus stearothermophilus and Bca DNA polymerase lacking 5'3'
exonuclease from Bacillus caldotenax as the DNA polymerase having a
strand displacement activity. An endoribonuclease such as an RNase
H can be used as the endonuclease. The RNase H is exemplified by an
RNase H from Escherichia coli, a bacterium of genus Thermotoga, a
bacterium of genus Thermus, a bacterium of genus Pyrococcus, a
bacterium of genus Archaeoglobus, a bacterium of genus Bacillus or
the like.
[0184] In one aspect, the composition of the thirty-fifth or
thirty-sixth invention contains Bca DNA polymerase lacking 5'3'
exonuclease from Bacillus caldotenax as the DNA polymerase having a
strand displacement activity and an RNase H from Escherichia coli,
a bacterium of genus Pyrococcus or a bacterium of genus
Archaeoglobus as the endonuclease. The RNase H is exemplified by
type I RNase H from Escherichia coli, or type II RNase H from a
bacterium of genus Pyrococcus or a bacterium of genus
Archaeoglobus.
[0185] The composition of the thirty-fifth or thirty-sixth
invention may contain a DNA polymerase having an endonuclease
activity. Bca DNA polymerase lacking 5'3' exonuclease from Bacillus
caldotenax can be used as such a DNA polymerase, which can be used
in the presence of a substance that allows the endonuclease
activity of the DNA polymerase to express. The substance that
allows the endonuclease activity of the Bca DNA polymerase to
express is exemplified by a manganese ion.
[0186] The composition of the thirty-fifth or thirty-sixth
invention can contain a substance that inhibits the reverse
transcription activity of the DNA polymerase. The substance that
inhibits the reverse transcription activity of the DNA polymerase
is exemplified by phosphonoformic acid. Furthermore, the
composition may contain a deoxynucleotide triphosphate analog such
as deoxyuridine triphosphate or a derivative thereof.
[0187] The thirty-seventh invention of the present invention
relates to a kit for amplifying a nucleic acid used for the method
for amplifying a nucleic acid of the twenth-fourth to twenty-sixth
of the present invention, which contains:
[0188] (a) an RNase H; and
[0189] (b) a DNA polymerase having a strand displacement
activity.
[0190] The thirty-eighth invention of the present invention relates
to a kit for amplifying a nucleic acid used for the method for
amplifying a nucleic acid of the twenty-seventh to thirtieth
invention of the present invention, which contains:
[0191] (a) an endonuclease; and
[0192] (b) a DNA polymerase having a strand displacement
activity.
[0193] An endoribonuclease such as an RNase H can be used as the
endonuclease for the kit of the thirty-eighth invention.
[0194] The kit of the thirty-seventh or thirty-eighth invention
which contains an RNase H is exemplified by a kit containing an
RNase H selected from the group consisting of an RNase H from
Escherichia coli, an RNase H from a bacterium of genus Thermotoga,
an RNase H from a bacterium of genus Thermus, an RNase H from a
bacterium of genus Pyrococcus, an RNase H from a bacterium of genus
Archaeoglobus and an RNase H from a bacterium of genus
Bacillus.
[0195] The kit of the thirty-seventh or thirty-eighth invention may
further contain a buffering component suitable for a nucleic acid
amplification reaction. For example, the composition can contain a
buffering component selected from the group consisting of Bicine
and HEPES. The kit may contain an annealing solution containing a
substance that enhances the annealing of the nucleic acid as the
template to the primer that is substantially complementary to the
nucleotide sequence of the nucleic acid. For example, the annealing
solution may contain spermidine and/or propylenediamine.
[0196] The DNA polymerase having a strand displacement activity
contained in the kit of the thirty-seventh or thirty-eighth
invention of the present invention is exemplified by a DNA
polymerase selected from the group consisting of Klenow fragment of
DNA polymerase I from Escherichia coli, Bst DNA polymerase lacking
5'3' exonuclease from Bacillus stearothermophilus and Bca DNA
polymerase lacking 5'3' exonuclease from Bacillus caldotenax.
[0197] In one aspect, the kit of the thirty-seventh or
thirty-eighth invention contains Bca DNA polymerase lacking 5'3'
exonuclease from Bacillus caldotenax and an RNase H from
Escherichia coli, a bacterium of genus Pyrococcus or a bacterium of
genus Archaeoglobus. The RNase H is exemplified by type I RNase H
from Escherichia coli, or type II RNase H from a bacterium of genus
Pyrococcus or a bacterium of genus Archaeoglobus.
[0198] The kit of the thirty-seventh or thirty-eighth invention of
the present invention may contain a DNA polymerase having an
endonuclease activity. Bca DNA polymerase lacking 5'3' exonuclease
from Bacillus caldotenax can be used as such a DNA polymerase. The
kit can contain a substance that allows the endonuclease activity
of the DNA polymerase to express. The substance that allows the
endonuclease activity of the Bca DNA polymerase to express is
exemplified by a manganese ion.
[0199] The kit of the thirty-seventh or thirty-eighth invention can
contain a substance that inhibits the reverse transcription
activity of the DNA polymerase. The substance that inhibits the
reverse transcription activity of the DNA polymerase is exemplified
by phosphonoformic acid. Furthermore, the kit may contain a
deoxynucleotide triphosphate analog such as deoxyuridine
triphosphate or a derivative thereof.
[0200] The thirty-ninth invention of the present invention relates
to a kit for amplifying a nucleic acid used for the method for
amplifying a nucleic acid of the twenty-fourth to twenty-sixth
invention of the present invention, which is in a packaged form and
contains instructions that direct the use of a DNA polymerase
having a strand displacement activity and an RNase H.
[0201] The fortieth invention of the present invention relates to a
kit for amplifying a nucleic acid used for the method for
amplifying a nucleic acid of the twenty-seventh to thirtieth
invention of the present invention, which is in a packaged form and
contains instructions that direct the use of a DNA polymerase
having a strand displacement activity and an endonuclease.
[0202] The forty-first invention of the present invention relates
to a product of a reagent for amplifying a nucleic acid consisting
of a packing material and a reagent for amplifying a nucleic acid
enclosed in the packing material, wherein the reagent for
amplifying a nucleic acid contains a DNA polymerase having a strand
displacement activity and/or an RNase H, and description that the
reagent for amplifying a nucleic acid can be used for nucleic acid
amplification under isothermal conditions is indicated in a label
stuck to the packaging material or instructions attached to the
packaging material.
[0203] The forty-second invention of the present invention relates
to a product of a reagent for amplifying a nucleic acid consisting
of a packing material and a reagent for amplifying a nucleic acid
enclosed in the packing material, wherein the reagent for
amplifying a nucleic acid contains a DNA polymerase having a strand
displacement activity and/or an endonuclease, and description that
the reagent for amplifying a nucleic acid can be used for nucleic
acid amplification under isothermal conditions is indicated in a
label stuck to the packaging material or instructions attached to
the packaging material.
[0204] The forty-third invention of the present invention relates
to a method for detecting a target nucleic acid in a sample,
characterized in that the method comprises:
[0205] (a) amplifying a nucleic acid by the method for amplifying a
nucleic acid of the twenty-fourth to thirtieth invention of the
present invention; and
[0206] (b) detecting a target nucleic acid amplified in step
(a).
[0207] The detection method of the forty-third invention of the
present invention can comprise detecting the amplified nucleic acid
using a probe for detection. The probe may be a probe that has been
labeled with a labeling substance. For example, an RNA probe
labeled with two or more fluorescent substances positioned at a
distance that results in a quenching state can be used.
[0208] The forty-fourth invention of the present invention relates
to a chimeric oligonucleotide primer used for the forty-third
invention. The chimeric oligonucleotide primer is exemplified by a
chimeric oligonucleotide primer represented by general formula
below:
5'-dNa-Nb-dNc-3' General formula
[0209] (a: an integer of 11 or more; b: an integer of 1 or more; c:
0 or an integer of 1 or more; dN: deoxyribonucleotide and/or
nucleotide analog; N: unmodified ribonucleotide and/or modified
ribonucleotide, wherein some of dNs in dNa may be replaced by Ns,
and the nucleotide at the 3'-terminus may be modified such that
extension from the 3'-terminus by the action of the DNA polymerase
does not take place).
[0210] Such chimeric oligonucleotide primers are exemplified by a
primer in which c is 0 and a primer in which the nucleotide analog
is deoxyriboinosine nucleotide or deoxyribouracil nucleotide, and
the modified ribonucleotide is (.alpha.-S) ribonucleotide.
[0211] The primer of the forty-fourth invention of the present
invention is exemplified by a primer for detecting a pathogenic
microorganism or a disease-related gene. A chimeric oligonucleotide
primer for detecting a pathogenic microorganism such as
enterohemorrhagic Escherichia coli, Clostridium botulinum,
Staphylococcus aureus, Mycobacterium tuberculosis, Chlamydia
trachomatis, papilloma virus, hepatitis C virus or a viroid is
encompassed by the present invention.
[0212] The forty-fifth invention of the present invention relates
to a chimeric oligonucleotide primer for detecting
enterohemorrhagic Escherichia coli having a nucleotide sequence
selected from the group consisting of SEQ ID NOS: 31 to 34, 47, 48,
51-53, 64-72, 84, 85, 113, 114, 130 and 131.
[0213] The forty-sixth invention of the present invention relates
to a chimeric oligonucleotide primer for detecting a viroid having
a nucleotide sequence selected from the group consisting of SEQ ID
NOS: 59, 60, 119, 120, 122 and 123.
[0214] The forty-seventh invention of the present invention relates
to a chimeric oligonucleotide primer for detecting Clostridium
botulinum having a nucleotide sequence represented by SEQ ID NO:
116 or 117.
[0215] The forty-eighth invention of the present invention relates
to chimeric oligonucleotide primer for detecting papilloma virus
having a nucleotide sequence represented by SEQ ID NO: 96 or
97.
[0216] The forty-ninth invention of the present invention relates
to a chimeric oligonucleotide primer for detecting hepatitis C
virus having a nucleotide sequence selected from the group
consisting of SEQ ID NOS: 101, 102, 138, 139, 200, 201, 205 and
206.
[0217] The fiftieth invention of the present invention relates to a
chimeric oligonucleotide primer for detecting Staphylococcus aureus
having a nucleotide sequence represented by SEQ ID NO: 136 or
137.
[0218] The fifty-first invention of the present invention relates
to a chimeric oligonucleotide primer for detecting Mycobacterium
tuberculosis having a nucleotide sequence selected from the group
consisting of SEQ ID NOS: 155, 156, 159 to 162, 194 and 195.
[0219] The fifty-second invention of the present invention relates
to a chimeric oligonucleotide primer for detecting Chlamydia
trachomatis having a nucleotide sequence selected from the group
consisting of SEQ ID NOS: 157, 158, 203 and 204.
[0220] The fifty-third invention of the present invention relates
to a kit for amplifying a nucleic acid used for the method for
amplifying a nucleic acid of the twenty-fourth to twenty-eighth
invention of the present invention, which contains the chimeric
oligonucleotide primer of the forty-fourth to fifty-second
invention.
[0221] The fifty-fourth invention of the present invention relates
to a kit for detecting a target nucleic acid used for the method
for detecting a target nucleic acid of the forty-third invention of
the present invention, which contains the chimeric oligonucleotide
primer of the forty-fourth to fifty-second invention.
[0222] The fifty-fifth invention of the present invention relates
to a probe used in the method of the forty-third invention.
[0223] The fifty-sixth invention of the present invention relates
to a probe which hybridizes to the nucleic acid amplified by the
method of the twenty-third to thirtieth invention.
[0224] The fifty-seventh invention of the present invention relates
to a probe which hybridizes to a region amplified using the
chimeric oligonucleotide primer of the forty-fourth to fifty-second
invention.
[0225] The probe of the fifty-fifth to fifty-seventh invention may
be a probe which has been labeled with a labeling substance, for
example, an RNA probe labeled with two or more fluorescent
substances positioned at a distance that results in a quenching
state
[0226] The fifty-eighth invention of the present invention relates
to a kit used for the detection of the target nucleic acid in the
method of the forty-third invention, which contains the probe of
the fifty-fifth to fifty-seventh invention.
[0227] The fifty-ninth invention of the present invention relates
to a method for amplifying a nucleic acid, which comprises using a
DNA polymerase having a strand displacement activity to effect a
template switching reaction.
[0228] The DNA polymerase having a strand displacement activity
used in the fifty-ninth invention is exemplified by Klenow fragment
of DNA polymerase I from Escherichia coli, Bst DNA polymerase
lacking 5'3' exonuclease from Bacillus stearothermophilus and Bca
DNA polymerase lacking 5'3' exonuclease from Bacillus
caldotenax.
[0229] The sixtieth invention of the present invention relates to a
method for producing a material having an immobilized nucleic acid
in which the nucleic acid is arrayed in a predefined region,
characterized in that the method comprises:
[0230] (a) amplifying a nucleic acid to be immobilized by the
method for amplifying a nucleic acid of the twenty-fourth to
thirtieth invention of the present invention; and
[0231] (b) arraying and immobilizing the nucleic acid amplified in
step (a) in a predefined region.
[0232] The sixty-first invention of the present invention relates
to a material having an immobilized nucleic acid in which the
nucleic acid is arrayed in a predefined region produced by the
method of the sixtieth invention.
[0233] The sixty-second invention of the present invention relates
to a method for producing a nucleic acid in large quantities,
characterized in that the method comprises:
[0234] (a) amplifying a nucleic acid by the method for amplifying a
nucleic acid of the twenty-fourth to thirtieth invention of the
present invention; and
[0235] (b) collecting the nucleic acid amplified in step (a).
[0236] The sixty-third invention of the present invention relates
to a method for amplifying a nucleic acid, characterized in that
the method comprises:
[0237] (a) duplicating a DNA or an RNA containing a sequence to be
amplified to prepare a nucleic acid as a template; and
[0238] (b) amplifying the nucleic acid as the template obtained in
step (a) by the method for amplifying a nucleic acid of the
twenty-fourth to thirtieth invention.
[0239] The sixty-fourth invention of the present invention relates
to a method for determining a nucleotide sequence of a nucleic
acid, characterized in that the method comprises amplifying a
nucleic acid according to the method of the twenty-fourth to
thirtieth, sixty-second or sixty-third invention.
[0240] The sixty-fifth invention of the present invention relates
to a method for preparing a single-stranded nucleic acid, the
method comprising a step of generating a single-stranded nucleic
acid using the method according to the twenty-fourth to thirtieth
invention. In the sixty-fifth invention, at least two primers at
different concentrations may be used.
BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS
[0241] FIG. 1 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0242] FIG. 2 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0243] FIG. 3 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0244] FIG. 4 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0245] FIG. 5 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0246] FIG. 6 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0247] FIG. 7 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0248] FIG. 8 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0249] FIG. 9 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0250] FIG. 10 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0251] FIG. 11 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0252] FIG. 12 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0253] FIG. 13 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0254] FIG. 14 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0255] FIG. 15 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0256] FIG. 16 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0257] FIG. 17 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0258] FIG. 18 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0259] FIG. 19 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0260] FIG. 20 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0261] FIG. 21 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0262] FIG. 22 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0263] FIG. 23 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0264] FIG. 24 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0265] FIG. 25 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0266] FIG. 26 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0267] FIG. 27 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0268] FIG. 28 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention and the results of dot blot hybridization.
[0269] FIG. 29 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0270] FIG. 30 is a graph which compares the amounts of
amplification products amplified according to the method of the
present invention and the PCR.
[0271] FIG. 31 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0272] FIG. 32 is a photograph of polyacrylamide gel
electrophoresis of amplified DNA fragments amplified according to
the method of the present invention.
[0273] FIG. 33 is a figure illustrating one aspect of the method
for amplifying a nucleic acid of the present invention.
[0274] FIG. 34 is a figure illustrating one aspect of the method
for amplifying a nucleic acid of the present invention.
[0275] FIG. 35 is a figure illustrating one aspect of the method
for amplifying a nucleic acid of the present invention.
[0276] FIG. 36 is a figure illustrating one aspect of the method
for amplifying a nucleic acid of the present invention.
[0277] FIG. 37 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0278] FIG. 38 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0279] FIG. 39 is a photograph of agarose gel electrophoresis of
amplified DNA fragments amplified according to the method of the
present invention.
[0280] FIG. 40 is a flow chart that illustrates an example of the
method of the present invention in which a single-stranded DNA is
used. In the figure, the released DNA strand marked with the closed
circle serves as a template DNA in (6).
[0281] FIG. 41 shows the results of agarose gel electrophoresis of
DNA fragments amplified by the method of the present invention
using varying reaction time.
DETAILED DESCRIPTION OF THE INVENTION
[0282] As used herein, a deoxyribonucleotide (also referred to as a
dN) refers to a nucleotide of which the sugar portion is composed
of D-2-deoxyribose. The deoxyribonucleotides include, for example,
ones having adenine, cytosine, guanine or thymine as the base
portion. Furthermore, the doxyribonucleotides also include a
deoxyribonucleotide having a modified base such as 7-deazaguanosine
and a deoxyribonucleotide analog such as deoxyinosine
nucleotide.
[0283] As used herein, a ribonucleotide (also referred to as an N)
refers to a nucleotide of which the sugar portion is composed of
D-ribose. The ribonucleotides include ones having adenine,
cytosine, guanine or uracil as the base portion. The
ribonucleotides also include modified ribonucleotides such as a
modified ribonucleotide in which the oxygen atom of the phosphate
group at the .alpha.-position is replaced by a sulfur atom (also
referred to as an (.alpha.-S) ribonucleotide or an (.alpha.-S)N) or
other derivatives.
[0284] As used herein, a chimeric oligonucleotide primer refers to
a primer that contains a deoxyribonucleotide and a ribonucleotide.
The primer may contain a nucleotide analog and/or a modified
ribonucleotide.
[0285] The chimeric oligonucleotide primers used in the present
invention include any chimeric oligonucleotide primer that has a
ribonucleotide being positioned at the 3'-terminus or on the
3'-terminal side of the primer, can be used to extend a nucleic
acid strand in the method of the present invention, can be cleaved
with an endonuclease, and can be used to effect a strand
displacement reaction.
[0286] As used herein, 3'-terminal side refers to a portion from
the center to the 3'-terminus of a nucleic acid such as a primer.
Likewise, 5'-terminal side refers to a portion from the center to
the 5'-terminus of a nucleic acid.
[0287] As used herein, an endonuclease may be any one that acts on
a double-stranded DNA generated by extending a DNA from the
chimeric oligonucleotide primer which have been annealed to a
nucleic acid as a template, and specifically cleaves it at a
portion of the primer that contains a ribonucleotide.
[0288] As used herein, a DNA polymerase refers to an enzyme that
synthesizes a DNA strand de novo using a DNA strand as a template.
The DNA polymerases include naturally occurring DNA polymerases and
variant enzymes having the above-mentioned activity. For example,
such enzymes include a DNA polymerase having a strand displacement
activity, a DNA polymerase lacking a 5'3' exonuclease activity and
a DNA polymerase having a reverse transcriptase activity or an
endonuclease activity.
[0289] As used herein, "a strand displacement activity" refers to
an activity that can effect a strand displacement, that is, that
can proceed DNA duplication on the basis of the sequence of the
nucleic acid as the template while displacing the DNA strand to
release the complementary strand that has been annealed to the
template strand. In addition, a DNA strand released from a nucleic
acid as a template as a result of a strand displacement is referred
to as "a displaced strand" herein.
[0290] Hereinafter, the present invention will be described in
detail.
[0291] (1) Chimeric Oligonucleotide Primer Used in the Present
Invention.
[0292] The primer used in the method of the present invention is a
chimeric oligonucleotide primer that contains a ribonucleotide as
well as at least one selected from the group consisitng of a
deoxyribonucleotide and a nucleotide analog. Such primers also
include an oligoribonucleotide primer that contains an unmodified
ribonucleotide and/or a modified ribonucleotide.
[0293] A chimeric oligonucleotide primer used in the method of the
present invention is a chimeric oligonucleotide primer that has a
nucleotide sequence substantially complementary to a part of the
nucleotide sequence of a nucleic acid as a template. It can
contribute to extension of a DNA strand under conditions used.
Furthermore, a ribonucleotide is positioned at the 3'-terminus or
on the 3'-terminal side of the chimeric oligonucleotide primer. The
primer is usually designed such that it is complementary to a
portion upstream of the region to be amplified, that is, a portion
3' to the nucleotide sequence corresponding to a region to be
amplified in a nucleic acid as a template. As used herein, "a
substantially complementary nucleotide sequence" means a nucleotide
sequence that can anneal to a DNA as a template under reaction
conditions used.
[0294] The chimeric oligonucleotide primer used in the method of
the present invention may contain one or more modified
ribonucleotide. As used herein, a ribonucleotide may be an
unmodified ribonucleotide and/or a modified ribonucleotide that can
be positioned at the 3'-terminus or on the 3'-terminal side of a
chimeric oligonucleotide primer and that is recognized by or
cleaved with an endonuclease. The ribonucleotides include both of
the unmodified ribonucleotide and the modified ribonucleotide as
described above. An unmodified ribonucleotide, a modified
ribonucleotide or a combination thereof can be used for the
chimeric oligonucleotide primer of the present invention as long as
it does not abolish the function of the primer. Examples of the
modified ribonucleotides include, but are not limited to, an
(.alpha.-S) ribonucleotide in which the oxygen atom bound to the
phosphate group is replaced by a sulfur atom, and a ribonucleotide
in which the hydroxy group at the 2-position of the ribose is
replaced by a methoxy group. Such a chimeric oligonucleotide primer
containing a modified ribonucleotide can be produced by using, for
example, an (.alpha.-S) ribonucleotide triphosphate, which is
prepared by a method using a sulfuration reaction reagent (Glen
Research) as described in U.S. Pat. No. 5,003,097, or a
2-OMe-RNA-CE phosphoramidite reagent (Glen Research).
[0295] A chimeric oligonucleotide primer that can be used in the
amplification method of the present invention may be designed to
contain a modified ribonucleotide that confers resistance to the
cleavage with an endonuclease. Such a primer is useful in that one
can control the cleavage site with an endonuclease during
amplification reaction steps.
[0296] One or two chimeric oligonucleotide primer may be used in
the method of the present invention depending on the desired form
of a DNA fragment after amplification (single-stranded or
double-stranded). Specifically, one chimeric oligonucleotide primer
is used when a single-stranded DNA is desired, whereas two primers
are used when a double-stranded DNA is desired.
[0297] The length of the chimeric oligonucleotide primer used in
the method of the present invention is not specifically limited,
but is preferably about 12 nucleotides to about 100 nucleotides,
more preferably about 15 nucleotides to about 40 nucleotides. It is
preferable that the nucleotide sequence of the chimeric
oligonucleotide is substantially complementary to a nucleic acid as
a template such that it anneals to the nucleic acid as the template
under reaction conditions used. The primer contains a sequence
recognized by an endonuclease, which is utilized in a step as
described below, at the 3'-terminus or on the 3'-terminal side.
[0298] For example, an oligonucleotide having a structure
represented by the following general formula can be used in the DNA
synthesis method of the present invention as a primer, although it
is not intended to limit the present invention:
5'-dNa-Nb-dNc-3' General formula
[0299] (a: an integer of 11 or more; b: an integer of 1 or more; c:
0 or an integer of 1 or more; dN: deoxyribonucleotide and/or
nucleotide analog; N: unmodified ribonucleotide and/or modified
ribonucleotide, wherein some of dNs in dNa may be replaced by Ns,
and the nucleotide at the 3'-terminus may be modified such that
extension from the 3'-terminus by the action of the DNA polymerase
does not take place).
[0300] For example, a chimeric oligonucleotide primer represented
by the general formula in which a=an integer of 11 or more; and b=1
and c=0, b=2 and c=0, b=3-5 and c=0, or b=2 and c=0-5 can be
preferably used in the present invention. The length of the
ribonucleotides at the 3'-terminus or on the 3'-termunal side of
the chimeric oligonucleotide primer used in the method of the
present invention is preferably 1-mer to 15-mer, more preferably
1-mer to 10-mer, most preferably 1-mer to 5-mer. The number of c in
the general formula is not specifically limited, but any number
that can be used in the method of the present invention may be
selected. Usually, 5 or less is preferably. Better results are
obtained in a reaction by selecting 3 rather than 4, 2 rather than
3, and 1 rather than 2 for c. In particular, the most efficient
reaction can be accomplished in case of c=0.
[0301] The chimeric oligonucleotide primer used in the present
invention has a structure in which an endonuclease recognizes or
cleaves a DNA strand extended from the primer using a DNA
polymerase (a primer-extended strand) at a site that contains a
ribonucleotide, which ribonucleotide being positioned at the
3'-terminus or on the 3'-terminal side of the chimeric
oligonucleotide primer. Although it is not intended to limit the
present invention, for example, when an RNase H acts on a
double-stranded DNA generated by extending a DNA from a chimeric
oligonucleotide primer represented by the general formula that has
been annealed to a nucleic acid as a template, the chimeric
oligonucleotide primer is cleaved at the ribonucleotide portion. A
double-stranded DNA in which a nick is introduced between the
oligonucleotide primer and the DNA strand synthesized by the
extension is then generated. Then, a strand displacement reaction
with a DNA polymerase proceeds from the nicked site. Thus, any
chimeric oligonucleotide primer that can be used to extend a
nucleic acid strand from the 3'-terminus of the primer, that can be
cleaved with an endonuclease, and with which a DNA polymerase can
effect a strand displacement reaction can be used in the method of
the present invention. Furthermore, the chimeric oligonucleotide
primers of the present invention include one whose 3'-terminus is
modified such that extension by the action of the DNA polymerase
can not take place, and DNA extension takes place from a
3'-terminus generated upon cleavage by the endonuclease. In
addition, a promoter sequence for an RNA polymerase may be included
on the 5'-terminal side of the chimeric oligonucleotide primer.
Such RNA polymerases are exemplified by T7 RNA polymerase and SP6
RNA polymerase.
[0302] Furthermore, the chimeric oligonucleotide primer used in the
method of the present invention may contain a nucleotide analog or
other substances. That is, one or more nucleotide analog(s) can be
contained in the chimeric oligonucleotide primer of the present
invention as long as the function of the primer is not abolished.
Plural types of the nucleotide analogs can be used in combination.
Examples of the nucleotide analogs include, but are not limited to,
nucleotide analogs having ribose derivatives such as deoxyinosine
nucleotide, deoxyuracil nucleotide and a deoxyribonucleotide analog
having a modified base such as 7-deazaguanine. Furthermore, the
chimeric oligonucleotides used in the present invention may contain
deoxynucleotides, ribonucleotides or nucleotide analogs having
various modifications such as addition of labeled compounds as long
as they retain the functions as described above.
[0303] Incorporation of a nucleotide analog into a primer is
effective for suppressing the formation of high-order structure of
the primer itself and stabilization of annealing formation with the
template. A ribonucleotide may be incorporated into a primer for
the same purpose. Although it is not intended to limit the present
invention, a modified ribonucleotide such as (.alpha.-S)
ribonucleotide can be preferably used in order to prevent the
digestion of the primer by a non-specific endonuclease (RNase).
[0304] The chimeric oligonucleotide primer can be synthesized to
have desired nucleotide sequence using, for example, the 394 type
DNA synthesizer from Applied Biosystems Inc. (ABI) according to a
phosphoramidite method. Alternatively, any methods including a
phosphate triester method, an H-phosphonate method and a
thiophosphonate method may be used to synthesize the chimeric
oligonucleotide primer.
[0305] (2) Endonuclease Used in the Present Invention.
[0306] Any endonuclease that can act on a double-stranded DNA
generated by DNA extension from the chimeric oligonucleotide primer
as described above in (1) that has been annealed to a nucleic acid
as a template and cleaves the extended strand to effect a strand
displacement reaction may be used in the present invention. That
is, the endonuclease is an enzyme that can generate a nick in the
chimeric oligonucleotide primer portion of the double-stranded DNA.
Examples of endonucleases that can be used in the present invention
include, but are not limited to, ribonucleases. Among these,
endoribonuclease H (RNase H) that acts on an RNA portion of a
double-stranded nucleic acid composed of a DNA and an RNA can be
preferably used. Any ribonuclease that has the above-mentioned
activities can be preferably used in the present invention,
including mesophilic and heat-resistant ones. For example, an RNase
H from E. coli can be used for a reaction at about 50 C to about 70
C in the method of the present invention as described below in
Examples. A heat-resistant ribonuclease can be preferably used in
the method of the present invention. Examples of the heat-resistant
ribonucleases which can be preferably used include, but are not
limited to, a commercially available ribonuclease, Hybridase.TM.
Thermostable RNase H (Epicenter Technologies) as well as an RNase
from a thermophilic bacterium of genus Bacillus, a bacterium of
genus Thermus, a bacterium of genus Pyrococcus, a bacterium of
genus Thermotoga, a bacterium of genus Archaeoglobus or the like.
Furthermore, both of naturally occurring ribonucleases and variants
can be preferably used. The enzymatic unit of RNase H indicated
herein is a value expressed according to a method of measuring an
enzymatic unit as described in Referential Examples.
[0307] The RNase H is not limited to a specific one as long as it
can be used in the method of the present invention. For example,
the RNase H may be derived from any organisms including various
viruses, phages, prokaryotes and eukaryotes. It may be either a
bacterial RNase H or a viral RNase H. The bacterial RNase H is
exemplified by Escherichia coli RNase H I and the viral RNase H is
exemplified by HIV-1. Type I, type II or type III RNase H can be
used in the method of the present invention. For example, type I
RNase H from Escherichia coli, or type II RNase H from a bacterium
of genus Pyrococcus or a bacterium of genus Archaeoglobus is
preferable, without limitation.
[0308] The efficiency of the cleavage reaction with an endonuclease
such as RNase H used in the method of the present invention may
vary depending on the nucleotide sequence around the 3'-terminus of
the primer and influence the amplification efficiency of the
desired DNA. Therefore, it is natural to design the optimal primer
for the RNase H used.
[0309] As used herein, the term "introducing a nick" or "nicking"
means internally cleaving one of the two strands of a
double-stranded nucleic acid. For example, an RNase H acts on a
hybrid double-stranded nucleic acid composed of a DNA and a
ribonucleotide-containing DNA to selectively cleave the
ribonucleotide-containing strand among the two strands at the
ribonucleotide portion, thereby introducing a nick into the hybrid
double-stranded nucleic acid.
[0310] (3) DNA Polymerase Used in the Present Invention.
[0311] A DNA polymerase having a strand displacement activity on a
DNA can be used in the present invention. Particularly, a DNA
polymerase substantially lacking a 5'3' exonuclease activity can be
preferably used.
[0312] As used herein, "a strand displacement activity" refers to
an activity that can effect a strand displacement, that is, that
can proceed DNA duplication on the basis of a sequence of a nucleic
acid as a template while displacing a DNA strand to release a
complementary strand that has been annealed to the template strand.
Additionally, a DNA strand released from a nucleic acid as a
template as a result of a strand displacement is referred to as "a
displaced strand" herein.
[0313] Any DNA polymerases having the strand displacement activity
can be used in the present invention. Examples thereof include
variants of DNA polymerases lacking their 5'3' exonuclease
activities derived from thermophilic bacteria of genus Bacillus
such as Bacillus caldotenax (hereinafter referred to as B. ca) and
Bacillus stearothermophilus (hereinafter referred to as B. st), as
well as large fragment (Klenow fragment) of DNA polymerase I from
Escherichia coli (E. coli). Both of mesophilic and heat-resistant
DNA polymerases can be preferably used in the present
invention.
[0314] B. ca is a thermophilic bacterium having an optimal growth
temperature of about 70.degree. C. Bca DNA polymerase from this
bacterium is known to have a DNA-dependent DNA polymerase activity,
an RNA-dependent DNA polymerase activity (a reverse transcription
activity), a 5'3' exonuclease activity and a 3' 5' exonuclease
activity. The enzyme may be either an enzyme purified from its
original source or a recombinant protein produced by using genetic
engineering techniques. The enzyme may be subjected to modification
such as substitution, deletion, addition or insertion by using
genetic engineering techniques or other means. Examples of such
enzymes include BcaBEST DNA polymerase (Takara Shuzo), which is Bca
DNA polymerase lacking its 5'3' exonuclease activity.
[0315] It is known that some DNA polymerases have an endonuclease
activity such as an RNase H activity under specific conditions.
Such a DNA polymerase can be used in the method of the present
invention. In one aspect, the DNA polymerase may be used under
conditions that allow the RNase H activity to express, e.g., in the
presence of Mn.sup.2+. In this case, the method of the present
invention can be conducted without the addition of an RNase H. The
present inventors have demonstrated that the Bca DNA polymerase
exhibits an RNase activity in a buffer containing Mn.sup.2+ for the
first time, and that the method for amplifying a nucleic acid of
the present invention can be carried out in a reaction mixture
containing no enzyme other than the Bca DNA polymerase. The
above-mentioned aspect is not limited to the use of the Bca DNA
polymerase. DNA polymerases that are known to have an RNase H
activity such as Tth DNA polymerase from Thermus thermophilus can
be used in the present invention.
[0316] (4) Composition of Reaction Buffer Used in the Present
Invention.
[0317] A reaction buffer that contains a buffering component, a
magnesium salt or another metal salt and dNTPs is used in the
present invention. Naturally, the type and the concentration of the
salt are optimized depending on the metal requirement or the like
of the enzyme to be used. Examples of the buffering components that
can be preferably used include, but are not limited to, Bicine,
Tricine, HEPES, tris and a phosphate (such as sodium phosphate and
potassium phosphate). Among these, a buffer that contains Bicine,
Tricine, HEPES or a phosphate as a buffering component is
preferable for the present invention. Although it is not intended
to limit the present invention, for example, when the reaction
temperature is high, a Bicine buffer of which the change in pH due
to the change in temperature is little is preferably used. A HEPES
buffer may be preferable depending on the type of RNase H used.
Thus, the optimal buffer may be selected depending on the reaction
temperature, the endonuclease or the DNA polymerase to be used and
the like. The final concentration of the buffering component ranges
5-100 mM, preferably 20-50 mM. The pH ranges 6.0-9.5, preferably
7.0-9.2. For example, a buffer containing 22-46 mM Tricine at pH
7.5-9.2 or a buffer containing 25-50 mM potassium phosphate at pH
7.0-8.0 is preferably used. Examples of magnesium salts that can be
preferably used include, but are not limited to, magnesium
chloride, magnesium acetate or magnesium sulfate. The final
concentration of the magnesium salt ranges 1-20 mM, preferably 2-10
mM. The final concentrations of dNTPs (a mixture of DATP, dCTP,
dGTP and dTTP) in a mixture as substrates for a DNA extension
reaction range 0.1-3.0 mM, preferably 0.2-1.2 mM. The amount of the
primers used in a reaction volume of 50 .mu.l ranges 1-1000 pmol,
preferably 10-150 pmol. Additionally, the reaction mixture may
contain an additive, for example, in order to stabilize the
amplification reaction. Bovine serum albumin (BSA) at a final
concentration of 0.1% or less, dimethyl sulfoxide (DMSO) at a final
concentration of 10% or less, putrescine dihydrochloride at a final
concentration of 4 mM or less, or propylenediamine at a final
concentration of 0.01% or less may be added. Additionally, NMP
(1-methyl-2-pyrrolidinone), glycerol, polyethylene glycol, dimethyl
sulfoxide and/or formamide may be contained. It is expected that
the addition of such an organic solvent reduces the non-specific
annealing of oligonucleotide primers.
[0318] The method of the present invention may be carried out by
adding a substance that inhibits the reverse transcription activity
of the DNA polymerase such as phosphonoformic acid (PFA). If a
substance that inhibits the reverse transcription activity is
added, the amplification of non-specific products other than the
target nucleic acid is reduced.
[0319] In another aspect, annealing of the nucleic acid as the
template to the chimeric oligonucleotide primer used in the present
invention before the amplification reaction is effective to reduce
non-specific annealing of an oligonucleotide primer in the
detection, amplification or production method of the present
invention. It is preferable to conduct the annealing using an
annealing solution that contains a substance that enhances the
annealing such as a polyamine (e.g., spermine or spermidine) or
propylenediamine. Preferably, the annealing solution containing the
polyamine also contains a salt. For example, without limitation,
the annealing solution may contain sodium chloride, potassium
chloride, potassium acetate, sodium acetate or the like and a
polyamine.
[0320] The annealing is usually conducted by incubating the
annealing solution containing the primer and the nucleic acid as
the template at a temperature at which a double-stranded nucleic
acid is denatured (e.g., 90 C or above) and then cooling the
solution to a reaction temperature used for the method of the
present invention or below.
[0321] After annealing, the nucleic acid amplification reaction of
the present invention is initiated by further adding other
necessary components such as a DNA polymerase, an RNase H and dNTPs
to the mixture.
[0322] The amount of an RNase H from Escherichia coli as an example
of endonucleases in a reaction volume of 50 .mu.l ranges preferably
3-200 U, more preferably 15-60 U. Similarly, the amount of an RNase
H from a bacterium of genus Pyrococcus or a bacterium of genus
Archaeoglobus as an example of endonuclease in a reaction volume of
50 .mu.l ranges preferably 3-200 U, more preferably 4-40 U. The
amount of BcaBEST DNA polymerase (Takara Shuzo) as an example of
DNA polymerases in a reaction volume of 50 .mu.l ranges preferably
0.5-100 U, more preferably 1-22 U.
[0323] When an endonuclease and a DNA polymerase is used in
combination in the method of the present invention, for example,
without limitation, a combination of an RNase H from Escherichia
coli, a bacterium of genus Pyrococcus or a bacterium of genus
Archaeoglobus and BcaBEST DNA polymerase is preferably used. It is
considered that the preferable units of the endonuclease and the
DNA polymerase may vary depending on the types the enzymes. In such
a case, the composition of the buffer used and the amount of the
enzymes added may be adjusted using the increase in detection
sensitivity or the amount of amplification product as an index. In
either case, it is natural to optimize the composition of the
reaction buffer and the like depending on the type of the enzyme to
be used.
[0324] (5) Method for Amplifying Nucleic Acid of the Present
Invention.
[0325] The method of the present invention can be conducted by
using at least one oligonucleotide primer as described above in (1)
in combination with the endonuclease as described above in (2) and
the DNA polymerase as described above in (3). Alternatively, a DNA
polymerase having an RNase H activity can be used under conditions
that allow the RNase H activity to express as described above.
[0326] dNTPs used for the PCR or the like (a mixture of DATP, dCTP,
dGTP and dTTP) can be preferably used as nucleotide triphosphates
that serve as substrates in the extension reaction in the method.
In addition, dUTP may be used as a substrate. The dNTPs may contain
a dNTP (deoxyribonucleotide triphosphate) analog such as
7-deaza-dGTP, triphosphate of dITP or the like as long as it serves
as a substrate for the DNA polymerase used. A derivative of a DNTP
or a dNTP analog may be used. A derivative having a functional
group such as a dUTP having an amino group may be contained. A
chimeric oligonucleotide primer is used in the method. The primer
can be prepared, for example, using a DNA synthesizer according to
a conventional synthesis method. A combination of the chimeric
oligonucleotide primer and a normal oligonucleotide primer can be
used in the method of the present invention.
[0327] If the activity of the enzyme used may be decreased in the
course of the reaction, the enzyme can be further added during the
reaction in the method of the present invention. Although it is not
intended to limit the present invention, for example, an RNase H
from Escherichia coli may be further added during a reaction in
which the RNase H is used. The added enzyme may be the same as that
contained in the reaction mixture at the beginning of the reaction
or it may be a different enzyme that exhibits the same activity.
Thus, the type or the property of the enzyme to be added is not
limited to a specific one as long as the addition during the
reaction provides effects such as increase in the detection
sensitivity or increase in the amount of amplification product.
[0328] The nucleic acid (DNA or RNA) used as a template in the
method of the present invention may be prepared or isolated from
any sample that may contain the nucleic acid. Alternatively, the
sample may be used directly in the method for amplifying a nucleic
acid of the present invention. Examples of the samples that may
contain the nucleic acid include, but are not limited to, samples
from organisms such as a whole blood, a serum, a buffy coat, a
urine, feces, a cerebrospinal fluid, a seminal fluid, a saliva, a
tissue (e.g., a cancerous tissue or a lymph node) and a cell
culture (e.g., a mammalian cell culture or a bacterial cell
culture), samples that contain a nucleic acid such as a viroid, a
virus, a bacterium, a fungi, a yeast, a plant and an animal,
samples suspected to be contaminated or infected with a
microorganism such as a virus or a bacterium (e.g., a food or a
biological formulation), and samples that may contain an organism
such as a soil and a waste water. The sample may be a preparation
containing a nucleic acid obtained by processing the
above-mentioned samples according to a known method. Examples of
the preparations that can be used in the present invention include
a cell destruction product or a sample obtained by fractionating
the product, the nucleic acid in the sample, or a sample in which
specific nucleic acid molecules such as mRNAs are enriched.
Furthermore, a nucleic acid such as a DNA or an RNA obtained
amplifying a nucleic acid contained in the sample by a known method
can be preferably used.
[0329] The preparation containing a nucleic acid can be prepared
from the above-mentioned materials by using, for example, lysis
with a detergent, sonication, shaking/stirring using glass beads or
a French press, without limitation. In some cases, it is
advantageous to further process the preparation to purify the
nucleic acid (e.g., in case where an endogenous nuclease exists).
In such cases, the nucleic acid is purified by a know method such
as phenol extraction, chromatography, ion exchange, gel
electrophoresis or density-gradient centrifugation.
[0330] When it is desired to amplify a nucleic acid having a
sequence derived from an RNA, the method of the present invention
may be conducted using as a template a cDNA synthesized by a
reverse transcription reaction that uses the RNA as a template. Any
RNA for which one can make a primer to be used in a reverse
transcription reaction can be applied to the method of the present
invention, including total RNA in a sample, RNA molecules such as,
mRNA, tRNA and rRNA as well as specific RNA molecular species.
[0331] Any primer that anneals to an RNA as a template under
reaction conditions used can be used in the reverse transcription
reaction. The primer may be a primer having a nucleotide sequence
that is complementary to a specific RNA as a template (a specific
primer), an oligo-dT (deoxythymine) primer and a primer having a
random sequence (a random primer). In view of specific annealing,
the length of the primer for reverse transcription is preferably 6
nucleotides or more, more preferably 9 nucleotides or more. In view
of oligonucleotide synthesis, the length is preferably 100
nucleotides or less, more preferably 30 nucleotides or less. A
chimeric oligonucleotide primer can be used as a primer for reverse
transcription. The chimeric oligonucleotide primer can also be
utilized as a primer for a strand displacement reaction in the
method for amplifying a nucleic acid of the present invention using
a cDNA obtained after reverse transcription as a template. Such a
primer may be any one that has the properties as described above in
(1) and that can be used in a reverse transcription reaction from
an RNA.
[0332] Any enzyme that has an activity of synthesizing a cDNA using
an RNA as a template can be used in the reverse transcription
reaction. Examples thereof include reverse transcriptases
originating from various sources such as avian myeloblastosis
virus-derived reverse transcriptase (AMV RTase), Molony murine
leukemia virus-derived reverse transcriptase (MMLV RTase) and
Rous-associated virus 2 reverse transcriptase (RAV-2 RTase). In
addition, a DNA polymerase that also has a reverse transcription
activity can be used. An enzyme having a reverse transcription
activity at a high temperature such as a DNA polymerase from a
bacterium of genus Thermus (e.g., Tth DNA polymerase) and a DNA
polymerase from a thermophilic bacterium of genus Bacillus is
preferable for the present invention. For example, DNA polymerases
from thermophilic bacteria of genus Bacillus such as a DNA
polymerase from B. st (Bst DNA polymerase) and Bca DNA polymerase
are preferable, although it is not intended to limit the present
invention. For example, Bca DNA polymerase does not require a
manganese ion for the reverse transcription reaction. Furthermore,
it can synthesize a cDNA while suppressing the formation of a
secondary structure of an RNA as a template under high-temperature
conditions. Both a naturally occurring one and a variant of the
enzyme having a reverse transcriptase activity can be used as long
as they have the activity.
[0333] In another aspect, after duplicating a DNA or an RNA
containing a nucleotide sequence to be amplified beforehand, the
duplicated product may be used as a nucleic acid as a template in
the method of the present invention. Examples of the methods for
duplication include, but are not limited to, a method in which an
appropriate host is transformed with a vector into which the
nucleic acid fragment containing the nucleotide sequence to be
amplified is inserted, the resulting transformant is cultured, the
vector into which the nucleic acid fragment containing the
nucleotide sequence to be amplified is inserted is extracted
therefrom and used. Any vectors can be used as long as they are
stably replicated in the host. For example, pUC series, pBluescript
series, pGEM series, cosmid type vectors and phage type vectors are
preferably used. Any hosts can be used as long as they can maintain
the vectors used. For example, Escherichia coli, which is readily
cultured, is exemplified.
[0334] In another aspect of the duplication method, after an RNA
having a nucleotide sequence to be amplified is transcribed using
an RNA polymerase and a nucleic acid fragment containing the
nucleotide sequence as a template, the RNA may be used as a
template for the method of the present invention directly or after
converting it into a cDNA by reverse transcription reaction. The
nucleic acid fragment containing the nucleotide sequence to be
amplified is not limited to a specific one as long as it has a
promoter sequence for an RNA polymerase. It may be inserted into a
vector having a promoter sequence for an RNA polymerase, ligated
with an adapter or a cassette having a promoter sequence for an RNA
polymerase at its end or enzymatically synthesized using a primer
having a promoter sequence for an RNA polymerase and an appropriate
template. Thus, a nucleic acid fragment containing a nucleotide
sequence to be amplified can be duplicated or amplified in a form
of an RNA using a promoter sequence for an RNA polymerase being
positioned as described above. Any vectors can be used as long as
they have promoter sequences for RNA polymerases. For example, pUC
series, pBluescript series, pGEM series, cosmid type vectors and
phage type vectors are preferably used. The vector can be
preferably used in its circular form or after being linearized. Any
RNA polymerases can be used for the duplication or amplification
method. For example, SP6 RNA polymerase, T7 RNA polymerase, T3 RNA
polymerase or the like can be preferably used.
[0335] Both of a double-stranded DNA such as a genomic DNA isolated
as described above or a PCR fragment and a single-stranded DNA such
as a cDNA prepared by a reverse transcription reaction from a total
RNA or an mRNA can be preferably used as a template DNA in the
present invention. The double-stranded DNA is preferably used
either after denaturing it into single-stranded DNAs or without the
denaturation.
[0336] The denaturing step may be eliminated in the nucleic acid
amplification method of the present invention if a linear
double-stranded DNA such as a PCR amplification product is used as
a template. The elimination may be accomplished by locating the
annealing site for the primer used in the method of the present
invention about 50 bases inside from the terminus of the DNA. If a
nucleic acid having a sequence from an RNA is to be amplified,
amplification reaction can be initiated by adding an RNA-cDNA
double-stranded nucleic acid obtained by reverse transcription
reaction using an RNA as a template to the amplification reaction
mixture of the present invention containing an RNase H to digest
the RNA strand and convert the nucleic acid into a single-stranded
cDNA. Furthermore, a reverse transcription reaction using an RNA as
a template and a DNA amplification reaction using a cDNA generated
by the reverse transcription reaction as a template can be
conducted with one DNA polymerase in the DNA synthesis method of
the present invention. Such a DNA polymerase has a reverse
transcriptase activity and a strand displacement activity.
[0337] The suitable length of the template is one that provides a
sufficient binding of the primer sequence due to the presence of
the whole target sequence or at least a sufficient part of the
target sequence in the fragment.
[0338] Without limitation, if a DNA as a template is a
double-stranded DNA, the DNA can be denatured into single-stranded
DNAs to allow a primer to bind to the DNA strand as the template in
the method of the present invention. Incubating the double-stranded
DNA at a temperature at which it is denatured (e.g., about
95.degree. C.) is preferable for the denaturation. Other processes
include one in which an elevated pH is used. In this case, the pH
should be lowered upon the amplification reaction in order to allow
an oligonucleotide primer to bind to a target. A nucleic acid is
successively amplified under isothermal conditions after denaturing
a double-stranded DNA into single-stranded DNAs or, if an RNA is
used as a template, preparing a cDNA (a single-stranded DNA) by a
reverse transcription reaction.
[0339] "Successively" means that a reaction proceeds without a
change in the reaction temperature or the composition of the
reaction mixture. As used herein, "isothermal" means conditions of
a substantially constant temperature under which an enzyme and a
nucleic acid strand function in each step.
[0340] The nucleic acid amplification reaction of the present
invention may be conducted at a normal temperature (e.g.,
37.degree. C.) by using a mesophilic DNA polymerase such as Klenow
fragment. It can also be conducted at a high temperature (e.g.,
50.degree. C. or higher, or 60.degree. C. or higher) by using
heat-resistant enzymes (an endonuclease and a DNA polymerase). In
this case, non-specific annealing of a primer is suppressed,
resulting in increase in the specificity of DNA amplification.
Furthermore, the problem of forming secondary structure of a DNA as
a template is solved, resulting in increase in the ability of
extension of a DNA polymerase. A reverse transcription reaction and
the nucleic acid amplification can be successively conducted in the
method. In this case, a DNA having a sequence derived from an RNA
can be amplified by combining the use of a reverse transcriptase
with the above-mentioned reaction or by using a DNA polymerase
having a reverse transcription activity.
[0341] In each aspect of the present invention, preferably, a
chimeric oligonucleotide primer that is complementary to a
single-stranded DNA as a template is first annealed to the DNA,
although it is not intended to limit the present invention. A DNA
that is complementary to the DNA as the template (a primer-extended
strand) is then extended along the remained sequence of the DNA as
the template from the 3'-terminus of the primer by the action of a
DNA polymerase to synthesize a double-stranded DNA. An endonuclease
acts on the double-stranded DNA and begins to reextend a DNA from
the primer portion of the primer-extended strand de novo. In one
aspect of the present invention, the endonuclease acts as a nicking
enzyme that introduces a nick into the double-stranded DNA or it
alters the structure of the double-stranded DNA composed of the
chimeric oligonucleotide primer and the DNA as the template,
although the present invention is not restricted by a theory. A DNA
polymerase having a strand displacement activity re-extends a DNA
strand from the 3'-terminus of the nick introduced in the
double-stranded DNA to generate a new primer-extended strand while
releasing the DNA downstream from the 3.sup.1-terminus of the nick.
Thus, the new primer-extended strand replaces the previously
synthesized primer-extended strand.
[0342] The method for amplifying a nucleic acid of the present
invention can be carried out using two primers, i.e., a chimeric
oligonucleotide primer that is complementary to a nucleic acid as a
template and another chimeric oligonucleotide primer that is
complementary to a displaced strand. In this case, one primer binds
to a DNA strand as a template to cause a strand displacement
reaction, whereas another primer binds to a displaced strand
released as a result of the strand displacement reaction to
initiate another strand displacement reaction. It is clear that a
reaction product with one primer can function as a template for
another primer if this aspect is used. Thus, the amount of
amplification product increases in a non-linear manner as the
amount of the template increases.
[0343] When the method for amplifying a nucleic acid of the present
invention is conducted using a double-stranded DNA as a template,
both strands can serve as templates in the amplification reaction
by using chimeric oligonucleotide primers that anneal to the
respective two strands. If the reaction is initiated after
denaturing the double-stranded DNA, a chimeric oligonucleotide
primer, four deoxyribonucleotide triphosphates (dNTPs), a DNA
polymerase and an endonuclease are added to a reaction mixture
before or after the double-stranded DNA is denatured. If heat
treatment is used for denaturing the double-stranded DNA and a
heat-resistant enzyme is not used, it is preferable to add the
enzyme after the denaturation.
[0344] In the aspect of the nucleic acid amplification method of
the present invention in which a double-stranded DNA as a template
and two chimeric oligonucleotide primers are used, switching of
templates may occur among the template-extended strand
intermediates during the extension reaction from the primers to
generate a double-stranded nucleic acid consisting of the
synthesized primer-extended strands being annealed each other,
although it depends on the reaction conditions or the like. The
double-stranded nucleic acid has chimeric oligonucleotide primers
at both ends. Then, reaction of extending complementary strands
comprising strand displacement can be initiated from both of the
ends again. As a result of the reaction, an amplification product
having the primer sequence at one end is generated. Furthermore, if
switching of templates occurs during the reaction, a
double-stranded nucleic acid similar to one that described above is
generated again.
[0345] The present invention provides a method for amplifying a
nucleic acid which comprises using a DNA polymerase having a strand
displacement activity to effect a template switching reaction. In
the template switching reaction in the presence of a
double-stranded nucleoc acid as a template, two chimeric
oligonucleotide primers substantially complementary to the
nucleotide sequences of the respective strands and a DNA polymerase
having a strand displacement activity, two primer-extended strands
complementary to the template are synthesized. Template switching
of each of the primer-extended strands from the template to the
other primer-extended strand takes place during the synthesis of
the primer-extended strands.
[0346] As used herein; a template switching reation refers to a
reaction in which when complementary strands are synthesized by
strand displacement reactions from the both sides of a
double-stranded nucleic acid, a DNA polymerase switches the
template and synthesizes a complementary strand thereafter using
the other complementary strand newly synthesized by another DNA
polymerase as a template. In other words, a template switching
reaction refers to a reaction in which a double-stranded nucleic
acid as a template is treated with primers and a DNA polymerase
having a strand displacement activity to generate extended strands
complementary to the template, wherein a DNA polymerase that
synthesized the primer-extended strands actively switches the
template from the original templates to the other primer-extended
strands during the synthesis of the extended strands. The ability
of the DNA polymerase to effect a template switching reaction can
be determined, for example, according to the method as described in
Example 45 below, although it is not intended to limit the present
invention.
[0347] A DNA polymerase capable of an effect the template switching
reaction during strand displacement reaction can be preferably used
for the present invention. For example, a variant enzyme of Bca DNA
polymerase lacking a 5'3' exonuclease activity is preferably used
in particular. Such an enzyme is commercially available as BcaBEST
DNA polymerase (Takara Shuzo). It can also be prepared from
Escherichia coli HB101/pU1205 (FERM BP-3720) which contains the
gene for the enzyme according to the method as described in
Japanese Patent No. 2978001.
[0348] Although it is not intended to limit the present invention,
the mode of reaction of the method for amplifying a nucleic acid of
the present invention is considered as follows, for example.
[0349] In the method for amplifying a nucleic acid of the present
invention, a double-stranded nucleic acid as a template is treated
in the presence of an RNase H with two chimeric oligonucleotide
primers that are substantially complementary to the nucleotide
sequences of the respective strands and a DNA polymerase having a
strand displacement activity to synthesize primer-extended strands
that are complementary to the template. A double-stranded nucleic
acid consisting of the synthesized primer-extended strands being
annealed each other and a double-stranded nucleic acid consisting
of the templates being annealed each other to which the two primers
are annealed as a result of template switching reaction can be
obtained. The latter double-stranded nucleic acid is reused as a
template.
[0350] The double-stranded nucleic acid consisting of the
primer-extended strands being annealed each other is cleaved with
an RNase H at sites that contain the ribonucleotides. Nucleic acids
that are complementary to the template are extended using a DNA
polymerase having a strand displacement activity from the
3'-termini of the respective primer portions of the double-stranded
nucleic acid by an effect of strand displacements. A
double-stranded nucleic acid consisting of the primer-extended
strands being annealed each other and a double-stranded nucleic
acid consisting of the templates being annealed each other to which
the two primers are annealed as a result of template switching
reaction can be obtained.
[0351] If the template switching reaction does not take place, two
types of double-stranded nucleic acids each consisting of the
template and the primer-extended strand can be obtained.
[0352] Nucleic acids that are complementary to the template are
extended using a DNA polymerase having a strand displacement
activity from the 3'-termini of the respective primer portions of
the double-stranded nucleic acid. As a result of template switching
reaction, a double-stranded nucleic acid consisting of the
primer-extended strands being annealed each other and a
double-stranded nucleic acid consisting of the templates being
annealed each other to which the two primers are annealed can be
obtained. The double-stranded nucleic acid to which the two primers
are annealed is reused as a template.
[0353] If the template switching reaction does not take place, two
types of double-stranded nucleic acids each consisting of the
template and the primer-extended strand can be obtained.
[0354] The two types of double-stranded nucleic acids are cleaved
with an RNase H at sites that contain the ribonucleotides. Nucleic
acids that are complementary to the template are extended using a
DNA polymerase having a strand displacement activity from the
3'-termini of the respective primer portions of the double-stranded
nucleic acid by an effect of strand displacements.
[0355] In the method for amplifying a nucleic acid of the present
invention, a double-stranded nucleic acid as a template is treated
in the presence of an RNase H with two chimeric oligonucleotide
primers that are substantially complementary to the nucleotide
sequences of the respective strands and a DNA polymerase having a
strand displacement activity and primer-extended strands that are
complementary to the template are synthesized. If the template
switching reaction does not take place, two types of
double-stranded nucleic acids each consisting of the template and
the primer-extended strand can be obtained.
[0356] In the amplification method of the present invention, the
chimeric oligonucleotide primer-extended strand may be cleaved at a
site that contains the ribonucleotide such that the 5' fragment
(primer portion) resulting from the cleavage does not contain the
ribonucleotide. A primer-extended strand extended from the thus
generated primer portion is no longer cleaved by an endonuclease.
As a result, an amplification product having the primer sequence at
its end is generated.
[0357] As described above, an amplification product without the
primer sequence and a product having the primer sequence(s) at one
or both of the ends may be generated in the nucleic acid
amplification method of the present invention. These products are
included in the amplification products herein.
[0358] An example of the method for amplifying a nucleic acid of
the present invention is illustrated in FIGS. 33 to 36. In other
words, FIGS. 33 to 36 illustrate an exemplary nucleic acid
amplification in the nucleic acid amplification method of the
present invention.
[0359] FIGS. 33 to 36 illustrate an exemplary nucleic acid
amplification in the presence of a DNA as a template which is a
double-stranded nucleic acid, a pair of chimeric oligonucleotide
primers synthesized on the basis of the nucleotide sequence
information of the DNA as the template (in the figures, the
chimeric oligonucleotide primers have three ribonucleotides at
their 3'-termini; open circles in the figures represent the
ribonucleotides), a strand displacement type DNA synthetase (DNA
polymerase) having a strand displacement activity, an RNase H which
is a ribonuclease that cleaves at a DNA-RNA hybrid site, and dNTPs
which are substrates to be incorporated into the extended
strands.
[0360] As shown in FIG. 33, the chimeric oligonucleotide primers
synthesized on the basis of the nucleotide sequence information of
the DNA as the template are annealed to the specific portions of
the DNA as the template. DNA strands are extended from the
3'-termini of the respective chimeric oligonucleotide primers as a
result of the strand displacement reaction as indicated with Step
1.
[0361] Next, as shown in FIG. 34, some of the primer-extended
strands extended from upstream and downstream are released from the
original templates as a result of the template switching reaction
as indicated with Step 2. The primer-extended strands are annealed
each other at their 3' portions. Complementary strands are extended
from the annealed extended strands, forming a double-stranded DNA
consisting of the primer-extended strands being annealed each
other. Additionally, a double-stranded DNA consisting of the
displaced strands being annealed each other to which the
above-mentioned chimeric oligonucleotide primers are annealed is
generated. This is utilized as the starting material in FIG.
34.
[0362] As indicated with Step 3 in FIG. 35, only one strand
containing an RNA derived from the chimeric oligonucleotide primer
of the double-stranded DNA in FIG. 34 consisting of the
primer-extended strands being annealed each other is cleaved by the
action of an RNase H at the DNA/RNA hybrid site of the
double-stranded DNA, resulting in introduction of a nick in the
double-stranded DNA.
[0363] Subsequently, the strand displacement reaction takes place
from the nick in the double-stranded DNA and a DNA is extend as
indicated with Step 4 in FIG. 35. Next, a template switching
reaction like that in Step 2 in FIG. 34 takes place in some degree
or at some ratio as indicated with Step 5 in FIG. 35, resulting in
a double-stranded DNA consisting of the amplification products,
i.e., the primer-extended strands being annealed each other.
[0364] In addition, a double-stranded DNA consisting of the
displaced strands being annealed each other to which the
above-mentioned chimeric oligonucleotide primers are annealed are
generated.
[0365] Next, as shown in FIG. 36, DNA strands are extended as a
result of the strand displacement reaction from the 3'-termini of
the respective chimeric oligonucleotide primers in the
double-stranded DNA in FIG. 35 which consists of the displaced
strands being annealed each other to which the chimeric
oligonucleotide primers are annealed. Similar template switching
reactions take place in Step 2 and Step 5 in some degree, resulting
in a double-stranded DNA consisting of the primer-extended strands
being annealed each other. This double-stranded DNA is brought back
to Step 3 in FIG. 35. The reaction starts on Step 3 again. A
double-stranded DNA which consists of the displaced strands being
annealed each other to which the chimeric oligonucleotide primers
are annealed is generated and utilized as a starting material in
FIG. 36. As a result, a chain reaction, in which these
double-stranded nucleic acids are repeatedly generated, takes place
to specifically amplify and produce a region bounded by a pair of
chimeric oligonucleotide primers.
[0366] In the nucleic acid amplification method of the present
invention using a chimeric oligonucleotide, a polymer in which the
regions to be amplified are connected each other may be generated.
The polymer has a structure in which plural regions to be amplified
are repeated in the same direction. The polymers are observed upon
electrophoretic analysis of amplification products as laddered
bands. It is considered that the generation of such polymers is
influenced by the region to be amplified, the size of the region,
the flanking regions, the nucleotide sequence of the chimeric
oligonucleotide primer to be used, the reaction conditions and the
like.
[0367] The polymer as described above contains plural regions to be
amplified. For example, the polymer is useful when detection of a
nucleic acid containing a region to be amplified is intended
because it hybridizes to a number of probes upon hybridization
using an appropriate probe and generates a intensive signal. The
region to be amplified or a portion thereof can be obtained from
the polymer as a monomer by using digestion with a restriction
enzyme or the like in combination.
[0368] The DNA polymerase used in the present invention should
synthesize an extended strand from the 3'-terminus of the primer
portion towards the downstream while displacing a previously
extended DNA strand. It is important that the DNA polymerase should
not exhibit a 5'3' exonuclease activity that may digest the
displaced strand. For example, Klenow fragment, which is an
exonuclease-deficient variant of DNA polymerase I from Escherichia
coli, a similar fragment derived from Bst DNA polymerase (New
England Biolabs), and BcaBEST DNA polymerase from B. ca (Takara
Shuzo) are useful as such a DNA polymerase. Sequenase 1.0 and
Sequenase 2.0 (United States Biochemical), and T5 DNA polymerase
and .phi.29 DNA polymerase as described in Gene, 97:13-19 (1991)
can also be used. A polymerase that normally has a 5'3' exonuclease
activity can be used in the DNA synthesis method of the present
invention if addition of an appropriate inhibitor can inhibit the
activity.
[0369] The method for amplifying a nucleic acid of the present
invention may be conducted at varying temperatures or it may be
conducted isothermally. Varying temperatures means that the
reaction temperatures are changed for respective steps such that
the change does not interfere with the reactions in the steps.
Specifically, varying temperatures refers to change in temperature
to that suitable for, for example, each of annealing of a primer,
synthesis reaction of a complementary strand, nicking of a
complementary strand and a displacement reaction.
[0370] On the other hand, isothermal means that the reaction
temperature for each step is unchanged and each step is conducted
at a substantially constant temperature. It is natural to select
the temperature to optimize the reaction conditions in both
cases.
[0371] One feature of the method for amplifying a nucleic acid of
the present invention is that the method does not require adjusting
the temperature up and down during the nucleic acid synthesis.
Thus, the present invention provides a method for isothermally
synthesizing a nucleic acid. Many of conventional nucleic acid
amplification methods require adjusting the temperature up and down
to dissociate a target from a synthesized strand. These methods
require a special reaction equipment such as a thermal cycler for
this purpose. However, the method of the present invention can be
conducted only using an equipment that can keep a constant
temperature. As described above, the method of the present
invention can be conducted at a single temperature. Preferably, it
is conducted by selecting the reaction temperature and the
stringency level such that non-specific annealing of a primer is
reduced and such that the primer specifically anneals to a nucleic
acid as a template. Although it is not intended to limit the
present invention, the method of the present invention can be
conducted under high-temperature conditions by using a
heat-resistant enzyme as described above. In addition, it is
preferable to conduct the method of the present invention at an
appropriate temperature for sufficiently retaining the activity of
the enzyme used in order to maintain the reaction efficiency at
high level. Thus, the reaction temperature is preferably about
20.degree. C. to about 80.degree. C., more preferably about
30.degree. C. to about 75.degree. C., most preferably about
50.degree. C. to about 70.degree. C. although it varies depending
on the enzyme used. When the reaction is conducted under
high-temperature conditions in particular, it is preferable to use
a longer primer than that for a reaction at a normal temperature.
The sequence and the length of the primer appropriate for the
reaction temperature may be determined, for example, with reference
to its Tm value. Alternatively, a commercially available software
for designing a primer such as OLIGO.TM. Primer Analysis software
(Takara Shuzo) may be used. For example, when a reaction
temperature of 55.degree. C. to 60.degree. C. or 65.degree. C. is
used, the primer used for the method of the present invention may
be, for example, without limitation, 12-100 nucleotides in length,
preferably 14-50 nucleotides in length, more preferably 15-40
nucleotides in length. An example of effects brought by the
elevated reaction temperature is the solution of a problem of
forming secondary structure of a DNA as a template. The elevated
reaction temperature enables amplification of a desired nucleic
acid even if a nucleic acid having a high GC content is used as a
template. Furthermore, it is similarly effective in amplifying a
region of a long chain length. Such effect is observed in a range
between about 60 bp and about 20 kbp, specifically between about
110 bp and about 4.3 kbp, more specifically about 130 bp and about
1500 bp.
[0372] The amplification efficiency can be increased by adjusting
the reaction temperature in accordance with the GC content of the
nucleic acid as the template. For example, if a nucleic acid having
a low GC content is used as a template, the amplification reaction
of the present invention can be conducted at 50 to 55 C, although
the temperature depends on the chain length to be amplified and the
Tm value of the primer.
[0373] Use of a DNA polymerase having a reverse transcriptase
activity (e.g., BcaBEST DNA polymerase) in the method of the
present invention can make the amplification of a nucleic acid from
an RNA, which comprises a step of preparing a cDNA from an RNA (a
reverse transcription reaction), be conveniently conducted.
Alternatively, a product obtained by independently conducting a
step of preparing a cDNA from an RNA, i.e., a cDNA, can be used in
the method of the present invention as the DNA as a template.
[0374] In each case, the reaction in the method of the present
invention is repeated until it is terminated by appropriate means,
for example, by inactivating the enzyme or by lowering the reaction
temperature, or until the reaction is deprived of one of the
substrates.
[0375] FIG. 40 illustrates one embodiment in which a
single-stranded DNA as a template and two primers are used.
Respective steps, which are successively conducted in parallel, are
described below:
[0376] (1) a step of annealing a single-stranded DNA as a template
with a chimeric oligonucleotide primer;
[0377] (2) a step of effecting a DNA extension reaction from the
3'-terminus of the primer to form a primer-extended strand;
[0378] (3) a step of cleaving at a site that contains a
ribonucleotide in the primer with an endonuclease;
[0379] (4) a step of effecting a strand displacement using a DNA
polymerase from the cleavage site in step (3);
[0380] (5) a step of reusing a double-stranded DNA, which is
composed of a template obtained in step (4) and a regenerated
primer-extended strand, in step (3), while utilizing a released
displaced strand in a reaction of step (6) and the following
steps;
[0381] (6) a step annealing an oligonucleotide primer that is
different from that in step (1) with the released displaced strand
in step (5) as a template;
[0382] (7) a step of effecting a DNA extension reaction from the
3'-terminus of the primer to form a primer-extended strand;
[0383] (8) a step of cleaving at a site that contains a
ribonucleotide in the primer with an endonuclease;
[0384] (9) a step of effecting a strand displacement using a DNA
polymerase from the cleavage site in step (8); and
[0385] (10) a step of reusing a template obtained in step (9) and a
regenerated primer-extended strand in step (8).
[0386] When a double-stranded DNA is used as a template, each of
the single-stranded DNAs obtained after denaturing the
double-stranded DNA serves as the template in step (1). Therefore,
the amount of amplification product is more than that obtained with
a single-stranded DNA as a template. In addition, detection of the
amplification product can be conducted in a shorter time than that
required when a single-stranded DNA is used as a template.
[0387] The method for amplifying a nucleic acid of the present
invention can be used for various experimental procedures that
utilize amplification of a nucleic acid including detection,
labeling and sequencing of a nucleic acid.
[0388] Furthermore, the method for amplifying a nucleic acid of the
present invention can be used for an in situ nucleic acid
amplification method, a method for amplifying a nucleic acid on a
solid substrate such as a DNA chip, or a multiplex nucleic acid
amplification method in which plural regions are simultaneously
amplified.
[0389] One of the features of the method for amplifying a nucleic
acid of the present invention is its ability to prepare a
single-stranded DNA. One or two chimeric oligonucleotide primers
can be used in the method for this purpose. For example, if two
oligonucleotide primers are used, the method of the present
invention can be conducted applying a similar primer ratio to the
so-called asymmetric-PCR in which an amplification reaction is
carried out by using an excess amount of one oligonucleotide primer
relative to another. The primer ratio is, without limitation,
preferably in a range of 1:10 to 1:500, more preferably in a range
of 1:10 to 1:100. As a result, the amount of the replacement
product from one strand becomes excessive relative to that from
another.
[0390] According to the method for amplifying a nucleic acid of the
present invention, a single-stranded DNA substantially free of a
complementary strand thereto can be prepared. For example, a
single-stranded DNA for producing a material having an immobilized
nucleic acid such as a DNA chip, a single-stranded DNA probe for
detecting a target nucleic acid, or a mega-primer for the
long-chain PCR can be readily produced in a short time. Only a
sense sequence or an antisense sequence can be selectively
amplified by using the method of the present invention. Thus, the
present invention is also useful as a method for producing a
nucleic acid having a sense sequence or a antisense sequence.
[0391] A region of a nucleic acid of interest can be amplified even
from a trace amount of a nucleic acid as a template by conducting
the method of the present invention in a buffer of Bicine, Tricine,
HEPES, phosphate or tris.
[0392] Furthermore, the methods for amplifying a nucleic acid of
the present invention does not require the specific reaction
equipment that can adjust a temperature with the passage of time.
Therefore, an amplification reaction can be conducted in a large
volume of reaction mixture. Thus, a nucleic acid (e.g., for medical
use) can be industrially produced in large quantities.
[0393] The utilization efficiency of the primer in the method for
amplifying a nucleic acid of the present invention is about 100%,
which may be 5- to 10-fold higher than that in a conventional
method such as the PCR.
[0394] The nucleic acid amplification method of the present
invention can produce an amplification product with high fidelity
to the nucleotide sequence of the template nucleic acid. When the
frequency of error in the DNA synthesis in the method of the
present invention was confirmed by analyzing the nucleotide
sequences of resulting amplification products, the frequency of
error found in amplification products obtained by the method of the
present invention was equivalent to that by LA-PCR which is known
to be able to amplify a nucleic acid with high fidelity. In other
words, the method of the present invention has fidelity equivalent
to that of the LA-PCR.
[0395] (6) Method for detecting target nucleic acid of the present
invention and kit for the method. A target nucleic acid in a sample
can be detected by using the method for amplifying a nucleic acid
of the present invention. The detection method comprises:
[0396] (a) amplifying a target nucleic acid by the method for
amplifying a nucleic acid of the present invention as described
above; and
[0397] (b) detecting the target nucleic acid amplified in the step
above.
[0398] In step (a) above, if an RNA is used as a template, the
reverse transcription reaction and the nucleic acid amplification
reaction may be conducted in one step. Although it is not intended
to limit the present invention, for example, a combination of AMV
RTase, MMLV RTase or RAV-2 RTase and Bca DNA polymerase lacking
5'3' exonuclease can be preferably used as a combination of a
reverse transcriptase and a strand displacement-type DNA
polymerase.
[0399] The method can be utilized to detect or quantify a specific
gene in a sample. In other words, a specific gene can be detected
or quantified from all samples suspected to contain a nucleic acid
such as a DNA or an RNA. Examples of the samples from which a
specific gene can be detected or quantified include, but are not
limited to, samples from organisms such as a whole blood, a serum,
a buffy coat, a urine, feces, a cerebrospinal fluid, a seminal
fluid, a saliva, a tissue (e.g., a cancerous tissue or a lymph
node) and a cell culture (e.g., a mammalian cell culture or a
bacterial cell culture), samples that contain a nucleic acid such
as a viroid, a virus, a bacterium, a fungi, a yeast, a plant and an
animal, samples suspected to be contaminated or infected with a
micoorganism such as a virus or a bacterium (e.g., a food or a
biological formulation), and samples that may contain an organism
such as a soil and a waste water. For example, a viroid, a virus, a
fungi, a bacterium or other microorganisms in a sample can be
detected or quantified on the basis of the presence or the content
of a specific gene derived from these microorganisms as a target.
Particularly, a method for detecting a pathogenic microorganism is
useful in fields of sanitation and environment. Furthermore, the
method of the present invention can be used to distinguish a
genotype of an organism or to determine the expression level of a
gene. Particularly, detection or confirmation of the expression
state of a disease-related gene, e.g., a gene related to
canceration of cells is useful in a field of medicine. Both of an
RNA and a DNA can be preferably used as the nucleic acid as the
template in the detection.
[0400] The method for detecting a target nucleic acid of the
present invention can be used to distinguish the difference in the
nucleotide sequence of the target nucleic acid. In this aspect, the
chimeric oligonucleotide primer to be used is designed such that
the 3'-terminal portion of the primer is positioned close to the
specific base of the target nucleotide sequence to be
distinguished. For example, it is designed such that a hydrogen
bond is formed between the base and the 3'-terminal base of the
primer. If a mismatch exists between the nucleotide sequence of the
3'-terminal portion of the primer and the nucleotide sequence of
the template, amplification from the target nucleic acid does not
take place and no amplification product is generated using the
above-mentioned chimeric oligonucleotide primer for amplification
reaction. Information concerning a specific base in a gene such as
a point mutation or a single nucleotide polymorphism (SNP) can be
obtained using the method.
[0401] The method for detecting a target nucleic acid of the
present invention can be conducted by amplifying the target nucleic
acid directly from a sample containing the nucleic acid. In this
case, the chain length of the target nucleic acid to be amplified
is not limited to a specific one. For example, a region of 200 bp
or shorter, preferably 150 bp or shorter is effective for sensitive
detection of the target nucleic acid. The target nucleic acid in
the sample can be detected with high sensitivity by designing the
chimeric oligonucleotide primers of the present invention to result
in the chain length to be amplified as described above.
[0402] In addition, a target nucleic acid can be detected with more
sensitivity even from a trace amount of a nucleic acid sample in
the detection method of the present invention by using a reaction
buffer containing Bicine, Tricine, HEPES, phosphate or tris as a
buffering component and an annealing solution containing spermidine
or propylenediamine as exemplified in (4) above. In this case, the
endonuclease and the DNA polymerase to be used are not limited to
specific ones. For example, a combination of an RNase H from
Escherichia coli, a bacterium of genus Pyrococcus or a bacterium of
genus Archaeoglobus and BcaBEST DNA polymerase is preferable. It is
considered that the preferable units of the endonuclease and the
DNA polymerase may vary depending on the types the enzymes. In such
a case, the composition of the buffer and the amount of the enzymes
added may be adjusted using the increase in detection sensitivity
or the amount of amplification product as an index.
[0403] In the detection method of the present invention, dUTP may
be incorporated as a substrate during amplification of a target
nucleic acid. Thus, if dUTP is used as a substrate, it is possible
to prevent carry-over contamination of amplification products by
degrading amplification products utilizing uracil N-glycosidase
(UNG).
[0404] Known methods for detecting a nucleic acid can be used for
step (b). Examples of such methods include detection of a reaction
product having a specific size by electrophoresis, and detection by
hybridization with a probe. Furthermore, a detection method in
which magnetic beads are combined can be preferably used. A
fluorescent substance such as ethidium bromide is usually used in
the detection by electrophoresis. The hybridization with a probe
may be combined with the detection by electrophoresis. The probe
may be labeled with a radioisotope or with a non-radioactive
substance such as biotin or a fluorescent substance. Additionally,
use of a labeled nucleotide in step (a) may facilitate the
detection of amplification product into which the labeled
nucleotide is incorporated, or may enhance the signal for detection
utilizing the label. Furthermore, a fluorescence polarization
method, a fluorescence energy transition or the like can also be
utilized for the detection. The target nucleic acid can be detected
automatically or quantified by constructing a suitable detection
system. In addition, detection with naked eyes by a hybrid
chromatography method can be preferably used.
[0405] A ribonucleotide (RNA) probe labeled with two or more
fluorescent substances positioned at a distance that results in a
quenching state can be used in the detection method of the present
invention. The probe does not emit fluorescence. When it is
annealed to a DNA amplified from a target nucleic acid that is
complementary to the probe, RNase H digests the probe. The distance
between the fluorescent substances on the probe then increases,
resulting in the emission of fluorescence. Thus, the emission
reveals the presence of the target nucleic acid. If RNase H is used
in the method for amplifying a nucleic acid of the present
invention, a target nucleic acid can be detected only by adding the
probe to the reaction mixture. For example, a combination of
fluorescent substances, 6-carboxyfluorescein (6-FAM) and
N,N,N',N'-tetramethyl-6-carb- oxyrhodamine (TAMRA), can be
preferably used for labeling the probe.
[0406] The present invention further provides a probe used in the
above-mentioned method for detecting a target nucleic acid. The
probe of the present invention is not limited to specific one as
long as it can hybridize to a target nucleic acid amplified by the
nucleic acid amplification method of the present invention under
normal hybridization conditions. In view of specific detection of
amplification product, a probe that hybridizes under conditions,
for example, known to those skilled in the art as being stringent
is preferable. The stringent hybridization conditons are described
in, for example, T. Maniatis et al. (eds.), Molecular Cloning: A
Laboratory Manual 2nd ed., 1989, Cold Spring Harbor Laboratory.
Specifically, the stringent conditions are exemplified by the
following: incubation at a temperature about 25 C lower than the Tm
of the probe to be used for 4 hours to overnight in 6.times.SSC
(1.times.SSC: 0.15 M NaCl, 0.015 M sodium citrate, pH 7.0)
containing 0.5% SDS, 5.times. Denhardt's (0.1% bovine serum albumin
(BSA), 0.1% polyvinylpyrrolidone, 0.1% Ficoll 400) and 100 mg/ml
salmon sperm DNA. A probe having a label as described above may be
used as the probe for facilitating the detection of the target
nucleic acid.
[0407] The method for amplifying a nucleic acid under isothermal
conditions of the present invention does not require the use of an
equipment such as a thermal cycler. The number of primers used in
the amplification method of the present invention can be one or
two, which is less than that used in a conventional method. Since
reagents such as dNTPs used for PCR and the like can be applied to
the method of the present invention, the running cost can be
reduced as compared with a conventional method. Therefore, the
method of the present invention can be preferably used, for
example, in a field of genetic test in which the detection is
routinely conducted. The method of the present invention provides a
greater amount of an amplification product in a shorter time than
the PCR. Therefore, the method of the present invention can be
utilized as a convenient, rapid and sensitive method for detecting
a gene.
[0408] In genetic analysis on a genomic level, attempts are made to
make the reaction system small and to increase the degree of
integration in order to analyze a large amount of nucleotide
sequences. An system has been developed for this purpose by
utilizing the latest hyperfine processing techniques in which basic
processes for genome analysis (e.g., extraction of DNA from cells,
DNA amplification reaction, electrophoresis, hybridization,
detection of the DNA of interest, etc.) are integrated on a
microchip of several square centimeters to fingertip size. Such a
system is called as a microchip or a nanochip.
[0409] Application of the PCR to the system as a gene amplification
reaction is currently considered. However, since the PCRs requires
means for repeatedly controlling temperature up and down over time,
the system would become complicated. By contrast, since the system
can be simplified using the method of the present invention which
can amplify a nucleic acid under isothermal conditions, the method
is quite suitably utilized for the integrated system as described
above. A highly integrated system can be constructed by utilizing
the techniques of the present invention.
[0410] (7) Kit of the Present Invention
[0411] The present invention provides a kit used for the method for
amplifying or detecting a nucleic acid of present invention as
described above. In one embodiment, the kit is in a packaged form
and contains instructions regarding the use of a DNA polymerase and
an endonuclease in a strand displacement reaction. Also, a kit that
contains a DNA polymerase having a strand displacement activity, an
endonuclease, and a buffer for a strand displacement reaction is
preferably used for the method of the present invention.
Alternatively, a commercially available DNA polymerase having a
strand displacement activity and/or endonuclease may be selected
and used according to the instructions. Additionally, the kit may
contain a reagent for a reverse transcription reaction that is used
when an RNA is used as a template. The DNA polymerase can be
selected from the DNA polymerases to be used in the present
invention as described above in (3). The endonuclease can be
selected from the endonucleases as described above in (2). One
having the reaction buffer composition as described above in (4)
can be preferably used as the buffer for the strand displacement
reaction.
[0412] "Instructions" are printed matters describing a method of
using the kit, e.g., a method for preparing a reagent solution for
a strand displacement reaction, recommended reaction conditions and
the like. The instructions include an instruction manual in a form
of a pamphlet or a leaflet, a label stuck to the kit, and
description on the surface of the package containing the kit. The
instructions also include information disclosed or provided through
electronic media such as the Internet.
[0413] The kit of the present invention may further contain a
reaction buffer containing Bicine, Tricine, HEPES, phosphate or
tris as a buffering component and an annealing solution as
exemplified in (4) above. Additionally, it may contain a DNA
polymerase having a strand displacement activity and an RNase H.
Furthermore, the kit may contain a modified deoxyribonucleotide or
a deoxynucleotide triphosphate analog.
[0414] The kit used in the method for detecting a target nucleic
acid may further contain an appropriate chimeric oligonucleotide
primer for amplifying the target nucleic acid and a reagent for
detecting the amplified target nucleic acid such as a probe in
addition to the instructions and the reagents for amplification
reaction as described above.
[0415] In addition, the kits of the present invention include a kit
containing the chimeric oligonucleotide primer used in the present
invention and/or the probe of the present invention as described
above.
[0416] (8) Composition of the Present Invention.
[0417] The present invention provides a composition used for the
method for amplifying a nucleic acid of the present invention or
the method for detecting a nucleic acid of the present invention as
described above. For example, the composition may contain the
endonuclease as described in (2) above and the DNA polymerase as
described in (3) above. The composition may further contain a
buffering component, a magnesium salt, dNTPs and the like as
components for conducting an amplification reaction. Furthermore,
it may contain a modified deoxyribonucleotide or a deoxynucleotide
triphosphate analog. Those as described in (4) above can be used as
the buffering component and other additives.
[0418] In a particularly preferable aspect, the composition may
contain suitable amounts of the various components as listed above
for the nucleic acid amplification method of the present invention.
Amplification reaction can be conducted only by adding an
appropriate template and chimeric oligonucleotide primer(s) to the
composition. If the object to be amplified is known beforehand, the
composition preferably contains chimeric oligonucleotide primer(s)
suitable for amplifying the object.
[0419] (9) Material Having Immobilized Nucleic Acid Arrayed in
Predefined Region of the Present Invention and Method for Producing
the Same.
[0420] A DNA chip (also referred to as a DNA microarray or a DNA
array) is a material having an immobilized nucleic acid in which
various fragments of genes or DNAs are arrayed and immobilized in a
predefined region or at a predefined position on a solid substrate
such as a slide glass. The DNA chip is used for examining the
presence of a nucleic acid in a nucleic acid sample that has a
sequence complementary to an arrayed and immobilized DNA in a
predefined region on the DNA chip. The examination is carried out
by contacting the DNA chip with the nucleic acid sample prepared
from a sample, preferably a labeled nucleic acid sample, for
hybridization. Since the DNA chip can be used to detect or quantify
a number of nucleic acids in a sample in one procedure, it is a
very useful means that dramatically promotes the analysis of gene
expression, or the analysis of a mutation or polymorphism. A DNA
chip in which a double-stranded nucleic acid is arrayed and
immobilized in a predefined region is used for hybridization after
it is subjected to appropriate denaturation. A DNA chip in which a
single-stranded DNA complementary to a target nucleic acid to be
detected is arrayed and immobilized in a predefined region is
particularly preferable for the detection of a target nucleic
acid.
[0421] As described above, a desired DNA can be amplified in a
single-stranded form by the method of the present invention.
Although any method for purifying an amplification product can be
used, purification using isopropanol precipitation is preferable.
The thus obtained DNA, preferably a single-stranded DNA
substantially free of a complementary strand thereto, can be
preferably used as a DNA fragment to be immobilized onto a DNA
chip. Thus, the method of the present invention is preferably used
as a method for preparing a DNA to be arrayed and immobilized in a
predefined region for producing a DNA chip. Any insoluble substrate
can be used as a substrate onto which the thus obtained DNA is
arrayed and immobilized in a predefined region, but a plate-shaped
substrate made from glass or plastic, and a membrane-shaped
substrate made from nitrocellulose or nylon are preferably used. A
known method for immobilizing a nucleic acid can be used for the
immobilization. The DNA may be directly immobilized onto a
substrate. Alternatively, the DNA may be immobilized through a
suitable linker or after ligating plural DNA molecules.
Furthermore, since a modified deoxyribonucleotide can be
incorporated into an amplified nucleic acid by the method of the
present invention, the material having an immobilized nucleic acid
can be produced utilizing the modification group.
[0422] A target nucleic acid that hybridizes with a nucleic acid on
a material having an immobilized nucleic acid in which a DNA
amplified by the method of the present invention is arrayed and
immobilized in a predefined region (e.g., a DNA chip) can be
detected or quantified. Such detection or quantification can be
accomplished by contacting the material with a nucleic acid sample
prepared from a sample suspected to contain the target nucleic acid
for hybridization. Among these, a DNA chip in which a
single-stranded DNA amplified by the method of the present
invention is arrayed and immobilized in a predefined region allows
the detection of a target nucleic acid with more convenient
operation, higher sensitivity and higher reproducibility as
compared with a conventional material.
[0423] (10) Method for Producing Nucleic Acid in large Quantities
of the Present Invention.
[0424] As described above, one aspect of the present invention
provides a method for amplifying a nucleic acid that can be carried
out under isothermal conditions. A desired nucleic acid can be
produced in the method by mixing a nucleic acid as a template for
the nucleic acid to be amplified and various components required
for a reaction and reacting the mixture under isothermal
conditions. Since the PCR requires changing the temperature of the
reaction mixture over time, the reaction volume is limited to one
in which the temperature can be controlled (usually, 200 .mu.l or
less). Therefore, it is difficult to scale up the volume. On the
other hand, there is no such limitation in the method of the
present invention. A large amount of nucleic acid can be produced
by increasing the volume of the reaction mixture. In the method of
the present invention, the volume is, for example, preferably more
than 200 .mu.l, more preferably 300 .mu.l or more, and most
preferably 500 .mu.l or more, although it is not intended to limit
the present invention. In the method of the present invention, a
number of complementary strand molecules are synthesized from one
template molecule. Furthermore, nucleic acids can be synthesized
using these complementary strand molecules as templates. Thus, a
desired nucleic acid can be efficiently produced in large
quantities by suitably selecting the template and the primer.
Additionally, the fact that, unlike the PCR, the method of the
present invention does not require a special equipment or a
complicated temperature change makes it advantageous in view of the
cost of equipment and energy. Therefore, the method is an excellent
industrial method for producing a nucleic acid in large
quantities.
[0425] The nucleic acid of interest can be amplified or produced
even from a trace amount of a nucleic acid as a template in the
production method of the present invention by using the reaction
buffer and the annealing solution as exemplified in (4) above. In
this case, the endonuclease and the DNA polymerase to be used are
not limited to specific ones. For example, a combination of an
RNase H from Escherichia coli and BcaBEST DNA polymerase is
preferable. It is considered that the preferable units of the
endonuclease and the DNA polymerase may vary depending on the types
of the enzymes. In such a case, the composition of the buffer and
the amount of the enzymes added may be adjusted using the maximal
amount of amplification product as an index.
[0426] Furthermore, the method of the present invention is useful
as a method for supplying a variety of DNA fragments in large
quantities, such as those to be immobilized onto the DNA chip.
Specifically, DNA fragments can be obtained in large quantities in
simple reaction steps in one embodiment. In another embodiment, a
limited number of primers can be used to obtain a variety of DNA
fragments. A step of amplifying the nucleic acid that serves as the
template in the method of the present invention beforehand by a
known nucleic acid amplification method such as the PCR can be
incorporated in the latter embodiment. All kinds of nucleic acids
as templates can be amplified using a limited number of primers,
for example, based on the method for amplifying a nucleic acid
using a random primer having a tag sequence (Nucleic Acids
Research, 24(19):3778-3783 (1996)) or the degenerate
oligonucleotide-primed PCR (DOP-PCR; Genomics, 13:718-725 (1992)),
which uses a degenerate primer. The nucleic acid amplification
method of the present invention can be conducted using one or
several primers for all of the nucleic acids as templates produced
in the above-mentioned step. This can be accomplished by designing
the primer used in the nucleic acid amplification method of the
present invention such that it corresponds to the tag sequence
added to the random or degenerate primer. Thus, a combination of a
suitable step for preparing a nucleic acid as a template and the
method of the present invention can supply a variety of DNA
fragments in larger quantities and at a lower cost as compared with
a conventional method.
[0427] A pharmaceutical composition containing a nucleic acid may
contain a double-stranded DNA for expressing a useful polypeptide
in a cell or a single-stranded antisense DNA for suppressing the
expression of a gene of interest. Such a nucleic acid is
administered into an organism using suitable means, for example, a
carrier for gene transfer such as liposome. The method for
producing a nucleic acid of the present invention is preferable for
producing a single-stranded or double-stranded nucleic acid for
medical use in large quantities. Additionally, a nucleic acid
containing a DNTP analog that, for example, suppresses the
degradation of the nucleic acid in vivo can be readily produced by
the method of the present invention.
[0428] Since the DNA fragment amplified in the present invention is
composed of normal nucleotides, the amplified DNA can be, for
example, subcloned into a suitable vector utilizing a restriction
enzyme site in the DNA. Furthermore, the DNA can be treated with a
restriction enzyme for RFLP without a problem, for example.
Therefore, the DNA can be widely utilized in a field of genetic
test. In addition, a promoter sequence for an RNA polymerase can be
incorporated into the amplified fragment. The amplified fragment
can be used as a template to synthesize an RNA, which can be used
as a probe, for example. Of course, a fluorescence-labeled DNA
probe can be produced by conducting the method for amplifying a
nucleic acid of the present invention using a fluorescence-labeled
DNTP instead of a normal DNTP.
[0429] Features of the method for amplifying a nucleic acid of the
present invention are listed below.
[0430] 1. It can amplify a large amount of a nucleic acid from a
small amount of a template. The amplification product increases
quadratically when two primers are used.
[0431] 2. It can be conducted isothermally. In this case, it does
not require the use of an equipment such as a thermal cycler.
Therefore, the reaction volume can be readily scaled up.
[0432] 3. Usually, the amplification reaction is conducted using
one or two chimeric oligonucleotide primer and two enzymes (a DNA
polymerase and an endonuclease).
[0433] 4. Since a number of DNA strands are synthesized from one
molecule of a primer, the amount of the primer does not restrict
the amount of the amplification product. Furthermore, the primer
utilization efficiency is about 100%, which is very higher than
that of the PCR.
[0434] 5. A single-stranded or double-stranded DNA can be
selectively amplified depending on the purpose.
[0435] 6. Since it does not require a DNTP analog such as an
(.alpha.-S) DNTP for the amplification reaction, the cost of
reagents is low. Furthermore, a nucleic acid in a natural form
without a dNTP analog can be obtained.
[0436] 7. It can supply an amplified DNA fragment at low cost and
in large quantities by combining the method of the present
invention with another nucleic acid duplication method.
[0437] 8. The detection method of the present invention has an
equal or higher detection sensitivity as compared with that of a
conventional method. The detection method of the present invention
can be conducted in a shorter time than that required for a
conventional method having the equal sensitivity.
[0438] 9. The method is suitable for amplification of a nucleic
acid, automated detection, detection in a small amount and highly
integrated detection on a microchip or a nanochip.
[0439] As described above, the method of the present invention is
suitable for detection of a gene and industrial production of a
nucleic acid.
EXAMPLES
[0440] The following Examples illustrate the present invention in
more detail, but are not to be construed to limit the scope
thereof.
Referential Example 1
Preparation of RNase H from Thermophile Bacillus Caldotenax
[0441] Bacillus caldotenax YT-G (purchased from Deutsche Sammlung
von Mikroorganismen; DSM406) was inoculated into 100 ml of a medium
containing 0.2% Tryptone (Difco Laboratories) and 1.5% yeast
extract (Difco Laboratories) (pH 6.5), cultured at 60 C for 140
minutes with shaking and used as a pre-culture. 30 ml of the
pre-culture was inoculated into 3 L of a medium having the same
composition and cultured with aeration at 2.5 L/minute and stirring
at 250 rpm at a temperature of 60 C for 5 hours.
[0442] The cells were collected by centrifuging the culture at
5000.times.g for 15 minutes. 402 g (wet weight) of the cells were
suspended in 1000 ml of 50 mM tris-HCl buffer (pH 7.5) containing
10 mM mercaptoethanol, 0.5 M NaCl, 1 mM EDTA and 20 .mu.M PAPMSF
and disrupted using MINI-Lab (APV GAULIN/RANNIE). Cell debris were
removed by centrifugation to recover a supernatant.
[0443] A polyethylene imine solution was added to the resulting
supernatant at a final concentration of 0.1%. After stirring, the
mixture was allowed to stand for 1 hour. A supernatant was then
recovered by centrifugation. Ammonium sulfate was added to the
supernatant to 50% saturation. A precipitate obtained by
centrifugation was dissolved in 20 mM tris-HCl buffer (pH 7.5)
containing 10 mM mercaptoethanol, 0.1 mM EDTA, 50 mM NaCl and 10%
glycerol. The solution was dialyzed against the same buffer. The
dialyzed sample was loaded onto a 280-ml DE52 column (Whatman)
equilibrated with the same buffer and non-adsorptive fractions were
collected.
[0444] The column was further washed with 420 ml of the buffer used
for the equilibration and washing fractions were collected. The
non-adsorptive fractions and the washing fractions from the DE52
column chromatography were mixed together and loaded onto a 240-ml
P-11 column (Whatman) equilibrated with 20 mM tris-HCl buffer (pH
7.5) containing 10 mM mercaptoethanol, 0.1 mM EDTA, 50 mM NaCl and
10% glycerol. Elution was then carried out using the equilibration
buffer containing 0 to 0.5 M NaCl.
[0445] The resulting active fractions were placed in a dialysis
tube. The tube was placed on solid polyethylene glycol 20000 for
dehydration-concentration at 4 C. The enzyme concentrate was then
loaded onto a 300-ml Superdex G-200 column (Amersham Pharmacia
Biotech) equilibrated with 25 mM tris-HCl buffer (pH 7.5)
containing 5 mM mercaptoethanol, 0.5 mM EDTA, 30 mM NaCl and 50%
glycerol. Elution was carried out using the buffer used for
equilibration to obtain active fractions. The active fractions were
loaded onto a 15-ml Heparin-Sepharose column (Amersham Pharmacia
Biotech) equilibrated with 20 mM tris-HCl buffer (pH 7.5)
containing 10 mM mercaptoethanol, 0.1 mM EDTA, 50 mM NaCl and 10%
glycerol. Elution was carried out using the equilibration buffer
containing 0 to 0.5 M NaCl.
[0446] The resulting active fractions were loaded onto a 5-ml
Hitrap-SP column (Amersham Pharmacia Biotech) equilibrated with 20
mM tris-HCl buffer (pH 7.5) containing 10 mM mercaptoethanol, 0.1
mM EDTA, 50 mM NaCl and 10% glycerol. Elution was carried out using
the equilibration buffer containing 0 to 0.5 M NaCl. The resulting
active fractions were loaded onto a 300-ml Superdex G-200 column
(Amersham Pharmacia Biotech) equilibrated with 25 mM tris-HCl
buffer (pH 7.5) containing 5 mM mercaptoethanol, 0.5 mM EDTA, 30 mM
NaCl and 50% glycerol again. The resulting active fractions were
used as an RNase H preparation (an enzyme solution).
[0447] A heat-resistant RNase H activity was measured as
follows.
[0448] 1 mg of poly(rA) or poly(dT) (both from Amersham Pharmacia
Biotech) was dissolved in 1 ml of 40 mM tris-HCl (pH 7.7)
containing 1 mM EDTA to prepare a poly(rA) solution and a poly(dT)
solution.
[0449] The poly(rA) solution (to a final concentration of 20
.mu.g/ml) and the poly(dT) solution (to a final concentration of 30
.mu.g/ml) were then added to 40 mM tris-HCl (pH 7.7) containing 4
mM MgCl.sub.2, 1 mM DTT, 0.003% BSA and 4% glycerol. The mixture
was reacted at 37 C for 10 minutes and then cooled to 4 C at
prepare a poly(rA)-poly(dT) solution.
[0450] 1 .mu.l of an enzyme solution was added to 100 .mu.l of the
poly(rA)-poly(dT) solution. The mixture was reacted at 40 C for 10
minutes. 10 .mu.l of 0.5 M EDTA was added thereto to terminate the
reaction. Absorbance at 260 nm was then measured. As a control, 10
.mu.l of 0.5 M EDTA was added to the reaction mixture, the
resulting mixture was reacted at 40 C for 10 minutes, and the
absorbance was then measured. A value (difference in absorbance)
was obtained by subtracting the absorbance for the control from the
absorbance for the reaction in the absence of EDTA. Thus, the
concentration of nucleotide released from poly(rA)-poly(dT) hybrid
by the enzymatic reaction was determined on the basis of the
difference in absorbance. One unit of an RNase H was defined as an
amount of enzyme that increases A.sub.260 corresponding to release
of 1 nmol of ribonucleotide in 10 minutes calculated according to
the following equation. If a diluted enzyme solution is used, the
value obtained using the following equation was corrected based on
the dilution rate:
Unit=[Difference in Absorbance.times.Reaction
Volume(ml)]/0.0152
Referential Example 2
Cloning of Bacillus Caldotenax RNase HII Gene
[0451] (1) Preparation of Genomic DNA from Bacillus Caldotenax
[0452] Bacillus caldotenax YT-G (DSM406) was inoculated into 60 ml
of LB medium (1% Tryptone, 0.5% yeast extract and 0.5% NaCl, pH
7.2) and cultured at 65 C for 20 hours. After culturing, the
culture was centrifuged to collect cells. The cells were suspended
in 2 ml of 25% sucrose and 50 mM tris-HCl (pH 8.0). 0.2 ml of 10
mg/ml lysozyme chloride (Nacalai Tesque) in water was added
thereto. The mixture was reacted at 20 C for 1 hour. After
reaction, 12 ml of a mixture containing 150 mM NaCl, 1 mM EDTA and
20 mM tris-HCl (pH 8.0), 0.1 ml of 20 mg/ml proteinase K (Takara
Shuzo) and 1 ml of a 10% aqueous solution of sodium lauryl sulfate
were added to the reaction mixture. The mixture was incubated at 37
C for 1 hour.
[0453] 2.1 ml of 5 M NaCl and 2 ml of a CTAB-NaCl solution [10%
cetyltrimethylammonium bromide (Nacalai Tesque) and 0.7 M NaCl]
were then added to the mixture and the resulting mixture was mixed
thoroughly and incubated at 65 C for 10 minutes. An equal volume of
a mixture of chloroform/isoamyl alcohol (24:1, v/v) was added
thereto. The resulting mixture was gently mixed for 10 minutes and
then centrifuged for 10 minutes at 10000.times.g. After
centrifugation, an equal volume of a mixture of phenol saturated
with 100 mM tris-HCl (pH 8.0)/chloroform/isoamyl alcohol (25:24:1,
v/v) was added to the resulting supernatant. The resulting mixture
was gently mixed for 10 minutes and then centrifuged for 10 minutes
at 10000.times.g. After centrifugation, 0.6 volume of 2-propanol
was added to the resulting supernatant. The resulting fibrous
precipitate was wound using a glass bar, washed with 70% ethanol in
water, air-dried and then dissolved in 0.5 ml of TE buffer to
obtain a genomic DNA solution.
[0454] (2) Cloning of a Middle Portion of RNase HII Gene
[0455] Oligonucleotides BsuII-3 and BsuII-6 represented by SEQ ID
NOS:97 and 98 were synthesized on the basis of Motif I and Motif
III, portions conserved among amino acid sequences of RNase HIIs
from various organisms (Biochemistry, 38:605-608 (1999)).
[0456] A PCR was carried out in a volume of 100 .mu.l using 1 .mu.l
of the Bacillus caldotenax genomic DNA solution as prepared in
Referential Example 2-(1) as a template, and 100 pmol of BsuII-3
and 100 pmol of BsuII-6 as primers. TaKaRa Taq polymerase (Takara
Shuzo) was used as a DNA polymerase for the PCR according to the
attached protocol. The PCR was carried out as follows: 50 cycles of
94 C for 30 seconds, 45 C for 30 seconds and 72 C for 1 minute.
After reaction, the reaction mixture was subjected to phenol
treatment followed by ethanol precipitation to purify a DNA. The
resulting DNA was blunt-ended using T4 DNA polymerase (Takara
Shuzo) and then subjected to agarose gel electrophoresis to recover
an amplified DNA fragment of about 0.4 kb from the gel. The about
0.4-kb DNA fragment was ligated with pUC119 (Takara Shuzo) digested
with Sma I (Takara Shuzo) using T4 DNA ligase (Takara Shuzo). The
ligation mixture was used to transform Escherichia coli JM109. The
resulting transformants were cultured to obtain a plasmid 21-12
into which the about 0.4-kb DNA was inserted.
[0457] (3) Cloning of Upstream Portion of RNase II Gene
[0458] The nucleotide sequence of the inserted fragment of about
0.4 kb in the plasmid 21-12 obtained in Referential Example 2-(2)
was determined. Oligonucleotides RNII-S1 and RNII-S2 represented by
SEQ ID NOS:99 and 100 were synthesized on the basis of the
determined nucleotide sequence.
[0459] The Bacillus caldotenax genomic DNA as prepared in
Referential Example 2-(1) was digested with BamHI (Takara Shuzo)
and ligated with a Sau3AI cassette (Takara Shuzo) using T4 DNA
ligase. A procedure was carried out according to the protocol
attached to TaKaRa LA PCR in vitro cloning kit (Takara Shuzo) using
the ligation mixture as a template, RNII-S2 as a primer for a
primary PCR and RNII-S1 as a primer for a secondary PCR. A DNA was
purified from the solution after the secondary PCR by phenol
extraction followed by ethanol precipitation. The DNA was
blunt-ended using T4 DNA polymerase and then subjected to agarose
gel electrophoresis to recover an amplified DNA fragment of about
1.5 kb from the gel. The about 1.5-kb DNA fragment was ligated with
pUC119 digested with Sma I using T4 DNA ligase. The ligation
mixture was used to transform Escherichia coli JM109.
[0460] The resulting transformants were cultured to obtain a
plasmid B25N16 into which the about 1.5-kb DNA was inserted.
[0461] (4) Cloning of the Entire RNase II Gene
[0462] Oligonucleotides RNII-S5 and RNII-S6 represented by SEQ ID
NOS:101 and 102 were synthesized on the basis of the nucleotide
sequence of the inserted fragment of about 0.4 kb in the plasmid
21-12 as determined in Referential Example 2-(3).
[0463] A PCR was carried out using the plasmid 21-12 as prepared in
Referential Example 2-(2) as a template, and RNII-S5 and RNII-S6 as
primers. TaKaRa Ex Taq polymerase (Takara Shuzo) was used as a DNA
polymerase for the PCR according to the attached protocol. The PCR
was carried out as follows: 25 cycles of 94 C for 30 seconds, 55 C
for 30 seconds and 72 C for 30 seconds. After reaction, the
reaction mixture was subjected to agarose gel electrophoresis. An
amplified DNA fragment of about 0.3 kb was recovered from the gel.
The about 0.3-kb DNA fragment was labeled with digoxigenin using
DIG High-prime (Roche Diagnostics).
[0464] Southern Hybridization was carried out for digests of the
Bacillus caldotenax genomic DNA as prepared in Referential Example
2-(1) with HindIII (Takara Shuzo), Sac I (Takara Shuzo), or HindIII
and SacI using the digoxigenin-labeled DNA as a probe.
Hybridization and detection were carried out using DIG Luminescent
Detection Kit (Roche Diagnostics) according to the protocol
attached thereto. As a result, DNA fragments of about 4.5 kb, about
5.8 kb and about 1.3 kb were hybridized with the probe for the
digests with HindIII, SacI, and HindIII and SacI, respectively.
[0465] Based on these results, the Bacillus caldotenax genomic DNA
was digested with HindIII and subjected to agarose gel
electrophoresis to recover DNAs of about 4.5 kb from the gel. The
resulting DNA fragments were digested with SacI and subjected to
agarose gel electrophoresis to recover DNAs of about 1.3 kb from
the gel. The resulting DNAs were ligated with pUC19 (Takara Shuzo)
digested with HindIII and SacI using T4 DNA ligase. The ligation
mixture was used to transform Escherichia coli HB101.
[0466] The resulting transformants were replica-plated onto
Hybond-N.TM. (Amersham Pharmacia Biotech). Colony hybridization was
then carried out using the above-mentioned digoxigenin-labeled
probe according to a conventional method. A plasmid pRHB1 was
prepared from the thus obtained positive clone.
[0467] The nucleotide sequence of the DNA inserted into pRHB1 was
then determined. Comparison of the amino acid sequence deduced from
the nucleotide sequence with the amino acid sequence of the RNase
HII from Bacillus subtilis suggested that a region of about 40 bp
from the initiation codon was missing in the DNA in pRHB1. Then,
the full-length RNase H gene was constructed as follows.
[0468] B25N16 as prepared in Referential Example 2-(3) was digested
with HindIII and subjected to agarose gel electrophoresis to
recover a DNA fragment of about 160 bp from the gel. The about
160-bp DNA fragment was ligated with pRHB1 digested with HindIII
using T4 DNA ligase. The ligation mixture was used to transform
Escherichia coli HB101. Plasmids were prepared from the resulting
transformants.
[0469] Next, an oligonucleotide RNII-Nde represented by
[0470] SEQ ID NO:103 was synthesized on the basis of the presumed
nucleotide sequence around the initiation codon. PCRs were carried
out using the plasmids prepared from the transformants as
templates, and RNII-Nde and RNII-S6 as primers. A plasmid from
which a DNA fragment of about 0.7 kb was amplified was selected and
designated as pRHB11.
[0471] The nucleotide sequence of the DNA fragment inserted into
the thus obtained plasmid pRHB11 was determined. Analysis of the
results revealed an open reading frame presumably encoding RNase
HII. This nucleotide sequence is shown in SEQ ID NO:104. The amino
acid sequence of RNase HII deduced from the nucleotide sequence is
shown in SEQ ID NO:105.
[0472] Escherichia coli HB101 transformed with the plasmid pRHB11
is designated and indicated as Escherichia coli JM109/pRHB11, and
deposited on Sep. 5, 2000 at the International Patent Organism
Depositary, National Institute of Advanced Industrial Science and
Technology under accession number FERM P-18021.
[0473] (5) Expression of Bacillus Caldotenax RNase HII Gene
[0474] Escherichia coli HB101 transformed with pRHB11 or pRHB1 was
inoculated into 5 ml of LB medium containing 100 .mu.g/ml of
ampicillin and cultured with shaking at 37 C overnight. After
cultivation, cells collected by centrifugation were suspended in
0.5 ml of TE buffer and sonicated. A supernatant obtained by
centrifugation was used as a cell crude extract.
[0475] 10 mM tris-HCl (pH 8.0), 1 mM dithiothreitol (Nacalai
Tesque), 0.003% bovine serum albumin (fraction V, Sigma), 4%
glycerol, 20 .mu.g/ml poly(dT) (Amersham Pharmacia Biotech) and 30
.mu.g/ml poly(rA) (Amersham Pharmacia Biotech) were mixed together.
The mixture was incubated at 37 C for 10 minutes and used as a
substrate solution for measuring an RNase H activity.
[0476] 1 .mu.l of 1 M MnCl.sub.2 was added to 100 .mu.l of the
substrate solution. The mixture was incubated at 40 C. 10 .mu.l of
a 10-fold dilution of the cell crude extract was added to the
mixture to initiate a reaction. After reacting at 40 C for 30
minutes, 10 .mu.l of 0.5 M EDTA was added thereto to terminate the
reaction. Absorbance at 260 nm was then measured. As a result, the
absorbance at 260 nm from a reaction in which a cell crude extract
prepared from Escherichia coli HB101 harboring pRHB11 was used was
clearly higher than that from a reaction in which a cell crude
extract prepared from Escherichia coli HB101 harboring pRHB1 was
used. Thus, it was demonstrated that pRHB11 contained an RNase H
gene and that Escherichia coli harboring pRHB11 expressed an RNase
H activity.
[0477] (6) Preparation of Purified RNase HII Preparation
[0478] Escherichia coli HB101 transformed with pRHB11 obtained in
Referential Example 2-(4) was inoculated into 1 L of LB medium
containing 100 .mu.g/ml of ampicillin and cultured with shaking at
37 C for 16 hours. After cultivation, cells collected by
centrifugation were suspended in 52.3 ml of a sonication buffer [50
mM tris-HCl (pH 8.0), 2 mM 2-mercaptoethanol, 10% glycerol, 2 mM
phenylmethanesulfonyl fluoride] and sonicated. A supernatant
obtained by centrifuging the sonicated suspension at 12000 rpm for
10 minutes was heated at 60 C for 15 minutes. It was then
centrifuged at 12000 rpm for 10 minutes again to collect a
supernatant. Thus, 50.0 ml of a heated supernatant was
obtained.
[0479] The solution was subjected to RESOURSE Q column (Amersham
Pharmacia Biotech) equilibrated with Buffer C [50 mM tris-HCl (pH
8.0), 2 mM 2-mercaptoethanol, 10% glycerol] and chromatographed
using FPLC system (Amersham Pharmacia Biotech). As a result, RNase
HII flowed through the RESOURSE Q column. 51 ml of the flow-through
RNase HII fraction was subjected to RESOURSE S column (Amersham
Pharmacia Biotech) equilibrated with Buffer C and eluted with a
linear gradient of 0 to 500 mM NaCl using FPLC system. A fraction
containing RNase II eluted with about 240 mM NaCl was obtained. 3.0
ml of the RNase II fraction was subjected in two portions to PD-10
column (Amersham Pharmacia Biotech) equilibrated with Buffer C
containing 50 mM NaCl. 7.0 ml the resulting eluate was subjected to
HiTrap-heparin column (Amersham Pharmacia Biotech) equilibrated
with Buffer C containing 50 mM NaCl and eluted with a linear
gradient of 50 to 550 mM NaCl using FPLC system. A fraction
containing RNase II eluted with about 310 mM NaCl was obtained. 4.4
ml of the RNase II fraction was concentrated by ultrafiltration
using Centricon-10 (Amicon). 280 .mu.l of the concentrate was
subjected to Superdex 200 gel filtration column (Amersham Pharmacia
Biotech) equilibrated with 50 mM tris-HCl (pH 8.0) containing 100
mM NaCl and 0.1 mM EDTA and eluted with the same buffer. As a
result, RNase HII was eluted at a position corresponding to a
molecular weight of 35 kilodalton. This molecular weight
corresponds to that of RNase HII in a form of a monomer. The thus
eluted RNase HII was used as Bca RNase HII preparation.
[0480] The enzymatic activity of the thus obtained Bca RNase HII
preparation was measured as follows.
[0481] 100 .mu.l of a reaction mixture [20 mM HEPES-potassium
hydroxide (pH 7.8), 0.01% bovine serum albumin (Takara Shuzo), 1%
dimethyl sulfoxide, 10 mM manganese chloride, 20 .mu.g/ml poly(dT)
(Amersham Pharmacia Biotech), 30 .mu.g/ml poly(rA) (Amersham
Pharmacia Biotech)] which had been incubated at 40 C was added to 1
.mu.l of the Bca RNase HII preparation. The mixture was reacted at
40 C for 10 minutes. The reaction was then terminated by adding 10
.mu.l of 0.5 M EDTA (pH 8.0). Absorbance at 260 nm was then
measured.
[0482] As a result, an RNase H activity was observed for the Bca
RNase HII preparation.
Referential Example 3
Cloning of Bacillus Caldotenax RNase HIII Gene
[0483] (1) Cloning of Fragment of RNase HIII Gene
[0484] Primers BsuIII-1, BsuIII-3, BsuIII-6 and BsuIII-8
represented by SEQ ID NOS:106-109 for screening a gene encoding
RNase HIII were synthesized based on the amino acid sequences of
regions well conserved among Bacillus subtilis and other organisms
determined on the basis of the homology among the amino acid
sequences of RNase HIIIs from Bacillus subtilis [Biochemistry,
38:605-608 (1999)] and other organisms.
[0485] A first PCR was carried out in a volume of 50 .mu.l using
200 ng of the Bacillus caldotenax genomic DNA as prepared in
Referential Example 2-(1) as a template, and 100 pmol of BsuIII-1
and 100 pmol of BsuIII-8 as primers. A second PCR was then carried
out in a volume of 100 .mu.l using 1 .mu.l of the reaction mixture
as a template, and 100 pmol of BsuIII-3 and 100 pmol of BsuIII-6 as
primers. TaKaRa Taq polymerase (Takara Shuzo) was used as a DNA
polymerase for the two PCRs according to the attached protocol. The
PCRs were carried out as follows: 25 (the first PCR) or 30 (the
second PCR) cycles of 94 C for 30 seconds, 45 C for 30 seconds and
72 C for 1 minute.
[0486] An amplified DNA fragment of about 450 bp was blunt-ended
using T4 DNA polymerase (Takara Shuzo) and then subjected to
agarose gel electrophoresis to recover the amplified DNA fragment
of about 450 bp. The about 450-bp DNA fragment was ligated with
pUC119 (Takara Shuzo) digested with Sma I (Takara Shuzo) using T4
DNA ligase (Takara Shuzo). The ligation mixture was used to
transform Escherichia coli JM109. The resulting transformants were
cultured to obtain a plasmid pBCA3204 into which the about 450-bp
DNA fragment was inserted.
[0487] (2) Cloning of RNase HIII Gene Using Southern Hybridization
Method
[0488] The nucleotide sequence of the DNA fragment inserted in
pBCA3204 obtained in Referential Example 3-(1) was determined.
Primers RNIII-S3 and BcaRNIII-3 represented by SEQ ID NOS:110 and
111 were synthesized on the basis of the determined nucleotide
sequence. A PCR was carried out in a volume of 100 .mu.l using
RNIII-S3 and BcaRNIII-3 as primers and pBCA3204 as a template.
TaKaRa Z-Taq (Takara Shuzo) was used as a DNA polymerase for the
PCR according to the attached protocol. The PCR was carried out as
follows: 30 cycles of 98 C for 0 second, 55 C for 0 second and 72 C
for 20 seconds. After reaction, the reaction mixture was subjected
to phenol-chloroform extraction, ethanol precipitation and agarose
gel electrophoresis to recover a DNA fragment of about 0.4 kb from
the gel. The about 0.4-kb DNA fragment was labeled using DIG DNA
Labeling Kit (Boehringer Mannheim) to prepare a probe.
[0489] 20 .mu.g of the Bacillus caldotenax genomic DNA prepared in
Referential Example 2-(1) was completely digested with BamHI,
EcoRI, HindIII, PstI or XbaI (all from Takara Shuzo). The half of
each of the digests was then subjected to agarose gel
electrophoresis. The DNAs were transferred from the agarose gel to
a nylon membrane using 0.4 N sodium hydroxide and fixed at 120 C
for 30 minutes. The membrane was pre-incubated in a sealed bag
containing 30 ml of a hybridization buffer [43.4 g/L sodium
chloride, 17.6 g/L sodium citrate, 1% blocking agent (Boehringer
Mannheim), 0.1% N-lauroyl sarcosine, 0.02% sodium lauryl sulfate
(SDS)] at 60 C for 4 hours and then incubated in a sealed bag
containing 5 ml of a hybridization buffer containing the probe at
60 C for 16 hours.
[0490] The membrane was washed twice in 50 ml of 2.times.SSC (17.5
g/L NaCl, 8.8 g/L sodium citrate) containing 0.1% SDS at room
temperature, and twice in 50 ml of 0.5.times.SSC (4.3 g/L sodium
chloride, 1.9 g/L sodium citrate) containing 0.1% SDS at 45 C.
Then, an EcoRI fragment of about 8 kb, a PstI fragment of about 4.5
kb and a HindIII fragment of about 1 kb which have sequences
complementary to the probe were detected using DIG nucleic acid
detection kit (Boehringer Mannheim).
[0491] The remaining half of the Bacillus caldotenax genomic DNA
completely digested with PstI was subjected to agarose gel
electrophoresis. PstI fragments of about 4.5 kb were recovered from
the gel. The DNA fragments were then ligated with a plasmid vector
pTV119N, which had been digested with PstI and dephosphorylated
with alkaline phosphatase (Takara Shuzo). The ligation mixture was
used to transform Escherichia coli JM109.
[0492] A PCR was carried out in a volume of 50 .mu.l using RNIII-S3
and BcaRNIII-3 as primers, and one of the colonies as a template to
select a colony presumably harboring an RNase HIII gene. TaKaRa-Z
Taq (Takara Shuzo) was used for the PCR according to the attached
protocol. The PCR was carried out as follows: 30 cycles of 98 C for
0 second, 55 C for 0 second and 72 C for 20 seconds. As a result,
it was found that the gene of interest was contained in the colony
No. 88.
[0493] A PCR was carried out using a plasmid prepared from the
colony No. 88 as a template, and a primer pair RN-N (Takara Shuzo)
and BcaRNIII-3 or a primer pair M4 (Takara Shuzo) and RNIII-S3 to
examine whether or not the entire RNase HIII gene was contained in
the plasmid. As a result, it was found that the entire RNase HIII
gene was contained in the plasmid, which was designated as
pBCA3P88.
[0494] (3) Determination of Nucleotide Sequence of DNA Fragment
Containing RNase HIII Gene
[0495] The nucleotide sequence of the DNA fragment inserted into
the plasmid pBCA3P88 obtained in Referential Example 3-(2) was
determined according to a dideoxy method.
[0496] Analysis of the determined nucleotide sequence revealed the
existence of an open reading frame encoding an amino acid sequence
including the N-terminal amino acid sequence of RNase HIII. The
nucleotide sequence of the open reading frame and the amino acid
sequence of RNase HIII deduced from the nucleotide sequence are
shown in SEQ ID NO:112 and SEQ ID NO:113, respectively.
[0497] (4) Construction of Plasmid for Expressing RNase HIII
[0498] A PCR was carried out in a volume of 100 .mu.l using the
plasmid pBCA3P88 as described in Referential Example 3-(2) as a
template, BcaRNIIINde represented by SEQ ID NO:114 designed with
reference to the sequence around the above-mentioned open reading
frame for RNase HIII and M13 primer M4 (Takara Shuzo). Pyrobest DNA
polymerase (Takara Shuzo) was used as a DNA polymerase for the PCR
according to the attached protocol. The PCR was carried out as
follows: 30 cycles of 94 C for 30 seconds, 55 C for 30 seconds and
72 C for 3 minutes. An amplified DNA fragment of about 4 kb was
digested with NdeI (Takara Shuzo) and subjected to agarose gel
electrophoresis to recover an NdeI fragment of about 1.4 kb from
the gel. The about 1.4-kb DNA fragment was ligated with pTV119Nd (a
plasmid in which the NcoI site in pTV119N is converted into a NdeI
site) which had been digested with NdeI and dephosphorylated with
alkaline phosphatase (Takara Shuzo). The ligation mixture was used
to transform Escherichia coli JM109.
[0499] Next, a PCR was carried out in a volume of 50 .mu.l using
one of the colonies as a template, and RN-N (Takara Shuzo) and
BcaRNIII-3 as primers in order to screen for a plasmid in which the
RNase HIII gene in the NdeI fragment was linked downstream from the
lac promoter in the vector pTV119Nd. A colony presumably harboring
the RNase HIII gene was then selected. TaKaRa-Z Taq (Takara Shuzo)
was used as a DNA polymerase for the PCR according to the attached
protocol. The PCR was carried out as follows: 30 cycles of 98 C for
0 second, 55 C for 0 second and 72 C for 20 seconds. As a result,
it was found that the colony No. 2 contained a plasmid in which the
RNase HIII gene in the NdeI fragment was linked downstream from the
lac promoter in the vector pTV119Nd. This plasmid was designated as
pBCA3Nd2.
[0500] The determination of the nucleotide sequence of the DNA
fragment inserted into the plasmid by a dideoxy method revealed
that there was no mutation due to the PCR except that the
initiation codon GTG was changed to ATG.
[0501] Escherichia coli JM109 transformed with the plasmid pBCA3Nd2
is designated and indicated as Escherichia coli JM109/pBCA3Nd2, and
deposited on Sep. 5, 2000 at the International Patent Organism
Depositary, National Institute of Advanced Industrial Science and
Technology under accession number FERM P-18019.
[0502] (5) Preparation of Purified RNase HIII Preparation
[0503] Escherichia coli JM109 transformed with pBCA3Nd2 obtained in
Referential Example 3-(4) was inoculated into 2 L of LB medium
containing 100 .mu.g/ml of ampicillin and cultured with shaking at
37 C for 16 hours. After cultivation, cells collected by
centrifugation were suspended in 39.6 ml of a sonication buffer [50
mM tris-HCl (pH 8.0), 1 mM EDTA, 2 mM phenylmethanesulfonyl
fluoride] and sonicated. A supernatant obtained by centrifuging the
sonicated suspension at 12000 rpm for 10 minutes was heated at 60 C
for 15 minutes. It was then centrifuged at 12000 rpm for 10 minutes
again to collect a supernatant. Thus, 39.8 ml of a heated
supernatant was obtained.
[0504] The heated supernatant was subjected to RESOURSE Q column
(Amersham Pharmacia Biotech) equilibrated with Buffer A [50 mM
tris-HCl (pH 8.0), 1 mM EDTA] and chromatographed using FPLC system
(Amersham Pharmacia Biotech). As a result, RNase HIII flowed
through the RESOURSE Q column.
[0505] 45 ml of the flow-through RNase HIII fraction was dialyzed
against 2 L of Buffer B [50 mM tris-HCl (pH 7.0), 1 mM EDTA] for 2
hours. The dialysis was repeated for two more times under the same
conditions. 55.8 ml of the dialyzed enzyme solution was subjected
to RESOURSE S column (Amersham Pharmacia Biotech) equilibrated with
Buffer B and eluted with a linear gradient of 0 to 500 mM NaCl
using FPLC system. A fraction containing RNase HIII eluted with
about 105 mM NaCl was obtained.
[0506] Buffer B containing 1 M NaCl was added to 7.0 ml of the
fraction to make the NaCl concentration to 150 mM. The mixture was
subjected to HiTrap-heparin column (Amersham Pharmacia Biotech)
equilibrated with Buffer B containing 150 mM NaCl. As a result,
RNase HIII flowed through the HiTrap-heparin column.
[0507] 7.5 ml of the flow-through RNase HIII fraction was
concentrated by ultrafiltration using Centricon-10 (Amicon). 190
.mu.l of the concentrate was subjected to Superdex 200 gel
filtration column (Amersham Pharmacia Biotech) equilibrated with 50
mM tris-HCl (pH 7.0) containing 100 mM NaCl and 0.1 mM EDTA and
eluted with the same buffer. As a result, RNase HIII was eluted at
a position corresponding to a molecular weight of 33 kilodalton.
This molecular weight corresponds to that of RNase HIII in a form
of a monomer.
[0508] The thus eluted RNase HIII was used as Bca RNase HIII
preparation.
[0509] The enzymatic activity of the thus obtained Bca RNase HIII
preparation was measured as follows.
[0510] 100 .mu.l of a reaction mixture [20 mM HEPES-potassium
hydroxide (pH 7.8), 0.01% bovine serum albumin (Takara Shuzo), 1%
dimethyl sulfoxide, 4 mM magnesium acetate, 20 .mu.g/ml poly(dT)
(Amersham Pharmacia Biotech), 30 .mu.g/ml poly(rA) (Amersham
Pharmacia Biotech)] which had been incubated at 40 C was added to 1
.mu.l of the Bca RNase HIII preparation. The mixture was reacted at
40 C for 10 minutes. The reaction was terminated by adding 10 .mu.l
of 0.5 M EDTA (pH 8.0). Absorbance at 260 nm was then measured. As
a result, an RNase H activity was observed for the Bca RNase HIII
preparation.
Referential Example 4
Cloning of Pyrococcus furiosus RNase HII Gene
[0511] (1) Preparation of Genomic DNA from Pyrococcus furiosus
[0512] 2 L of a medium containing 1% Tryptone (Difco Laboratories),
0.5% yeast extract (Difco Laboratories), 1% soluble starch (Nacalai
Tesque), 3.5% Jamarine S Solid (Jamarine Laboratory), 0.5% Jamarine
S Liquid (Jamarine Laboratory), 0.003% MgSO.sub.4, 0.001% NaCl,
0.0001% FeSO.sub.4.7H.sub.2O, 0.0001% COSO.sub.4, 0.0001%
CaCl.sub.2.7H.sub.2O, 0.0001% ZnSO.sub.4, 0.1 ppm
CuSO.sub.4.5H.sub.2O, 0.1 ppm KAl(SO.sub.4).sub.2, 0.1 ppm
H.sub.3BO.sub.4, 0.1 ppm Na.sub.2MoO.sub.4.2H.sub.2O and 0.25 ppm
NiCl.sub.2.6H.sub.2O was placed in a 2 L medium bottle, sterilized
at 120 C for 20 minutes, bubbled with nitrogen gas to remove
dissolved oxygen, then Pyrococcus furiosus (purchased from Deutsche
Sammlung von Mikroorganismen; DSM3638) was inoculated into the
medium and cultured at 95 C for 16 hours without shaking. After
cultivation, cells were collected by centrifugation.
[0513] The resulting cells were then suspended in 4 ml of 25%
sucrose, 50 mM tris-HCl (pH 8.0). 0.4 ml of 10 mg/ml lysozyme
chloride (Nacalai Tesque) in water was added thereto. The mixture
was reacted at 20 C for 1 hour. After reaction, 24 ml of a mixture
containing 150 mM NaCl, 1 mM EDTA and 20 mM tris-HCl (pH 8.0), 0.2
ml of 20 mg/ml proteinase K (Takara Shuzo) and 2 ml of 10% aqueous
solution of sodium lauryl sulfate and were added to the reaction
mixture. The mixture was incubated at 37 C for 1 hour. After
reaction, the mixture was subjected to phenol-chloroform extraction
followed by ethanol precipitation to prepare about 1 mg of genomic
DNA.
[0514] (2) Cloning of RNase HII Gene
[0515] The entire genomic sequence of Pyrococcus horikoshii was
published [DNA Research, 5:55-76 (1998)]. The existence of a gene
encoding a homologue of RNase HII (PH1650) in the genome was known
(SEQ ID NO:115, the home page of National Institute of Technology
and Evaluation, Ministry of International Trade and Industry of
Japan: http://www/nite.go.jp/).
[0516] Homology between the PH1650 gene and the partially published
genomic sequence of Pyrococcus furiosus (the home page of
University of Utah, Utah Genome Center:
http://www.genome.utah.edu/sequence.html) was searched. As a
result, a highly homologous sequence was found. Primers 1650Nde
(SEQ ID NO:116) and 1650Bam (SEQ ID NO:117) were synthesized on the
basis of the homologous sequence.
[0517] A PCR was carried out in a volume of 100 .mu.l using 200 ng
of the Pyrococcus furiosus genomic DNA obtained in Referential
Example 4-(1) as a template, and 20 pmol of 1650Nde and 20 pmol of
1650Bam as primers. TaKaRa Ex Taq (Takara Shuzo) was used as a DNA
polymerase for the PCR according to the attached protocol. The PCR
was carried out as follows: 30 cycles of 94 C for 30 seconds, 55 C
for 30 seconds and 72 C for 1 minute. An amplified DNA fragment of
about 0.7 kb was digested with NdeI and BamHI (both from Takara
Shuzo). The resulting DNA fragment was inserted between the NdeI
site and the BamHI site in a plasmid vector pET3a (Novagen) to make
a plasmid pPFU220.
[0518] (3) Determination of Nucleotide Sequence of DNA Fragment
Containing RNase HII Gene
[0519] The nucleotide sequence of the DNA fragment inserted into
pPFU220 obtained in Referential Example 4-(2) was determined
according to a dideoxy method.
[0520] Analysis of the determined nucleotide sequence revealed the
existence of an open reading frame presumably encoding RNase HII.
The nucleotide sequence of the open reading frame is shown in SEQ
ID NO:118. The amino acid sequence of RNase HII deduced from the
nucleotide sequence is shown in SEQ ID NO:119.
[0521] Escherichia coli JM109 transformed with the plasmid pPFU220
is designated and indicated as Escherichia coli JM109/pPFU220, and
deposited on Sep. 5, 2000 at the International Patent Organism
Depositary, National Institute of Advanced Industrial Science and
Technology under accession number FERM P-18020.
[0522] (4) Preparation of Purified RNase HII Preparation
[0523] Escherichia coli HMS174(DE3) (Novagen) was transformed with
pPFU220 obtained in Referential Example 4-(2). The resulting
Escherichia coli HMS174(DE3) harboring pPFU220 was inoculated into
2 L of LB medium containing 100 .mu.g/ml of ampicillin and cultured
with shaking at 37 C for 16 hours. After cultivation, cells
collected by centrifugation were suspended in 66.0 ml of a
sonication buffer [50 mM tris-HCl (pH 8.0), 1 mM EDTA, 2 mM
phenylmethanesulfonyl fluoride] and sonicated. A supernatant
obtained by centrifuging the sonicated suspension at 12000 rpm for
10 minutes was heated at 60 C for 15 minutes. It was then
centrifuged at 12000 rpm for 10 minutes again to collect a
supernatant. Thus, 61.5 ml of a heated supernatant was
obtained.
[0524] The heated supernatant was subjected to RESOURSE Q column
(Amersham Pharmacia Biotech) equilibrated with Buffer A [50 mM
tris-HCl (pH 8.0), 1 mM EDTA] and chromatographed using FPLC system
(Amersham Pharmacia Biotech). As a result, RNase HII flowed through
the RESOURSE Q column.
[0525] 60.0 ml of the flow-through RNase HII fraction was subjected
to RESOURSE S column (Amersham Pharmacia Biotech) equilibrated with
Buffer A and eluted with a linear gradient of 0 to 500 mM NaCl
using FPLC system. A fraction containing RNase HII eluted with
about 150 mM NaCl was obtained. 2.0 ml of the RNase HII fraction
was concentrated by ultrafiltration using Centricon-10 (Amicon).
250 .mu.l of the concentrate was subjected to Superdex 200 gel
filtration column (Amersham Pharmacia Biotech) equilibrated with 50
mM tris-HCl (pH 8.0) containing 100 mM NaCl and 0.1 mM EDTA and
eluted with the same buffer. As a result, RNase HII was eluted at a
position corresponding to a molecular weight of 17 kilodalton. This
molecular weight corresponds to that of RNase HII in a form of a
monomer.
[0526] The thus eluted RNase HII was used as Pfu RNase HII
preparation.
[0527] The enzymatic activity of the thus obtained Pfu RNase HII
preparation was measured as described in Referential Example 3-(5).
As a result, an RNase H activity was observed for the Pfu RNase HII
preparation.
Referential Example 5
Cloning of Thermotoga maritima RNase HII Gene
[0528] (1) Preparation of Genomic DNA from Thermotoga maritima
[0529] 2 L of a medium containing 1% Tryptone, 0.5% yeast extract,
1% soluble starch, 3.5% Jamarine S Solid, 0.5% Jamarine S Liquid,
0.003% MgSO.sub.4, 0.001% NaCl, 0.0001% FeSO.sub.4.7H.sub.2O,
0.0001% COSO.sub.4, 0.0001% CaCl.sub.2.7H.sub.2O, 0.0001%
ZnSO.sub.4, 0.1 ppm CuSO.sub.4.5H.sub.2O, 0.1 ppm
KAl(SO.sub.4).sub.2, 0.1 ppm H.sub.3BO.sub.3, 0.1 ppm
Na.sub.2MoO.sub.4.2H.sub.2O and 0.25 ppm NiCl.sub.2.6H.sub.2O was
placed in a 2 L medium bottle, sterilized at 120 C for 20 minutes,
bubbled with nitrogen gas to remove dissolved oxygen, then
Thermotoga maritima (purchased from Deutsche Sammlung von
Mikroorganismen und Zellkulturen GmbH; DSM3109) was inoculated into
the medium and cultured at 85 C for 16 hours without shaking.
[0530] Cells collected by centrifugation from 300 ml of the culture
were then suspended in 3 ml of TE buffer [10 mM tris-HCl (pH 7.5),
1 mM EDTA]. 150 .mu.l of 10% aqueous solution of sodium lauryl
sulfate (Nacalai Tesque) and 15 .mu.l of 20 mg/ml proteinase K
(Takara Shuzo) were added thereto. The mixture was incubated at 37
C for 1 hour. After reaction, 0.5 ml of 5 M NaCl was added to the
mixture. After thoroughly mixing, 0.4 ml of a CTAB-NaCl solution
[10% cetyltrimethylammonium bromide (Nacalai Tesque), 0.7 M NaCl]
was added to the mixture. After thoroughly mixing, the mixture was
incubated at 65 C for 10 minutes. 1.5 ml of a mixture of
chloroform/isoamyl alcohol (24:1, v/v) was added thereto. The
mixture was gently mixed for 10 minutes and centrifuged at
20000.times.g for 5 minutes. After centrifugation, an equal volume
of a mixture of phenol saturated with 100 mM tris-HCl (pH
8.0)/chloroform/isoamyl alcohol (25:24:1, v/v) was added to the
resulting supernatant. The mixture was gently mixed for 10 minutes
and then centrifuged at 20000.times.g for 5 minutes. After
centrifugation, 0.6 volume of 2-propanol was added to the
supernatant. The precipitate obtained by centrifugation at
10000.times.g for 5 minutes was washed with 70% ethanol in water,
air-dried and then dissolved in 200 .mu.l of TE to obtain a genomic
DNA solution.
[0531] (2) Cloning of RNase HII Gene
[0532] Oligonucleotides 915-F1, 915-F2, 915-R1 and 915-R2
represented by SEQ ID NOS:120-123 were synthesized on the basis of
the nucleotide sequence of a portion that had been identified as an
RNase HII gene in the nucleotide sequence of the genomic DNA of
Thermotoga maritima
(http://www.tigr.org/tdb/CMR/btm/htmls/SplashPage.html) in order to
obtain an amplified DNA fragment containing an RNase H gene by
carrying out a PCR using the Thermotoga maritima genomic DNA as a
template.
[0533] PCRs were carried out using the Thermotoga maritima genomic
DNA as prepared in Referential Example 5-(1) as a template, and
915-F1 and 915-R1, 915-F1 and 915-R2, 915-F2 and 915-R1, or 915-F2
and 915-R2 as a primer pair. TaKaRa Ex Taq was used as a DNA
polymerase for the PCRs according to the attached protocol. The
PCRs were carried out as follows: 25 cycles of 95 C for 0.5 minute,
55 C for 0.5 minute and 72 C for 1.5 minute. After reactions, the
respective PCR products were subjected to agarose gel
electrophoresis to extract and purify amplified DNA fragments of
about 0.7 kb. The DNAs amplified using a primer pair 915-F1 and
915-R1 or 915-F1 and 915-R2 were digested with HindIII and XbaI
(both from Takara Shuzo) and ligated with pUC19 digested with
HindIII and XbaI using T4 DNA ligase. The ligation mixture was used
to transform Escherichia coli JM109. The resulting transformants
were cultured to prepare plasmid DNAs into which the about 0.7-kb
DNAs were inserted. As a result, plasmids No. 1 and No. 2 having
DNAs amplified using 915-F1 and 915-R1, and plasmids No. 3 and No.
4 having DNAs amplified using 915-F1 and 915-R2 were obtained.
[0534] In addition, the DNAs amplified using a primer pair 915-F2
and 915-R1 or 915-F2 and 915-R2 were doubly digested with NcoI
(Takara Shuzo) and XbaI and ligated with pTV119N (Takara Shuzo)
doubly digested with NcoI and XbaI using T4 DNA ligase. The
ligation mixture was used to transform Escherichia coli JM109.
[0535] The resulting transformants were cultured to prepare plasmid
DNAs into which the about 0.7-kb DNAs were inserted. As a result,
plasmids No. 5 and No. 6 having DNAs amplified using 915-F2 and
915-R1, and a plasmid No. 7 having a DNA amplified using 915-F2 and
915-R2 were obtained.
[0536] Escherichia coli JM109 transformed with the plasmid No. 7 is
designated and indicated as Escherichia coli JM109/pTM-RNH, and
deposited on Sep. 5, 2000 at the International Patent Organism
Depositary, National Institute of Advanced Industrial Science and
Technology under accession number FERM P-18018.
[0537] (3) Expression of Thermotoga maritima RNase HII Gene
[0538] Escherichia coli JM109 transformed with one of the plasmids
No. 1 to 7 or pUC19 was inoculated into 5 ml of LB medium (10 g/L
Tryptone, 5 g/L yeast extract, 5 g/L NaCl, pH 7.2) containing 100
.mu.g/ml of ampicillin and cultured with shaking at 37 C. When the
absorbance at 660 nm reached 0.5,
isopropyl-.beta.-D-thiogalactopyranoside was added thereto to a
final concentration of 1 mM and the cells were cultured overnight.
After cultivation, cells collected by centrifugation were suspended
in 1 ml of TE buffer and sonicated. The sonicated suspension was
heated at 80 C for 10 minute. A supernatant obtained by
centrifugation was used as a cell crude extract. Absorbance was
measured using the cell crude extract as described in Referential
Example 2-(5). As a result, when reactions were carried out in the
presence of MnCl.sub.2, the absorbance at 260 nm from each of the
reactions in which cell crude extracts prepared from Escherichia
coli JM109 harboring the plasmid No. 3, 5, 6 or 7 were used was
clearly higher than that from a reaction in which a crude extract
prepared from Escherichia coli JM109 harboring pUC19 was used.
Thus, it was demonstrated that the plasmids No. 3, 5, 6 and 7
contained RNase H genes and that Escherichia coli harboring one of
these plasmids expressed an RNase H activity.
[0539] The partial nucleotide sequences of the DNA fragments
inserted into the plasmids which were demonstrated to express RNase
activities in Escherichia coli as described above were determined.
Analysis of the determined nucleotide sequences revealed an open
reading frame presumably encoding RNase HII. The nucleotide
sequence of the open reading frame is shown in SEQ ID NO:232. The
amino acid sequence of RNase HII deduced from the nucleotide
sequence is shown in SEQ ID NO:233. Then, it was found that one
base substitution that was presumably generated upon the PCR was
observed in a portion of the nucleotide sequence of the DNA
fragment inserted in the plasmid No. 7, resulting in the change in
the encoded amino acid residue.
[0540] (4) Preparation of Purified RNase HII Preparation
[0541] Escherichia coli JM109 was transformed with pTM-RNH obtained
in Referential Example 5-(2). The resulting Escherichia coli JM109
harboring pTM-RNH was inoculated into 1 L of LB medium containing
100 .mu.g/ml of ampicillin and cultured with shaking at 37 C for 16
hours. After cultivation, cells collected by centrifugation were
suspended in 31.0 ml of a sonication buffer [50 mM tris-HCl (pH
8.0), 2 mM 2-mercaptoethanol, 10% glycerol, 2 mM
phenylmethanesulfonyl fluoride] and sonicated. A supernatant
obtained by centrifuging the sonicated suspension at 12000 rpm for
10 minutes was heated at 70 C for 15 minutes. It was then
centrifuged at 12000 rpm for 10 minutes again to collect a
supernatant. Thus, 32.0 ml of a heated supernatant was
obtained.
[0542] The heated supernatant was subjected to RESOURSE Q column
(Amersham Pharmacia Biotech) equilibrated with Buffer C [50 mM
tris-HCl (pH 8.0), 2 mM 2-mercaptoethanol, 10% glycerol] and
chromatographed using FPLC system (Amersham Pharmacia Biotech). As
a result, RNase HII flowed through the RESOURSE Q column. 32.5 ml
of the flow-through RNase HII fraction was subjected to RESOURSE S
column (Amersham Pharmacia Biotech) equilibrated with Buffer C and
eluted with a linear gradient of 0 to 500 mM NaCl using FPLC
system. A fraction containing RNase II eluted with about 240 mM
NaCl was obtained. 2.0 ml of the RNase II fraction was subjected to
PD-10 column (Amersham Pharmacia Biotech) equilibrated with Buffer
C containing 50 mM NaCl. 3.5 ml of the resulting eluate was
subjected to HiTrap-heparin column (Amersham Pharmacia Biotech)
equilibrated with Buffer C containing 50 mM NaCl and eluted with a
linear gradient of 50 to 550 mM NaCl using FPLC system. As a
result, a fraction containing RNase II eluted with about 295 mM
NaCl was obtained. The thus eluted RNase HII was used as Tma RNase
HII preparation.
[0543] The enzymatic activity of the thus obtained Tma RNase HII
preparation was measured as described in Referential Example 2-(6).
As a result, an RNase H activity was observed for the Tma RNase HII
preparation.
Referential Example 6
Cloning of RNase HII Gene from Pyrococcus horikoshii
[0544] (1) Preparation of Genomic DNA from Pyrococcus
horikoshii
[0545] 2 L of a medium containing 1% Tryptone (Difco Laboratories),
0.5% yeast extract (Difco Laboratories), 1% soluble starch (Nacalai
Tesque), 3.5% Jamarine S Solid (Jamarine Laboratory), 0.5% Jamarine
S Liquid (Jamarine Laboratory), 0.003% MgSO.sub.4, 0.001% NaCl,
0.0001% FeSO.sub.4.7H.sub.2O, 0.0001% CoSO.sub.4, 0.0001%
CaCl.sub.2.7H.sub.2O, 0.0001% ZnSO.sub.4, 0.1 ppm
CuSO.sub.4.5H.sub.2O, 0.1 ppm KAl(SO.sub.4).sub.2, 0.1 ppm
H.sub.3BO.sub.4, 0.1 ppm Na.sub.2MoO.sub.4.2H.sub.2O and 0.25 ppm
NiCl.sub.2.6H.sub.2O was placed in a 2-L medium bottle, sterilized
at 120 C for 20 minutes, bubbled with nitrogen gas to remove
dissolved oxygen, then Pyrococcus horikoshii OT3 (purchased from
the Institute of Physical and Chemical Research (RIKEN); JCM9974)
was inoculated into the medium and cultured at 95 C for 16 hours
without shaking. After cultivation, cells were collected by
centrifugation.
[0546] The cells were then suspended in 4 ml of 25% sucrose, 50 mM
tris-HCl (pH 8.0). 0.4 ml of 10 mg/ml lysozyme chloride (Nacalai
Tesque) in water was added thereto. The mixture was reacted at 20 C
for 1 hour. After reaction, 24 ml of a mixture containing 150 mM
NaCl, 1 mM EDTA and 20 mM tris-HCl (pH 8.0), 0.2 ml of 20 mg/ml
proteinase K (Takara Shuzo) and 2 ml of 10% aqueous solution of
sodium lauryl sulfate were added to the reaction mixture. The
mixture was incubated at 37 C for 1 hour.
[0547] After reaction, the mixture was subjected to
phenol-chloroform extraction followed by ethanol precipitation to
prepare about 1 mg of genomic DNA.
[0548] (2) Cloning of RNase HII Gene
[0549] The entire genomic sequence of the Pyrococcus horikoshii has
been published [DNA Research, 5:55-76 (1998)]. The existence of one
gene encoding a homologue of RNase HII (PH1650) was known (SEQ ID
NO:234, the home page of National Institute of Technology and
Evaluation: http://www/nite.go.jp/).
[0550] Primers PhoNde (SEQ ID NO:235) and PhoBam (SEQ ID NO:236)
were synthesized on the basis of the sequence of the PH1650 gene
(SEQ ID NO:234).
[0551] A PCR was carried out using 100 ng of the Pyrococcus
horikoshii genomic DNA prepared in Referential Example 6-(1) as a
template, and 20 pmol each of PhoNde and PhoBam as primers in a
volume of 100 .mu.l. TaKaRa Ex Taq (Takara Shuzo) was used as a DNA
polymerase for the PCR according to the attached protocol. The PCR
was carried out as follows: 40 cycles of 94 C for 30 seconds, 55 C
for 30 seconds and 72 C for 1 minute. An amplified DNA fragment of
about 0.7 kb was digested with NdeI and BamHI (both from Takara
Shuzo). Then, a plasmid pPHO238 was constructed by incorporating
the resulting DNA fragment between NdeI and BamHI sites in a
plasmid vector pET3a (Novagen).
[0552] (3) Determination of Nucleotide Sequence of DNA Fragment
Containing RNase HII Gene
[0553] The nucleotide sequence of the DNA fragment inserted into
pPHO238 obtained in Referential Example 6-(2) was determined
according to a dideoxy method.
[0554] Analysis of the determined nucleotide sequence revealed an
open reading frame presumably encoding RNase HII. The nucleotide
sequence of the open reading frame is shown in SEQ ID NO:237. The
amino acid sequence of RNase HII deduced from the nucleotide
sequence is shown in SEQ ID NO:238.
[0555] Escherichia coli JM109 transformed with the plasmid pPHO238
is designated and indicated as Escherichia coli JM109/pPHO238, and
deposited on Feb. 22, 2001 at International Patent Organism
Depositary, National Institute of Advanced Industrial Science and
Technology under accession number FERM P-18222.
[0556] (4) Preparation of Purified RNase HII Preparation
[0557] Escherichia coli HMS174(DE3) (Novagen) was transformed with
pPHO238 obtained in Referential Example 6-(2). The resulting
Escherichia coli HMS174(DE3) harboring pPHO238 was inoculated into
1 L of LB medium containing 100 .mu.g/ml of ampicillin and cultured
with shaking at 37 C for 16 hours. After cultivation, cells
collected by centrifugation were suspended in 34.3 ml of a
sonication buffer [50 mM tris-HCl (pH 8.0), 1 mM EDTA, 2 mM
phenylmethanesulfonyl fluoride] and sonicated. A supernatant
obtained by centrifuging the sonicated suspension at 12000 rpm for
10 minutes was heated at 80 C for 15 minutes. It was then
centrifuged at 12000 rpm for 10 minutes again to collect a
supernatant. Thus, 33.5 ml of a heated supernatant was
obtained.
[0558] The heated supernatant was subjected to RESOURSE Q column
(Amersham Pharmacia Biotech) equilibrated with Buffer A [50 mM
tris-HCl (pH 8.0), 1 mM EDTA] and chromatographed using FPLC system
(Amersham Pharmacia Biotech). As a result, RNase HII flowed through
the RESOURSE Q column.
[0559] 35.0 ml of the flow-through RNase HII fraction was dialyzed
against 2 L of Buffer B (50 mM tris-HCl (pH 7.0), 1 mM EDTA) for 2
hours. The dialysis was repeated two more times. 34.5 ml of the
dialyzed enzyme solution was subjected to RESOURSE S column
(Amersham Pharmacia Biotech) equilibrated with Buffer B and eluted
with a linear gradient of 0 to 500 mM NaCl using FPLC system. A
fraction containing RNase HII eluted with about 155 mM NaCl was
obtained.
[0560] Buffer B was added to 4.0 ml of the fraction to make the
NaCl concentration to 50 mM. The mixture was subjected to
HiTrap-heparin column (Amersham Pharmacia Biotech) equilibrated
with Buffer B containing 50 mM NaCl and eluted with a linear
gradient of 50 to 550 mM NaCl using FPLC system. As a result, a
fraction containing RNase HII eluted with about 160 mM NaCl was
obtained.
[0561] 6.9 ml of the RNase HII fraction was concentrated by
ultrafiltration using Centricon-10 (Amicon). Two portions each
separated from 250 .mu.l of the concentrate were subjected to
Superose 6 gel filtration column (Amersham Pharmacia Biotech)
equilibrated with 50 mM tris-HCl (pH 7.0) containing 100 mM NaCl
and 0.1 mM EDTA and eluted with the same buffer. As a result, RNase
HII was eluted at a position corresponding to a molecular weight of
24.5 kilodalton. This molecular weight corresponds to that of RNase
HII in a form of a monomer.
[0562] The RNase HII eluted as described above was used as Pho
RNase HII preparation.
[0563] The enzymatic activity of the thus obtained Pho RNase HII
preparation was measured as described in Referential Example 3-(5).
As a result, an RNase H activity was observed for the Pho RNase HII
preparation.
Referential Example 7
Cloning of RNase HII Gene from Archaeoglobus fulgidus
[0564] (1) Preparation of Genomic DNA from Archaeoglobus
fulgidus
[0565] Cells of Archaeoglobus fulgidus (purchased from Deutsche
Sammlung von Mikroorganismen und Zellkulturen GmbH; DSM4139)
collected from 8 ml of a culture was suspended in 100 .mu.l of 25%
sucrose, 50 mM tris-HCl (pH 8.0). 20 .mu.l of 0.5 M EDTA and 10
.mu.l of 10 mg/ml lysozyme chloride (Nacalai Tesque) in water was
added thereto. The mixture was reacted at 20 C for 1 hour. After
reaction, 800 .mu.l of a mixture containing 150 mM NaCl, 1 mM EDTA
and 20 mM tris-HCl (pH 8.0), 10 .mu.l of 20 mg/ml proteinase K
(Takara Shuzo) and 50 .mu.l of 10% aqueous solution of sodium
lauryl sulfate and were added to the reaction mixture. The mixture
was incubated at 37 C for 1 hour. After reaction, the mixture was
subjected to phenol-chloroform extraction, ethanol precipitation
and air-drying, and then dissolved in 50 .mu.l of TE to obtain a
genomic DNA solution.
[0566] (2) Cloning of RNase HII Gene
[0567] The entire genomic sequence of the Archaeoglobus fulgidus
has been published [Nature, 390:364-370 (1997)]. The existence of
one gene encoding a homologue of RNase HII (AF0621) was known (SEQ
ID NO:239,
http://www.tigr.org/tdb/CMR/btm/htmls/SplashPage.htlm).
[0568] Primers AfuNde (SEQ ID NO:240) and AfuBam (SEQ ID NO:241)
were synthesized on the basis of the sequence of the AF0621 gene
(SEQ ID NO:239).
[0569] A PCR was carried out using 30 ng of the Archaeoglobus
fulgidus genomic DNA prepared in Referential Example 7-(1) as a
template, and 20 pmol each of AfuNde and AfuBam as primers in a
volume of 100 .mu.l. Pyrobest DNA polymerase (Takara Shuzo) was
used as a DNA polymerase for the PCR according to the attached
protocol. The PCR was carried out as follows: 40 cycles of 94 C for
30 seconds, 55 C for 30 seconds and 72 C for 1 minute. An amplified
DNA fragment of about 0.6 kb was digested with NdeI and BamHI (both
from Takara Shuzo). Then, a plasmid pAFU204 was constructed by
incorporating the resulting DNA fragment between NdeI and BamHI
sites in a plasmid vector pTV119Nd (a plasmid in which the NcoI
site in pTV119N is converted into a NdeI site).
[0570] (3) Determination of Nucleotide Sequence of DNA Fragment
Containing RNase HII Gene
[0571] The nucleotide sequence of the DNA fragment inserted into
pAFU204 obtained in Referential Example 7-(2) was determined
according to a dideoxy method.
[0572] Analysis of the determined nucleotide sequence revealed an
open reading frame presumably encoding RNase HII. The nucleotide
sequence of the open reading frame is shown in SEQ ID NO:242. The
amino acid sequence of RNase HII deduced from the nucleotide
sequence is shown in SEQ ID NO:243.
[0573] Escherichia coli JM109 transformed with the plasmid pAFU204
is designated and indicated as Escherichia coli JM109/pAFU204, and
deposited on Feb. 22, 2001 at International Patent Organism
Depositary, National Institute of Advanced Industrial Science and
Technology under accession number FERM P-18221.
[0574] (4) Preparation of Purified RNase HII Preparation
[0575] Escherichia coli JM109 was transformed with pAFU204 obtained
in Referential Example 7-(2). The resulting Escherichia coli JM109
harboring pAFU204 was inoculated into 2 L of LB medium containing
100 .mu.g/ml of ampicillin and cultured with shaking at 37 C for 16
hours. After cultivation, cells collected by centrifugation were
suspended in 37.1 ml of a sonication buffer [50 mM tris-HCl (pH
8.0), 1 mM EDTA, 2 mM phenylmethanesulfonyl fluoride] and
sonicated. A supernatant obtained by centrifuging the sonicated
suspension at 12000 rpm for 10 minutes was heated at 70 C for 15
minutes. It was then centrifuged at 12000 rpm for 10 minutes again
to collect a supernatant. Thus, 40.3 ml of a heated supernatant was
obtained.
[0576] The heated supernatant was subjected to RESOURSE Q column
(Amersham Pharmacia Biotech) equilibrated with Buffer A [50 mM
tris-HCl (pH 8.0), 1 mM EDTA] and chromatographed using FPLC system
(Amersham Pharmacia Biotech). As a result, RNase HII flowed through
the RESOURSE Q column.
[0577] The flow-through RNase HII fraction was subjected to
RESOURSE S column (Amersham Pharmacia Biotech) equilibrated with
Buffer A and chromatographed using FPLC system (Amersham Pharmacia
Biotech). As a result, RNase HII flowed through the RESOURSE S
column.
[0578] 40.0 ml of the flow-through RNase HII fraction was dialyzed
against 2 L of Buffer B (50 mM tris-HCl (pH 7.0), 1 mM EDTA)
containing 50 mM NaCl for 2 hours. The dialysis was repeated two
more times. 40.2 ml of the dialyzed enzyme solution was subjected
to HiTrap-heparin column (Amersham Pharmacia Biotech) equilibrated
with Buffer B containing 50 mM NaCl and eluted with a linear
gradient of 50 to 550 mM NaCl using FPLC system. As a result, a
fraction containing RNase HII eluted with about 240 mM NaCl was
obtained.
[0579] 7.8 ml of the RNase HII fraction was concentrated by
ultrafiltration using Centricon-10 (Amicon). Four portions each
separated from about 600 .mu.l of the concentrate were subjected to
Superose 6 gel filtration column (Amersham Pharmacia Biotech)
equilibrated with 50 mM tris-HCl (pH 7.0) containing 100 mM NaCl
and 0.1 mM EDTA and eluted with the same buffer. As a result, RNase
HII was eluted at a position corresponding to a molecular weight of
30.0 kilodalton. This molecular weight corresponds to that of RNase
HII in a form of a monomer.
[0580] The RNase HII eluted as described above was used as Afu
RNase HII preparation.
[0581] The enzymatic activity of the thus obtained Afu RNase HII
preparation was measured as described in Referential Example 3-(5).
As a result, an RNase H activity was observed for the Afu RNase HII
preparation.
Referential Example 8
[0582] Unit value of RNase H from Escherichi coli used in the
method of the present invention was measured according to the
following method.
[0583] (1) Preparation of Reagent Solutions Used
[0584] Reaction mixture for determining activity: The following
substances at the indicated final concentrations were contained in
sterile water: 40 mM tris-hydrochloride (pH 7.7 at 37 C), 4 mM
magnesium chloride, 1 mM DTT, 0.003% BSA, 4% glycerol and 24 .mu.M
poly(dT).
[0585] Poly[8-.sup.3H]adenylic acid solution: 370 kBq of a
poly[8-.sup.3H]adenylic acid solution was dissolved in 200 .mu.l of
sterile water.
[0586] Polyadenylic acid solution: Polyadenylic acid was diluted to
a concentration of 3 mM with sterile ultrapure water.
[0587] Enzyme dilution solution: The following substances at the
indicated final concentrations were contained in sterile water: 25
mM tris-hydrochloride (pH 7.5 at 37 C), 5 mM 2-mercaptoethanol, 0.5
mM EDTA (pH 7.5 at 37 C), 30 mM sodium chloride and 50%
glycerol.
[0588] Preparation of heat-denatured calf thymus DNA: 200 mg of
calf thymus DNA was suspended and allowed to swell in 100 ml of TE
buffer. The solution was diluted to a concentration of 1 mg/ml with
sterile ultrapure water based on the absorbance measured at UV 260
nm. The diluted solution was heated at 100.degree. C. for 10
minutes and then rapidly cooled in an ice bath.
[0589] (2) Method for Measuring Activity
[0590] 7 .mu.l of the poly[8-.sup.3H]adenylic acid solution was
added to 985 .mu.l of the reaction mixture for determining activity
prepared in (1) above. The mixture was incubated at 37.degree. C.
for 10 minutes. 8 .mu.l of polyadenylic acid was added to the
mixture to make the final concentration to 24 .mu.M. The mixture
was further incubated at 37.degree. C. for 5 minutes. Thus, 1000
.mu.l of a poly[8-.sup.3H]rA-poly-dT reaction mixture was prepared.
200 .mu.l of the reaction mixture was then incubated at 30.degree.
C. for 5 minutes. 1 .mu.l of an appropriate serial dilution of an
enzyme solution was added thereto. 50 .mu.l each of samples was
taken from the reaction mixture over time for use in subsequent
measurement. The period of time in minutes from the addition of the
enzyme to the sampling is defined as Y. 50 .mu.l of a reaction
mixture for total CPM or for blank was prepared by adding 1 .mu.l
of the enzyme dilution solution instead of an enzyme solution. 100
.mu.l of 100 mM sodium pyrophosphate, 50 .mu.l of the
heat-denatured calf thymus DNA solution and 300 .mu.l of 10%
trichloroacetic acid (300 .mu.l of ultrapure water for measuring
total CPM) were added to the sample. The mixture was incubated at
0.degree. C. for 5 minutes, and then centrifuged at 10000 rpm for
10 minutes. After centrifugation, 250 .mu.l of the resulting
supernatant was placed in a vial. 10 ml of Aquasol-2 (NEN Life
Science Products) was added thereto. CPM was measured in a liquid
scintillation counter.
[0591] (3) Calculation of Units
[0592] Unit value for each enzyme was calculated according to the
following equation.
Unit/ml={(measuredCPM-blankCPM).times.1.2*.times.20.times.1000.times.dilut-
ion
rate}200(.mu.l)/(totalCPM.times.Y(min.).times.50(.mu.l).times.9**)
[0593] 1.2*: Amount in nmol of poly[8-.sup.3H]rA-poly-dT contained
in total CPM per 50 .mu.l.
[0594] 9**: Correction coefficient.
Example 1
[0595] (1) Synthesis of Template DNA and Primers
[0596] A single-stranded DNA of 99 bases as a template and primers
used in this Example were synthesized using a DNA synthesizer
(Applied Biosystems). The nucleotide sequence of the
single-stranded DNA of 99 bases is shown in
[0597] SEQ ID NO:1 of the Sequence Listing. The structures of the
primers used in this Example are described below in detail:
[0598] Primer Pair 1: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:2 or 3 of the Sequence Listing and
wholly composed of deoxyribonucleotides;
[0599] Primer Pair 2: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:4 or 5 of the Sequence Listing in
which the first and second nucleotides from the 3'-terminus are
ribonucleotides and the phosphate bond on the 5'-terminal side of
the second ribonucleotide from the 3'-terminus is replaced by a
phosphorothioate bond;
[0600] Primer Pair 3: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:6 or 7 of the Sequence Listing in
which the nucleotide at the 3'-terminus is a ribonucleotide and the
phosphate bond on the 5'-terminal side of the ribonucleotide is
replaced by a phosphorothioate bond;
[0601] Primer Pair 4: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:8 or 9 of the Sequence Listing in
which the first and second nucleotides from the 3'-terminus are
ribonucleotides; and
[0602] Primer Pair 5: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:10 or 11 of the Sequence Listing in
which the third and fourth nucleotides from the 3'-terminus are
ribonucleotides and the phosphate bond on the 5'-terminal side of
the fourth ribonucleotide form the 3'-terminus is replaced by a
phosphorothioate bond.
[0603] (2) Amplification Reaction
[0604] Bca BEST DNA polymerase (Takara Shuzo), which is a DNA
polymerase lacking a 5'3' exonuclease activity from Bacillus
caldotenax, and cloned ribonuclease H (Takara Shuzo), which is
RNase H from E. coli, were used to examine the reaction systems of
Models 1 to 7 as described below.
[0605] A reaction mixture was prepared as follows.
[0606] 35 mM tris-hydrochloride buffer (pH 7.5), 0.1 mg/ml bovine
serum albumin (BSA), 2.7% glycerol, 5% dimethyl sulfoxide, 1.4 mM
each of dNTPs, 10 mM magnesium chloride, 20 pmol of one or both of
the primers of one of the primer pairs as described above in (1),
0.6 ng of the synthetic single-stranded DNA as the template, 5 U of
Bca BEST DNA polymerase and 60 U of cloned ribonuclease H to a
final reaction volume of 50 .mu.l. The reaction mixture was mixed
to homogeneity, incubated at 55.degree. C. for 60 minutes, and then
heated at 90.degree. C. for 2 minutes to inactivate the enzymes. 8
.mu.l of the reaction mixture was subjected to electrophoresis on
3% NuSieve 3:1 agarose (Takara Shuzo) gel. The primers used in the
respective Models are described below:
[0607] Models 1-5: One of the Primer Pairs 1-5 was used;
[0608] Model 6: Only the downstream primer of the Primer Pair 2 was
used; and
[0609] Model 7: The Primer Pair 4 was used without the addition of
RNase H.
[0610] As a result, amplified fragments having a size of interest
ranging from about 40 base pairs (bp) to about 90 bp were observed
when the reaction mixtures of the Models 2 to 5 were used,
indicating that DNAs are amplified using these reaction systems. An
amplified fragment having an expected size of about 70 bases (b) (a
single-stranded DNA fragment) was observed for the Model 6 in which
only one of the two primers was used. No DNA amplification was
observed for the reaction of the Model 1 or 7.
[0611] (3) Confirmation of Amplification Products
[0612] The reaction mixture obtained by the reaction of the Model 4
as described in (2) was filtrated using Microcon-100 (Takara Shuzo)
to recover an amplified DNA fragment entrapped on the filter. The
nucleotide sequence of the DNA fragment was determined by the
dideoxy method. As a result, the fragment amplified by the
above-mentioned reaction was confirmed to be a DNA having the same
nucleotide sequence as that of the DNA as the template.
[0613] (4) Examination of Reaction Time
[0614] The reaction mixture of the Model 2 as described above in
(2) was prepared to study the change in the amount of the
amplification product when it was reacted for a varying time. The
reaction mixture was incubated for 0, 15, 30, 60, 90 or 120 minutes
at 55.degree. C. The mixture was then treated at 90.degree. C. for
2 minutes to inactivate the enzymes. 8 .mu.l of the reaction
mixture was analyzed by electrophoresis on 3% NuSieve 3:1 agarose
gel. The results of the electrophoresis are shown in FIG. 41.
Numbers 1 to 6 in the figure represent lanes to which the reaction
mixture reacted for 0, 15, 30, 60, 90 or 120 minutes was applied,
respectively. M represents a lane to which 100 bp DNA ladder marker
(Takara Shuzo) was applied as a molecular weight marker.
[0615] As shown in FIG. 41, no amplification product was observed
for a reaction time of 0 minute. It was confirmed that the amount
of the amplification product increased as the reaction time became
longer from 15 minutes to 30 or 60 minutes. However, the amount of
the amplification product as observed by electrophoresis was almost
unchanged for a reaction time of 60 minutes or longer, indicating
that the amplification in the reaction system used reached the
plateau at about 60 minutes.
Example 2
[0616] (1) Preparation of RNA
[0617] An RNA used as a template in this Example was prepared from
human cultured cell HT29 (ATCC HTB-38) (Dainippon Pharmaceutical)
using TRIzol reagent (Life Technologies). The concentration of the
resulting total RNA was adjusted to 1 .mu.g/.mu.l. The OD260/OD280
value was 1.8, which indicates the spectrophotometric purity of the
RNA.
[0618] (2) Amplification Reaction
[0619] Bca BEST DNA polymerase, which has a reverse transcription
activity and a DNA polymerase activity, as well as RNase H
endonuclease were used to determine if a cDNA is amplified from an
RNA.
[0620] A reaction mixture having the composition as described in
Example 2 was prepared with the addition of 1 .mu.g of the
above-mentioned total RNA. A targeted region encoding human
transferrin receptor (GenBank accession no. X01060) was amplified
using the Primer Pair 2 in Example 1 as primers.
[0621] The reaction mixture was incubated at 55.degree. C. for 60
minutes, and then heated at 90.degree. C. for 2 minutes to
inactivate the enzymes. When 8 .mu.l of the reaction mixture was
subjected to electrophoresis on 3% NuSieve 3:1 agarose gel, an
amplified fragment having an expected size of 56 bp was observed.
Furthermore, Southern hybridization was carried out using a probe
having the targeted nucleotide sequence. A DNA probe having a
nucleotide sequence as shown in SEQ ID NO:12 of the Sequence
Listing labeled with biotin at the 5'-terminus was used to conduct
Southern hybridization. As a result, the probe hybridized with the
above-mentioned amplified fragment, confirming that the targeted
region was correctly amplified by the method of the present
invention.
Example 3
[0622] (1) Synthesis of Primers
[0623] The amplification method of the present invention was
examined using a double-stranded DNA as a template. Primers used
were synthesized using a DNA synthesizer (Applied Biosystems).
Nucleotide sequences of primers are shown in SEQ ID NOS:13-22 of
the Sequence Listing. The structures of the primers used in this
Example are described below in detail. The pUC19 DNA (Takara Shuzo)
was used as a template for the Primer Pairs A-F. The nucleotide
sequence of pUC19 is available from a database (GenBank accession
no. L09137). An amplified double-stranded DNA fragment was used as
a template for the Primer Pair G. The fragment was prepared from
the human total RNA obtained in Example 2 using primers having a
sequence as shown in SEQ ID NOS:95 or 96 of the Sequence Listing
and TaKaRa RNA PCR Kit (AMV) Ver. 2.1 (Takara Shuzo) according to
the attached standard protocol.
[0624] Primer Pair A (amplified fragment length: about 450 bp): A
combination of primers having a nucleotide sequence as shown in SEQ
ID NO:13 or 14 of the Sequence Listing in which the first and
second bases from the 3'-terminus are ribonucleotides;
[0625] Primer Pair B (amplified fragment length: about 250 bp): A
combination of primers having a nucleotide sequence as shown in SEQ
ID NO:13 or 15 of the Sequence Listing in which the first and
second bases from the 3'-terminus are ribonucleotides;
[0626] Primer Pair C (amplified fragment length: about 520 bp): A
combination of primers having a nucleotide sequence as shown in SEQ
ID NO:13 or 16 of the Sequence Listing in which the first and
second bases from the 3'-terminus are ribonucleotides;
[0627] Primer Pair D (amplified fragment length: about 890 bp): A
combination of primers having a nucleotide sequence as shown in SEQ
ID NO: 13 or 17 of the Sequence Listing in which the first and
second bases from the 3'-terminus are ribonucleotides;
[0628] Primer Pair E (amplified fragment length: about 130 bp): A
combination of primers having a nucleotide sequence as shown in SEQ
ID NO:18 or 19 of the Sequence Listing in which the first to third
bases from the 3'-terminus are ribonucleotides;
[0629] Primer Pair F (amplified fragment length: about 220 bp): A
combination of primers having a nucleotide sequence as shown in SEQ
ID NO:20 or 19 of the Sequence Listing in which the first to third
bases from the 3'-terminus are ribonucleotides; and
[0630] Primer Pair G (amplified fragment length: about 320 bp): A
combination of primers having a nucleotide sequence as shown in SEQ
ID NO:21 or 22 of the Sequence Listing in which the first to third
bases from the 3'-terminus are ribonucleotides.
[0631] (2) Amplification Reaction
[0632] A reaction mixture was prepared as follows.
[0633] 35 mM potassium phosphate buffer (pH 7.5), 0.1 mg/ml bovine
serum albumin (BSA), 5% dimethyl sulfoxide, 1.4 mM each of dNTPs,
10 mM magnesium chloride, 60 pmol each of the primers of one of the
primer pairs as described above in (1), 100 ng of the pUC19 DNA as
the template, 5.5 U of Bca BEST DNA polymerase and 60 U of RNase H
to a final reaction volume of 50 .mu.l.
[0634] The reaction conditions were as follows. The reaction
mixture without the DNA polymerase or RNase H was heat-denatured at
98.degree. C. for 1 minute, and then cooled to 55.degree. C. The
DNA polymerase and RNase H were then added thereto and the mixture
was incubated at 55.degree. C. for 60 minutes. After the completion
of the reaction, the mixture was heated at 90.degree. C. for 2
minutes to inactivate the enzymes. 8 .mu.l of the reaction mixture
was then subjected to electrophoresis on 3% NuSieve 3:1 agarose
gel.
[0635] As a result, it was confirmed that an amplified fragment of
interest was obtained using either of the Primer Pairs. Thus, it
was confirmed that a double-stranded DNA can be used as a template
to conduct an amplification reaction in the amplification method of
the present invention.
[0636] (3) Digestion of Amplification Product with Restriction
Enzyme
[0637] Digestion of an amplified fragment obtained using the
amplification method of the present invention with a restriction
enzyme was examined. The pUC19 plasmid DNA was used as a template
DNA. pUC19 upper (2) NN primer and pUC19 lower NN primer as shown
in SEQ ID NOS:13 and 14 of the Sequence Listing, respectively, were
used. In the primers, the first and second bases from the
3'-terminus are ribonucleotides. The composition of the reaction
mixture was as follows.
[0638] Reaction Mixture A: 35 mM potassium phosphate buffer (pH
7.5), 10 mM magnesium chloride, 1.4 mM each of dNTPs, 0.01% BSA, 5%
DMSO, 2.7% glycerol, 100 pmol each of the pUC19 upper (2) NN primer
and the pUC19 lower NN primer, 500 ng of the pUC19 DNA and sterile
distilled water to a reaction volume of 48 .mu.l.
[0639] The reaction mixture was heat-denatured at 98.degree. C. for
1 minute, and then cooled to 55.degree. C. 60 U of E. coli RNase H
and 5.5 U of Bca BEST were then added thereto to make the reaction
volume to 50 .mu.l. The reaction mixture was incubated at
55.degree. C. for 1 hour. After the completion of the reaction, the
mixture was heated at 90.degree. C. for 2 minutes to inactivate the
enzymes. The reaction mixture was subjected to electrophoresis on
3% agarose gel to purify the resulting amplification product. The
recovered amplification product was resupended in 100 .mu.l of
sterile distilled water.
[0640] The thus obtained DNA solution was used for restriction
enzyme digestion. Restriction enzymes used were AccII (Takara
Shuzo) and BcnI (Takara Shuzo). The composition of the reaction
mixture was as follows.
[0641] 3 .mu.l of the DNA solution, 1 .mu.l of 10.times.AccII
buffer or 10.times.BcnI buffer attached to each of the enzymes, 1
.mu.l of the restriction enzyme AccII or BcnI and sterile distilled
water to a reaction volume of 10 .mu.l. The reaction mixture was
reacted at 37.degree. C. for 30 minutes. 1.5 .mu.l of 10.times.
loading buffer was added thereto. 6 .mu.l of the mixture was
subjected to electrophoresis on 3% NuSieve agarose gel.
[0642] As a result, restriction enzyme-digested DNA fragments of
interest were obtained using both of the restriction enzymes AccII
and BcnI.
[0643] (4) Detection of Mutation
[0644] Detection of a mutation using the amplification method of
the present invention was examined. pUC19 was used as a template.
Nucleotide sequences of pUC19 upper (2) NN-U primer, pUC19 upper
(2) NN-A primer, pUC19 upper (2) NN-C primer and pUC19 upper (2)
NN-G primer are shown in SEQ ID NOS:23-26 of the Sequence Listing,
respectively. Nucleotide sequences of pUC19 lower NN primer is
shown in SEQ ID NOS:14 of the Sequence Listing. Any one of these
primers is a chimeric oligonucleotide primer in which the first and
second bases from the 3'-terminus are ribonucleotides. The
combinations of these primers were as follows.
[0645] Primer Pair 1: pUC19 upper (2) NN-U and pUC19 lower NN;
[0646] Primer Pair 2: pUC19 upper (2) NN-A and pUC19 lower NN;
[0647] Primer Pair 3: pUC19 upper (2) NN--C and pUC19 lower NN;
and
[0648] Primer Pair 4: pUC19 upper (2) NN-G and pUC19 lower NN.
[0649] A reaction mixture was prepared as follows.
[0650] 30 mM potassium phosphate buffer (pH 7.3), 0.01% bovine
serum albumin (BSA), 5% DMSO, 1 mM each of dNTPs, 8 mM magnesium
acetate, 60 pmol each of the primers, 50 ng of the DNA as the
template and sterile distilled water to a reaction volume of 48
.mu.l.
[0651] The reaction mixture was heat-denatured at 98.degree. C. for
1 minute, and then cooled to 55.degree. C. 5.5 U of Bca BEST DNA
polymerase and 60 U of E. coli RNase H were then added thereto and
the reaction mixture was incubated at 55.degree. C. for 60 minutes.
The mixture was then heated at 90.degree. C. for 2 minutes to
inactivate the enzymes. 8 .mu.l of the reaction mixture was
subjected to electrophoresis on 4% NuSieve 3:1 agarose (Takara
Shuzo) gel. As a result, an amplified fragment of about 450 bp of
interest was detected only when the combination of the primers that
included the primer having a complementary base at the
3.sup.1-terminus of pUC19 upper (2) NN was used. On the other hand,
no amplified fragment was observed for the combinations including
the primer having a mismatched base at the 3.sup.1-terminus of
pUC19 upper (2) NN.
Example 4
[0652] (1) Reaction in Microtube
[0653] Reaction volume for the amplification method of the present
invention was examined. A region encoding human transferrin
receptor was selected as a region to be amplified. Primers having a
sequence as shown in SEQ ID NO:27 or 28 of the Sequence Listing
were used. In the primers, the first and second bases from the
3'-terminus are ribonucleotides. A fragment of about 750 bp
amplified by RT-PCR was used as a template DNA. The reaction volume
was adjusted to 50, 100, 300 or 500 .mu.l. The composition of the
reaction mixture was as follows.
[0654] Reaction Mixture A: 10 .mu.l of 5.times. specialized buffer
(135 mM potassium phosphate buffer (pH 7.5), 0.5 mg/ml BSA, 2.5%
DMSO), 4 .mu.l of 100 mM magnesium acetate, 5 .mu.l of 10 mM dNTPs,
10 .mu.l of 10 .mu.M ATP, 1 .mu.l of Bca BEST DNA polymerase (22
U/.mu.l), 1 .mu.l of RNase H (60 U/.mu.l) and sterile distilled
water to 39 .mu.l.
[0655] Reaction Mixture B: 3 .mu.l each of 20 .mu.M human
transferrin receptor S primer (SEQ ID NO:27) and 20 .mu.M human
transferrin receptor A primer (SEQ ID NO:28), about 100 ng of the
DNA as the template and sterile distilled water to 11 .mu.l. If the
volume became 50 .mu.l or more, it was scaled up to have the
above-mentioned composition.
[0656] For an amplification reaction, the Reaction Mixture B was
treated at 98.degree. C. for 2 minutes, and then incubated at
55.degree. C. for 3 minutes. The Reaction Mixture B was added to
the Reaction Mixture A which had been pre-incubated in a 1500-.mu.l
microtube at 55.degree. C. After mixing, the reaction mixture was
incubated at 55.degree. C. for 1 hour. After the completion of the
reaction, the mixture was transferred to an ice bath. 8 .mu.l of
the reaction mixture was subjected to electrophoresis on 3% agarose
gel.
[0657] As a result, a fragment of about 300 bp of interest was
efficiently amplified using each of the reaction volumes. In
addition, it was confirmed that an amplified fragment of interest
can be obtained without a problem using a PCR-amplified fragment as
a template DNA.
[0658] (2) Reaction in Petri Dish
[0659] Use of a Petri dish for preventing the heterogeneous
temperature in a reaction mixture due to increased reaction volume
was examined. A region encoding human transferrin receptor was
selected as a region to be amplified. Primers having a sequence as
shown in SEQ ID NO:12 or 13 of the Sequence Listing were used. In
the primers, the first and second bases from the 3'-terminus are
ribonucleotides. A fragment of about 750 bp amplified by RT-PCR was
used as a template DNA. The reaction volume was adjusted to 10 ml.
The composition of the reaction mixture was as follows.
[0660] Reaction Mixture A: 2000 .mu.l of 5.times. specialized
buffer (135 mM potassium phosphate buffer (pH 7.5), 0.5 mg/ml BSA,
2.5% DMSO), 800 .mu.l of 100 mM magnesium acetate, 1000 .mu.l of 10
mM dNTPs and sterile distilled water to 9.1 ml.
[0661] Reaction Mixture B: 200 .mu.l each of 60 .mu.M human
transferrin receptor S primer (SEQ ID NO:12) and 60 .mu.M human
transferrin receptor primer (SEQ ID NO:13), about 10 .mu.g of the
DNA as the template and sterile distilled water to 500 .mu.l.
[0662] Reaction Mixture C: 200 .mu.l of Bca BEST DNA polymerase (22
U/.mu.l) and 200 .mu.l of RNase H (60 U/.mu.l)
[0663] For an amplification reaction, the Reaction Mixture B was
treated at 98.degree. C. for 1 minute, and then incubated at
55.degree. C. for 3 minutes. The Reaction Mixture B was added to
the Reaction Mixture A which had been pre-incubated in a 60-mm
(diameter) plastic Petri dish at 55.degree. C. The Reaction Mixture
C was further added thereto. After mixing, the reaction mixture was
incubated at 55.degree. C. for 1 hour. After the completion of the
reaction, the reaction mixture was transferred to an ice bath. 8
.mu.l of the reaction mixture was then subjected to electrophoresis
on 3% agarose gel.
[0664] As a result, a fragment of about 300 bp of interest was
efficiently amplified even if the reaction volume of 10 ml was
used. In addition, it was confirmed that an amplified fragment of
interest can be obtained without a problem using a PCR-amplified
fragment as a template DNA. Thus, it was confirmed that the method
of the present invention can be more preferably used for making a
DNA chip, which requires a large amount of a DNA fragment, as
compared to the conventional PCR method.
Example 5
[0665] (1) Relationship Between Type of Buffer and Amount of RNase
H Used
[0666] The relationship between the type of buffer and the amount
of RNase H used was examined. Plasmid DNAs, in which a fragment of
249 bp or 911 bp was cloned into the pUC19 vector (designated as
pUC19-249 and pUC19-911) were used as templates. Chimeric
oligonucleotide primers, in which the first to third bases from the
3'-terminus of MF2N3 (24) primer or MR1N3 (24) primer having a
sequence as shown in SEQ ID NO:29 or 30 of the Sequence Listing are
ribonucleotides, were used as primers. By using the combination of
these primers, amplified fragments of about 450 bp and about 1100
bp are obtained for pUC19-249 and pUC19-911, respectively.
[0667] A tris-hydrochloride buffer, a potassium phosphate buffer
and Tricine buffer were selected as buffer systems to be examined.
The amounts of RNase H examined were no addition and a final
concentration ranging from 0.3 to 1.2 U/.mu.l. The
tris-hydrochloride buffer system was prepared as described in
Example 1 (2), except that 10 ng of pUC19-249 or 200 ng of
pUC19-911, 60 pmol each of the primers and 11 U/50 .mu.l reaction
volume of Bca BEST DNA polymerase were used. The potassium
phosphate buffer system was prepared to have a similar composition.
The Tricine buffer system was prepared to contain the following at
the indicated final concentration: 34 mM Tricine buffer (pH 8.7),
10 mM potassium chloride, 10 mM ammonium sulfate, 0.01% BSA, 1%
DMSO, 4 mM magnesium acetate and 0.5 mM each of dNTPs. 10 ng/50
.mu.l reaction volume of the pUC19-249 plasmid or 200 ng/50 .mu.l
reaction volume of the pUC19-911 plasmid, 60 pmol/50 .mu.l reaction
volume each of primers, RNase H at a predetermined concentration
and 11 U/50 .mu.l reaction volume of Bca BEST DNA polymerase were
added to the buffer system.
[0668] For an amplification reaction, a mixture of pUC19-249 or
pUC19-911 as a template and the respective primers was
heat-denatured at 98.degree. C. for 1 minute, and then cooled to
55.degree. C. A mixture of the remaining reaction components was
added thereto. The mixture was reacted at 55.degree. C. for 60
minutes. After the completion of the reaction, the mixture was
cooled to 4.degree. C. and {fraction (1/10)} volume of 0.5 M EDTA
was added thereto to terminate the reaction. 3 .mu.l of the
reaction mixture was subjected to electrophoresis on 3% NuSieve 3:1
agarose (Takara Shuzo) gel.
[0669] As a result, when pUC19-249 was used as a template, increase
in amplification efficiency was observed depending on the buffer
system used in the following order: tris-hydrochloride<potassium
phosphate<Tricine. When pUC19-911 was used as a template,
increase in amplification efficiency was observed depending on the
buffer system used in the following order:
tris-hydrochloride<Tricine<potassium phosphate. The use of
RNase H at a final concentration ranging from 0.3 to 1.2 U/.mu.l
resulted in the amplified fragment of interest, although no
amplified fragment of interest was observed for no addition.
[0670] (2) Examination of Amount of Primer
[0671] The effect of the amount of a primer used on the
amplification method of the present invention was examined. A
reaction mixture system having a composition in which pUC19-249 was
used as a template among the compositions as described above in (1)
was used. 60 U/50 .mu.l reaction volume of RNase H was used for the
potassium phosphate buffer system, whereas 30 U/50 .mu.l reaction
volume of RNase H was used for the tris-hydrochloride or Tricine
buffer system. The examined concentration of the primer ranged from
10 to 100 pmol/50 .mu.l. Reaction conditions and confirmation of
amplification were as described above in (1).
[0672] As a result, an amplified fragment of interest was observed
using each of the reaction buffer systems containing the primer at
a concentration ranging from 10 to 100 pmol/50 .mu.l.
[0673] (3) Effect of pH of Reaction Buffer
[0674] The effect of the pH of a reaction mixture on the
amplification method of the present invention was examined. The
composition of the reaction mixture was as described above in (2).
The pH examined were 7.0-8.0 for the potassium phosphate buffer
system, 7.5-9.2 for the Tricine buffer system, and 7.5-9.0 for the
tris-hydrochloride buffer system. Reaction conditions and
confirmation of amplification were as described above in (1).
[0675] As a result, an amplified fragment of interest was observed
at pH within the range used for the respective buffer systems.
[0676] (4) Effect of Additive
[0677] The effect of addition of dimethyl sulfoxide (DMSO) was
examined using the reaction mixture composition of the phosphate
buffer system (pH 7.5) as described above in (3). Additionally, the
effect of addition of a polyamine was also examined. The examined
amount of added DMSO ranged from no addition to 10%. On the other
hand, spermine tetrahydrochloride (Sigma), spermidine
trihydrochloride (Sigma), acetylputrescine (Nacalai Tesque),
putrescine dihydrochloride (Nacalai Tesque), trimethylene diamine
(Nacalai Tesque), propylenediamine (Nacalai Tesque) and
diaminomethane dihydrochloride (Nacalai Tesque) were used as a
polyamine. The amounts of propylenediamine and trimethylene diamine
added were within the range between no addition and 2%. Other
polyaminies were used within the range between no addition and 5
mM. Reaction conditions and confirmation of amplification were as
described above in (1).
[0678] As a result, a DNA fragment of interest was efficiently
amplified using the additive at a concentration within the
indicated range: no addition to 5% of DMSO; no addition to 200
.mu.M of spermine tetrahydrochloride or spermidine; 40 .mu.M to 40
mM of acetylputrescine or putrescine dihydrochloride; 0.002% to
0.02% of trimethylene diamine; 0.0001% to 0.01% of
propylenediamine; and 0.1 .mu.M to 10 .mu.M of diaminomethane
dihydrochloride.
[0679] (5) Examination of Type of Magnesium Salt
[0680] The effect of the type of a magnesium salt on the
amplification method of the present invention was examined. The
pUC19 DNA was used as a template. pUC19 upper NN 249 primer and
pUC19 lower NN primer having sequences as shown in SEQ ID NOS:31
and 14 of the Sequence Listing, respectively, were used as primers.
An amplified fragment of about 225 bp is obtained using a pair of
these primers. Magnesium chloride, magnesium acetate and magnesium
sulfate were used as magnesium salts. The composition of the
reaction mixture was as follows.
[0681] 35 mM potassium phosphate buffer (pH 7.3), 8 mM (final
concentration) magnesium chloride, magnesium acetate or magnesium
sulfate, 1.0 mM (final concentration) each of dNTPs, 50 ng of the
pUC19 DNA, 60 pmol each of the primers, 60 U of RNase H, 5.5 U of
Bca BEST DNA polymerase and sterile distilled water to a reaction
volume of 50 .mu.l. Reaction conditions and confirmation of
amplification were as described above in (3).
[0682] As a result, an amplified fragment of interest was observed
using each of the magnesium salts.
[0683] (6) Examination of Concentrations of Magnesium and dNTPs
[0684] The effects of the concentrations of magnesium and dNTPs on
the amplification method of the present invention were examined.
The composition of the reaction mixture was as described above in
(5), except that 25 ng of the pUC19 DNA, and magnesium and dNTPs at
various concentrations were used. Reaction conditions and
confirmation of amplification were as described above in (1).
[0685] In a reaction system in which the final concentration of
each of dNTPs was fixed at 1 mM, an amplified fragment of interest
was obtained when a final magnesium concentration ranging from 6 mM
to 10 mM was used. In a reaction system in which the final
magnesium concentration of was fixed at 8 mM, an amplified fragment
of interest was obtained when a final concentration of each of
dNTPs ranging from 0.6 mM to 1.2 mM was used. Furthermore, in a
reaction system in which the final concentration of each of dNTPs
was fixed at 0.5 mM, an amplified fragment of interest was obtained
when a final magnesium concentration ranging from 2 mM to 6 mM was
used. In a reaction system in which the final magnesium
concentration was fixed at 4 mM, an amplified fragment of interest
was obtained when a final concentration of each of dNTPs ranging
from 0.2 mM to 0.8 mM was used.
[0686] (7) Examination of Change in Concentration of Potassium
Phosphate Buffer or Tricine Buffer and Reactivity
[0687] The effect of the concentration of the potassium phosphate
buffer or the Tricine buffer on the amplification method of the
present invention was examined. The composition of the reaction
mixture was as described above in (1) for a case where pUC19-249
was used as a template, except that a potassium phosphate buffer at
a final concentration of 20-50 mM or a Tricine buffer at a final
concentration of 22-46 mM was used.
[0688] As a result, an amplified fragment of interest was obtained
when the potassium phosphate buffer at a final concentration
ranging from 20 to 50 mM or the Tricine buffer at a final
concentration ranging from 22 to 46 mM was used.
[0689] (8) Examination of Concentration of Bca BEST DNA
Polymerase
[0690] The effect of the concentration of Bca BEST DNA polymerase
on the amplification method of the present invention was examined.
The composition of the reaction mixture was as described above in
(1) for a case where pUC19-249 was used as a template, except that
a potassium phosphate buffer system or a Tricine buffer system and
Bca BEST DNA polymerase at a concentration within a range of 1-22
U/50 .mu.l reaction volume was used. Reaction conditions and
confirmation of amplification were as described above in (1).
[0691] As a result, an amplified fragment of interest was obtained
when Bca BEST DNA polymerase was used at a concentration within a
range of 1-22 U/50 .mu.l.
Example 6
[0692] Comparison with the PCR Method
[0693] The amplification method of the present invention was
compared with the PCR method. Ones in which a DNA fragment of about
150 bp or about 250 bp is inserted into a multi-cloning site in the
pUC19 plasmid DNA were used as templates. The templates were
prepared as follows.
[0694] pUC19 upper 150 PCR primer, pUC19 upper 249 PCR primer and
pUC19 lower PCR primer, which have sequences as shown in SEQ ID
NOS:32, 33 and 34 of the Sequence Listing, respectively, were used
to conduct a PCR reaction using 100 .mu.g of the pUC19 plasmid DNA
as a template. An amplified fragment of about 150 bp was obtained
by using a combination of the pUC19 upper 150 primer and the pUC19
lower NN primer. An amplified fragment of about 250 bp was obtained
by using a combination of the pUC19 upper 249 primer and the pUC19
lower NN primer. Each of these amplified fragments was purified
using Microcon-100, blunt-ended using DNA blunting kit (Takara
Shuzo), and then subcloned into a HincII site in the pUC19 plasmid.
Plasmids into which one of the amplified fragments is inserted were
used to transform E. coli JM109. The resulting transformants were
cultivated and plasmids with inserted DNA were purified from the
cells using QIAGEN plasmid mini kit (Qiagen). The plasmids with
inserted DNA were used as templates.
[0695] The sequences of the primers used in this Example are shown
in SEQ ID NOS:35 and 36 of the Sequence Listing. Primers in which
the first to third bases from the 3'-terminus are ribonucleotides
were used for the amplification method of the present invention.
The composition of the reaction mixture was as follows.
[0696] 27 mM phosphate buffer (pH 7.3), 0.01% bovine serum albumin
(BSA), 5% DMSO, 1 mM each of dNTPs, 8 mM magnesium acetate, 60 pmol
each of the primers, 1 ng of the DNA as the template and sterile
distilled water to a reaction volume of 48 .mu.l.
[0697] The reaction mixture was heat-denatured at 98.degree. C. for
1 minute, and then cooled to 55.degree. C. 5.5 U of Bca BEST DNA
polymerase and 60 U of E. coli RNase H were added thereto, and the
mixture was incubated at 55.degree. C. for 60 minutes. Thereafter,
the mixture was heated at 90.degree. C. for 2 minutes to inactivate
the enzymes. 3 .mu.l of the reaction mixture was subjected to
electrophoresis on 4% NuSieve 3:1 agarose (Takara Shuzo) gel.
[0698] On the other hand, amplification using the PCR method was
conducted as a control. PCR Amplification kit (Takara Shuzo), 10
pmol each of primers having a sequence as shown in SEQ ID NO:37 or
38 of the Sequence Listing, 1 ng of the DNA as the template and
sterile distilled water to a reaction volume of 50 .mu.l were used
for the reaction. The reaction conditions were 25 cycles of
94.degree. C. for 30 seconds, 55.degree. C. for 30 seconds and
72.degree. C. for 40 seconds. After the completion of the reaction,
3 .mu.l of the reaction mixture was subjected to electrophoresis on
4% NuSieve 3:1 agarose (Takara Shuzo) gel.
[0699] As a result, more amount of a fragment of interest was
amplified from each of the plasmids having an insert of 150 bp or
249 bp as a template in the amplification method of the present
invention as compared with the PCR method. 20 .mu.l of the reaction
mixture was purified using Microcon-100, and the amount of the
amplification product was quantified using Beckman DU-640
spectrophotometer (Beckman) in order to express numerically the
amount of the amplification product. The amount of the fragment
amplified from the plasmid having an insert of 150 bp as the
template in the amplification method of the present invention was
confirmed to be about 60-fold higher than that in the PCR method.
The amount of the fragment amplified from the plasmid having an
insert of 250 bp as the template in the amplification method of the
present invention was confirmed to be about 40-fold higher than
that in the PCR methods. Based on these results, it was confirmed
that the method of the present invention can be more preferably
used for making a DNA chip, for which a large amount of a DNA
fragment is required, as compared with the conventional PCR
method.
Example 7
[0700] (1) Preparation of RNA Probe
[0701] A method for detecting an amplified fragment obtained by the
amplification method of the present invention was examined. A probe
for detection composed of ribonucleotides in which two different
fluorescent substances are attached to the ribonucleotides on both
ends of the probe was prepared. The RNA probe for detection was
synthesized using a DNA synthesizer (Applied Biosystems). The
nucleotide sequence of the probe is shown in SEQ ID NO:39 of the
Sequence Listing. 6-FAM (Glen Research) and TAMRA (Glen Research)
were used as fluorescent substances to label the probe at the
5'-terminus and the 3'-terminus, respectively.
[0702] (2) Amplification Reaction and Detection
[0703] 0.1 or 1 ng of the pUC19 DNA was used as a template. pUC19
upper 150 2N primer and pUC19 lower 542 2N primer having sequences
as shown in SEQ ID NOS:40 and 16 of the Sequence Listing,
respectively, in which the first and second bases from the
3'-terminus of the primer are ribonucleotides were used as
primers.
[0704] The composition of the reaction mixture was as follows.
[0705] 27 mM phosphate buffer (pH 7.3), 0.01% BSA, 5% DMSO, 1 mM
each of dNTPs, 8 mM magnesium acetate, 60 pmol each of the primers,
0.1 or 1 ng of the DNA as the template, 0.1 .mu.g of the RNA probe
and sterile distilled water to a reaction volume of 48 .mu.l. One
without the DNA as the template was also prepared as a control.
[0706] The reaction mixture was heat-denatured at 98.degree. C. for
1 minute, and then cooled to 55.degree. C. 22 U of Bca BEST DNA
polymerase or sterile water, and 60 U of E. coli RNase H were added
thereto, and the mixture was incubated at 55.degree. C. for 60
minutes. Thereafter, 5 .mu.l of 10% sodium dodecyl sulfate (SDS;
Nacalai Tesque) was added to the mixture to inactivate the enzymes.
50 .mu.l of the reaction mixture was diluted with an equal volume
of sterile water and transferred to a microplate. An image analyzer
FM BIO II Multi-View (Takara Shuzo) was used for detection at an
excitation wavelength of 505 nm.
[0707] As a result, no fluorescent signal was detected using either
of the templates when Bca BEST DNA polymerase was not added. Also,
no fluorescent signal was detected for the reaction mixture
containing Bca BEST DNA polymerase when the DNA as the template was
not added. On the other hand, a fluorescent signal was detected
when either 0.1 or 1 ng of the DNA as the template was added. An
amplified fragment of about 190 bp of interest was also observed by
electrophoresis on 3% agarose gel containing 0.00003% ethiduim
bromide only when 0.1 or 1 ng of the DNA as the template was added
in the presence of Bca BEST DNA polymerase. That is, the same
results were obtained by the detection method using an RNA probe
and the conventional electrophoretic detection method. Thus, a
method for detecting an amplified fragment obtained by the
amplification method of the present invention using an RNA probe
was established.
Example 8
[0708] Use of a primer composed of deoxyribonucleotides as one of
the two primers in the method of the present invention was
examined. MR1N3 (30) having a sequence as shown in SEQ ID NO:41 of
the Sequence Listing and M4 primer (Takara Shuzo) having a sequence
as shown in SEQ ID NO:42 of the Sequence Listing were used as
primers. In the MR1N3 primer, the first to third bases from the
3'-terminus are ribonucleotides. The composition of the reaction
mixture was as follows.
[0709] 27 mM phosphate buffer (pH 7.3), 0.01% bovine serum albumin
(BSA), 5% DMSO, 1 mM each of dNTPs, 8 mM magnesium acetate, 30 pmol
each of the primers, 1 ng of the DNA as the template and sterile
distilled water to a reaction volume of 24 .mu.l.
[0710] The reaction mixture was heat-denatured at 98.degree. C. for
2 minutes, and then cooled to 55.degree. C. 11 U of Bca BEST DNA
polymerase and 30 U of E. coli RNase H were added thereto to make
the reaction volume to 25 .mu.l. The reaction mixture was incubated
at 55.degree. C. for 60 minutes. Thereafter, the mixture was heated
at 90.degree. C. for 2 minutes to inactivate the enzymes. 5 .mu.l
of the reaction mixture was subjected to electrophoresis on 4%
NuSieve 3:1 agarose gel. As a result, an amplified fragment of
interest was observed.
Example 9
[0711] The method of the present invention was used to detect
hemorrhagic E. coli O-157.
[0712] Sequences of the primers used in this Example are shown in
SEQ ID NOS:43-46 of the Sequence Listing. In the primers, the
first, second and the third bases from the 3'-terminus are
ribonucleotides. A combination of primers having a sequence of SEQ
ID NO:40 or 41, and a combination of primers having a sequence of
SEQ ID NO:42 or 43 were constructed for detecting a sequence
encoding vero toxin 1 or vero toxin 2 of O-157 according to the
description of Rinsho To Biseibutsu (Clinical Microbiology),
18(4):507-513 (1991). Primers in which the first to third bases
from the 3'-terminus are ribonucleotides were used for the
amplification method of the present invention. A heat-extract
prepared by harvesting a culture of hemorrhagic E. coli O-157 (ATCC
accession no. 43895), suspending it in sterile water at an
appropriate cell density and treating it at 98.degree. C. for 10
minutes was used as a template. The composition of the reaction
mixture was as follows.
[0713] 27 mM phosphate buffer (pH 7.3), 0.01% bovine serum albumin
(BSA), 5% DMSO, 1 mM each of dNTPs, 8 mM magnesium acetate, 60 pmol
each of the primers, the DNA as the template (the heat-extract)
corresponding to 10.sup.4-10.sup.6 cells and sterile distilled
water to a reaction volume of 48 .mu.l.
[0714] The reaction mixture was heat-denatured at 98.degree. C. for
1 minute, and then cooled to 55.degree. C. 5.5 U of Bca BEST DNA
polymerase and 60 U of E. coli RNase H were added thereto. The
reaction mixture was incubated at 55.degree. C. for 60 minutes.
Thereafter, the mixture was heated at 90.degree. C. for 2 minutes
to inactivate the enzymes. 3 .mu.l of the reaction mixture was
subjected to electrophoresis on 4% NuSieve 3:1 agarose (Takara
Shuzo) gel.
[0715] As a result, O-157 vero toxin 1 and 2 could be detected
using either one of the primer pairs and the DNA as the template
corresponding to 10.sup.4 cells, confirming that the method of the
present invention can be utilized as a method for detecting a
virulent bacterium.
Example 10
[0716] Amplification of a long-chain DNA fragment by the method of
the present invention was examined. A double-stranded DNA as a
template was prepared as follows. First, a library was constructed
from mRNA derived from a normal gastric tissue using Uni-ZAP XR
vector (Stratagene) according to a conventional method. The library
was screened to select clones having an insert of about 2.1 kbp or
about 4.3 kbp. The clones were used to obtain pBluescript SK (-)
phage vectors by in vitro excision. Amplified fragments of about
2.2 kbp and about 4.4 kbp were obtained using the plasmids as
templates, MCR-F primer and MCR-R primer having sequences as shown
in SEQ ID NOS:47 and 48 of the Sequence Listing, respectively, and
PCR Amplification kit (Takara Shuzo). These PCR fragments were used
as templates for the amplification method of the present invention.
MF2N3 (24) primer and MR1N3 (24) primer having sequences as shown
in SEQ ID NOS:49 and 50 of the Sequence Listing, respectively, in
which the first to third bases from the 3'-terminus are
ribonucleotides were used as primers. The composition of the
reaction mixture was as follows.
[0717] 28 mM phosphate buffer (pH 7.5), 0.01% bovine serum albumin
(BSA), 1% DMSO, 0.5 mM each of dNTPs, 4 mM magnesium acetate, 30
pmol each of the primers, 0.2 mM putrescine and sterile distilled
water to 24.25 .mu.l. The reaction mixture was treated at
92.degree. C. for 2 minutes, and then cooled to 55.degree. C. 30 U
of RNase H and 5.5 U of Bca BEST DNA polymerase were added thereto
to make the reaction volume to 25 .mu.l. The reaction mixture was
incubated for 1 hour. After the completion of the reaction, the
mixture was cooled at 4.degree. C., and 2.5 .mu.l of a 0.5 M EDTA
solution added thereto to terminate the reaction. 5 .mu.l of the
mixture was subjected to electrophoresis on 1% agarose gel.
[0718] As a result, an amplified fragment of about 2.2 kbp or about
4.4 kbp was obtained by the method of the present invention,
confirming that the method of the present invention can be used to
amplify a long-chain DNA fragment.
Example 11
[0719] A DNA microarray onto which a .lambda. DNA fragment of about
400 bp amplified by the amplification method of the present
invention and .lambda. DNA fragments of 300 bp and 1000 bp
amplified by PCR were spotted was produced. The nucleotide sequence
of the .lambda. DNA is available from GenBank accession nos.
V00636, J02459, M17233 and X00906. A reaction mixture for the
amplification method of the present invention was prepared as
follows.
[0720] 34 mM Tricine-hydrochloride buffer (pH 8.7), 10 mM potassium
chloride, 10 mM ammonium sulfate, 0.01% bovine serum albumin (BSA),
1% dimethyl sulfoxide, 4 mM magnesium acetate, 0.5 mM each of
dNTPs, 500 pmol each of the primers, 100 ng of the PCR
amplification product as the template, 110 U of Bca BEST DNA
polymerase and 300 U of cloned RNase H in a final reaction volume
of 500 .mu.l. The reaction mixture was mixed to homogeneity,
incubated at 55.degree. C. for 60 minutes, and then heated at
90.degree. C. for 2 minutes to inactivate the enzymes. This
solution was used in the subsequent steps. The spotted DNA
fragments were as follows.
[0721] 1. Sample: A PCR amplification product (300 bp) obtained by
using a .lambda. DNA as a template and a combination of primers
having a sequence as shown in SEQ ID NO:51 or 52 of the Sequence
Listing was subcloned into the pUC19 vector. The subcloned product
was then PCR-amplified using MCR-F primer and MCR-R primer as shown
in example 10. The thus obtained product as a template and chimeric
oligonucleotide primers having a sequence as shown in SEQ ID NO:53
or 54 of the Sequence Listing, in which the first and second bases
from the 3'-terminus of the primer are ribonucleotides, were used
to amplify a product of about 400 bp by the amplification method of
the present invention to obtain the Sample. Five DNA solutions,
i.e., the reaction mixture at its original concentration or 2-, 4-,
8- or 16-fold dilutions of the reaction mixture with a carbonate
buffer (a carbonate buffer at a concentration of 50 mM were used
for dilution in each case) were used for spotting.
[0722] 2. Sample: The DNA fragment amplified in 1 above was treated
with Microcon-100 (Takara Shuzo). Then, five DNA solutions were
prepared by adjusting the concentrations to 0.125 .mu.g/.mu.l, 0.25
.mu.g/.mu.l, 0.5 .mu.g/.mu.l, 1.0 .mu.g/.mu.l and 2.0 .mu.g/.mu.l
with the 50 mM carbonate buffer.
[0723] 3. Positive Control: A PCR amplification product (300 bp)
amplified in 1 above was treated with Microcon-100. Then, five DNA
solutions were prepared by adjusting the concentrations to 0.125
.mu.g/.mu.l, 0.25 .mu.g/.mu.l, 0.5 .mu.g/.mu.l, 1.0 .mu.g/.mu.l and
2.0 .mu.g/.mu.l with the 50 mM carbonate buffer.
[0724] 4. Positive Control: A PCR amplification product (1000 bp)
obtained by using the .lambda. DNA as a template and a combination
of primers having a sequences as shown in SEQ ID NO:55 or 56 of the
Sequence Listing was treated with Microcon-100. Then, four DNA
solutions were prepared by adjusting the concentrations to 0.125
.mu.g/.mu.l, 0.25 .mu.g/.mu.l, 0.5 .mu.g/.mu.l and 1.0 .mu.g/.mu.l
with the 50 mM carbonate buffer.
[0725] 5. Negative Control: A PCR amplification product (300 bp)
obtained by using the .lambda. DNA as a template and a combination
of primers having a sequence as shown in SEQ ID NO:55 or 57 of the
Sequence Listing was subcloned into the pUC19 vector. The subcloned
product was then PCR-amplified using primers having a sequence as
shown in SEQ ID NO:47 or 48 of the Sequence Listing. The thus
obtained product as a template and primers having a sequence as
shown in SEQ ID NO:53 or 54 of the Sequence Listing as primers were
used to amplify a product of about 400 bp by the amplification
method of the present invention to obtain the Negative Control.
Five DNA solutions, i.e., the reaction mixture at its original
concentration or 2-, 4-, 8- or 16-fold dilutions of the reaction
mixture with a carbonate buffer (a carbonate buffer at a
concentration of 50 mM were used for dilution in each case) were
used for spotting.
[0726] 6. Negative Control: The DNA fragment obtained in 5 above
was treated with Microcon-100. Then, five DNA solutions were
prepared by adjusting the concentrations to 0.125 .mu.g/.mu.l, 0.25
.mu.g/.mu.l, 0.5 .mu.g/.mu.l, 1.0 .mu.g/.mu.l and 2.0 .mu.g/.mu.l
with the 50 mM carbonate buffer.
[0727] The respective DNA solutions thus prepared were spotted onto
a slide glass to which amino groups had been introduced (Matsunami
Glass) using an equipment for making DNA chips (Genetic
Microsystems (GMS)), and were immobilized using UV irradiation. The
slide was washed with 0.2% SDS followed by distilled water, dried,
and then used as a DNA array.
[0728] A PCR amplification product (300 bp) amplified in 1 above
was labeled with Cy5 using Label IT Cy5.sup.R Labeling Kit (Takara
Shuzo) for use as a probe. Hybridization was carried out using a
prehybridization solution and a hybridization solution as described
in the instructions attached to IntelliGene (Takara Shuzo). First,
the DNA array was subjected to prehybridization at room temperature
for 2 hours. The hybridization solution containing the denatured
Cy5-labeled probe was dripped onto the DNA array. A cover glass was
mounted thereon. The sides of the cover glass were sealed with a
film. The sealed DNA array was incubated at 65.degree. C. for 13
hours. After the cover glass was removed, the DNA array was washed
in 2.times.SSC at 65.degree. C. for 5 minutes, in a solution
containing 0.2.times.SSC and 0.1% SDS at 65.degree. C. for 5
minutes, and finally in 0.2.times.SSC at room temperature for 5
minutes, and air-dried. The DNA array was then subjected to a
microarray scanner (GMS) to analyze the fluorescent signals from
the respective spots.
[0729] As a result, a fluorescent signal was observed at each of
the positions onto which fragments amplified by the PCR method (the
Positive Controls as described above in 3 and 4) and the method of
the present invention (the Samples as described above in 1 and 2)
were spotted. The intensities of the signals were as follows: the
Sample 2>the Positive Control 4>the Sample 1>the Positive
Control 3. On the other hand, no signal was observed at all for the
Negative Controls 5 and 6. From these results, it was confirmed
that an unpurified or purified DNA fragment amplified by the method
of the present invention can be preferably used as a DNA fragment
to be immobilized to make a DNA chip.
Example 12
[0730] (1) The designing of a primer used in the method of the
present invention in which a PCR-amplified fragment was used as a
template was examined. First, R1-S1 primer, R1-A3 primer, R2-S1
primer, R2-A3 primer, R3-S1 primer and R3-A3 primer having
sequences as shown in SEQ ID NOS:58-63 of the Sequence Listing
respectively, were synthesized according to a conventional method.
The structures of the respective primers are as follows.
[0731] (i) R1-S1 primer: From the 5'-terminus, 7 bases of a spacer
sequence, 17 bases of a M13RV sequence (or RV sequence; the
nucleotide sequence of M13RV primer (Takara Shuzo)) and 20 bases of
a sense primer sequence for .lambda. DNA-specific PCR;
[0732] (ii) R1-A3 primer: From the 5'-terminus, 7 bases of a spacer
sequence, 17 bases of the M13RV sequence and 20 bases of an
antisense primer sequence for .lambda. DNA-specific PCR;
[0733] (iii) R2-S1 primer: From the 5'-terminus, 25 bases of a
spacer sequence, 17 bases of the M13RV sequence and 20 bases of a
sense primer sequence for .lambda. DNA-specific PCR;
[0734] (iv) R2-A3 primer: From the 5'-terminus, 25 bases of a
spacer sequence, 17 bases of the M13RV sequence and 20 bases of an
antisense primer sequence for .lambda. DNA-specific PCR;
[0735] (v) R3-S1 primer: From the 5'-terminus, 58 bases of a spacer
sequence, 17 bases of the M13RV sequence and 20 bases of a sense
primer sequence for .lambda. DNA-specific PCR; and
[0736] (vi) R3-A3 primer: From the 5'-terminus, 58 bases of a
spacer sequence, 17 bases of the M13RV sequence and 20 bases of an
antisense primer sequence for .lambda. DNA-specific PCR.
[0737] M13RV 20mer has a sequence of a total of 20 bases consisting
of 17 bases of the M13RV sequence and 3 bases at the 5'-terminus.
Therefore, when M13RV 20 mer is used in the method of the present
invention, the lengths of the spacer sequences in the
above-mentioned primers become 4 bases, 22 bases and 55 bases,
respectively. Primers without a spacer sequence were also made as
controls for the above-mentioned primers.
[0738] For example, when the primer pair, R1-S1 primer/R1-A3
primer, is used, an amplified fragment of 348 bp is obtained. 7
bases on both ends of the amplified fragment correspond to the
spacer portions. The RV sequences are located inside the spacer
portions. The .lambda. DNA sequences are located inside the RV
sequences.
[0739] Similarly, when the primer pair, R2-S1 primer/R2-A3 primer,
is used, an amplified fragment of 384 bp in which 25 bases on both
ends of the amplified fragment correspond to the spacer portions is
obtained. In addition, when the primer pair, R3-S1 primer/R3-A3
primer, is used, an amplified fragment of 450 bp in which 58 bases
on both ends of the amplified fragment correspond to the spacer
portions is obtained. On the other hand, a fragment amplified using
control primers has no spacer portion. These PCR-amplified
fragments were used as templates for the following examination.
[0740] One of two primers, M13RV-2N 17mer primer or M13RV-2N 20mer
having a sequence as shown in SEQ ID NO:64 or 65 of the Sequence
Listing was used in this Example. In the primers, the first and
second bases from the 3'-terminus are ribonucleotides. The reaction
was carried out as follows. 5 .mu.l of a mixture of 20 .mu.M of the
primer, about 20 ng of the template and 0.01% propylenediamine was
denatured at 98.degree. C. for 2 minutes, and then cooled to
55.degree. C. Thereafter, 34 mM Tricine buffer (pH 8.7), 10 mM
potassium chloride, 10 mM ammonium sulfate, 0.01% BSA, 1% DMSO, 4
mM magnesium acetate, 0.5 mM each of dNTPs, 1 U of Bca BEST DNA
polymerase and 15 U of RNase H were added thereto to make the final
reaction volume to 25 .mu.l. The reaction mixture was incubated at
55.degree. C. for 1 hour. After the completion of the reaction, the
mixture was cooled to 4.degree. C., and then 2.5 .mu.l of a 0.5 M
EDTA solution was added thereto to terminate the reaction. 3 .mu.l
of the reaction mixture was subjected to electrophoresis on 3%
NuSieve 3:1 agarose (Takara Shuzo) gel. As a result, when M13RV-2N
17mer was used, increase in amplification efficiency was observed
depending on the length of the spacer sequence in the following
order: 25mer>7mer>58mer>- no spacer sequence. When
M13RV-2N 20mer was used, increase in amplification efficiency was
observed depending on the length of the spacer sequence in the
following order: 22mer>4mer>55mer>no spacer sequence.
Furthermore, when the M13RV sequences in the primers described
above in (i) to (vi) were replaced by M13M4 sequences, a similar
tendency was observed for the relationship between the spacer
sequence and the amplification efficiency. Thus, it was confirmed
that, when a linear DNA fragment such as a PCR-amplified fragment
is used as a template, the designing of primers used in the method
of the present invention to generate a spacer sequence (portion)
leads to an increased amplification efficiency.
[0741] (2) Amplification of a template having a high GC content in
the method for amplifying a nucleotide sequence using an elevated
reaction temperature was examined. First, primers having a sequence
as shown in SEQ ID NO:66 or 67 of the Sequence Listing for PCR
amplification of a 307-bp region (GC content: 62.5%) of
CDC2-related protein kinase PISS LRE gene (GenBank accession no.
AA789328) were produced. In addition, primers having a sequence as
shown in SEQ ID NO:68 or 69 of the Sequence Listing for PCR
amplification of a 284-bp region (GC content: 61.3%) of Type II
cytoskeltal 1 keratin gene (GenBank accession no. AA706022) were
produced. PCR amplification was carried out using these primers and
commercially available DNA fragments (Research Genetics) as
templates. The respective PCR-amplified fragments obtained by using
the above-mentioned primer pairs have spacer sequences and the
M13RV sequences on both ends. The fragments were used as templates
for the present invention.
[0742] M13RV-2N 17mer primer having a sequence as shown in SEQ ID
NO:64 of the Sequence Listing or M13RV-2N 20mer primer having a
sequence as shown in SEQ ID NO:65 of the Sequence Listing was used
in this Example. In the primers, the first and second bases from
the 3'-terminus are ribonucleotides. The reaction was carried out
as follows. .mu.l of a mixture of 100 pmol of the primer, 20 ng of
the template and 0.01% propylenediamine was denatured at 980 C for
2 minutes, and then cooled to 550 C or 600 C. Thereafter, 34 mM
Tricine buffer (pH 8.7), 10 mM KCl, 10 mM ammonium sulfate, 0.01%
BSA, 1% DMSO, 4 mM magnesium acetate, 0.5 mM each of dNTPs, 11 U of
Bca BEST DNA polymerase and 30 U of RNase H were added thereto to
make the final reaction volume to 50 .mu.l. The reaction mixture
was incubated at 55.degree. C. or 60.degree. C. for 1 hour. After
the completion of the reaction, the mixture was cooled to 4.degree.
C. 3 .mu.l of the reaction mixture was subjected to electrophoresis
on 3% agarose gel. The results are shown in Table 1 below.
1 TABLE 1 Gene and results of amplification Reaction Primers Type
II temperature used CDC2-related cytoskeltal 55.degree. C. M13RV-2N
17mer ++ ++ M13RV-2N 20mer ++ ++ 60.degree. C. M13RV-2N 17mer + +
M13RV-2N 20mer ++++ ++++ + to ++++: The degree of amplification was
scored in four grades. -: No amplification was observed.
[0743] As shown in Table 1, the region of interest was efficiently
amplified even if a template having a high GC content was used.
This amplification was accomplished by elevating the reaction
temperature (from 55.degree. C. to 60.degree. C.) and by using a
primer having a higher Tm value as compared with an optimal primer
for a reaction at 55.degree. C. when the reaction was carried at
60.degree. C.
[0744] (3) The relationship between the length of an amplified
fragment and the amount of the amplification product in the method
for amplifying a nucleotide sequence under high reaction
temperature conditions was examined. First, a pair of primers
having a sequence as shown in SEQ ID NO:70 or 71 of the Sequence
Listing for amplifying a 800-bp region of the lambda DNA (Takara
Shuzo) and a pair of primers having a sequence as shown in SEQ ID
NO:72 or 73 of the Sequence Listing for amplifying a 400-bp region
of the lambda DNA were synthesized according to a conventional
method. PCR was conducted using one of these primer pairs and the A
DNA as a template to obtain an amplified fragment. An amplified
fragment of about 1.1 kbp was also prepared using the pUC19-911
plasmid as described in Example 5 (1) as a template and MF2 (24)
PCR primer and MR1 (24) PCR primer, which have sequences as shown
in SEQ ID NOS:74 and 75 of the Sequence Listing, respectively. The
PCR-amplified fragments obtained by using the above-mentioned
primer pairs have spacer sequences and the M13RV or M4 sequences on
both ends. These fragments were used as templates for the present
invention.
[0745] M13RV-2N 17mer primer or M13RV-2N 20mer primer as shown in
(2) above was used as a primer in this Example. In the primers, the
first and second bases from the 3'-terminus are ribonucleotides. A
combination of M13M4-3N 20mer primer having a sequence as shown in
SEQ ID NO:76 of the Sequence Listing and M13RV-3N 20mer primer
having a sequence as shown in SEQ ID NO:77 of the Sequence Listing,
and a combination of M13M4-3N 24mer primer and M13RV-3N 24mer
primer having sequences as shown in SEQ ID NO:78 and 79 of the
Sequence Listing, respectively, were used for amplifying a region
of about 1 kbp. In the primers, the first to third bases from the
3'-terminus are ribonucleotides. The reaction was carried out as
follows. 10 .mu.l of a mixture of 10 pmol of the primer, about 20
ng of the template and 0.01% propylenediamine was denatured at
98.degree. C. for 2 minutes, and then cooled to 55.degree. C. or
60.degree. C. Thereafter, 34 mM Tricine buffer (pH 8.7), 10 mM
potassium chloride, 10 mM ammonium sulfate, 0.01% BSA, 1% DMSO, 4
mM magnesium acetate, 0.5 mM each of dNTPs, 11 U of Bca BEST DNA
polymerase and 30 U of RNase H were added thereto to make the final
reaction volume to 50 .mu.l. The reaction mixture was incubated at
55.degree. C. or 60.degree. C. for 1 hour. After the completion of
the reaction, the mixture was cooled to 4.degree. C., and then 5
.mu.l of a 0.5 M EDTA solution was added thereto to terminate the
reaction. 3 .mu.l of the reaction mixture was subjected to
electrophoresis on 3% NuSieve 3:1 agarose (Takara Shuzo) gel. The
results are shown in Tables 2 and 3 below.
2 TABLE 2 Length of amplified fragment Reaction Primers and results
temperature used 400 bp 800 bp 55.degree. C. M13RV-2N 17mer ++ ++
M13RV-2N 20mer ++ ++ 60.degree. C. M13RV-2N 17mer + + M13RV-2N
20mer ++++ ++++ + to ++++: The degree of amplification was scored
in four grades. -: No amplification was observed.
[0746] As shown in Table 2, fragments for regions of 400 bp and 800
bp were efficiently amplified by making the length of the primer
for amplification from 17mer to 20mer and by elevating the reaction
temperature from 55.degree. C. to 60.degree. C.
3 TABLE 3 Length of amplified Reaction Primers fragment and results
temperature used 1034 bp 55.degree. C. M13RV-3N 20mer & ++
M13M4-3N 20mer M13RV-3N 24mer & ++ M13M4-3N 24mer 65.degree. C.
M13RV-3N 20mer & + M13M4-3N 20mer M13RV-3N 24mer & ++++
M13M4-3N 24mer + to ++++: The degree of amplification was scored in
four grades. -: No amplification was observed.
[0747] Furthermore, as shown in Table 3, a fragment for a region of
about 1 kbp was efficiently amplified by making the length of the
primer for amplification from 20mer to 24mer and by elevating the
reaction temperature from 55.degree. C. to 65.degree. C.
Additionally, similar results were obtained for amplification of a
long-chain DNA fragment as described in Example 10 by using longer
primers and an elevated reaction temperature. Increase in
amplification efficiency was observed when a region of about 2 kbp
or longer was amplified.
Example 13
[0748] (1) Use of a heat-resistant DNA polymerase other than Bca
BEST DNA polymerase in the method of the present invention was
examined. Bst DNA polymerase (New England Biolabs) was used as a
heat-resistant DNA polymerase. A pair of primers, 5'-ID primer and
3'-ID primer having sequences as shown in SEQ ID NOS:80 and 81 of
the Sequence Listing, respectively, were synthesized according to a
conventional method. PCR was carried out using the primer pair and
a commercially available DNA fragment for cyclin A gene (Research
Genetics) as a template, resulting in an amplified fragment of
about 300 bp. The PCR-amplified fragment obtained by using the
primer pair has the M13RV sequences on both ends. The fragment was
used as a template for the present invention.
[0749] M13RV-2N 17mer primer having a sequence as shown in SEQ ID
NO:64 of the Sequence Listing was used as a primer in this Example.
In the primer, the first and second bases from the 3'-terminus are
ribonucleotides. The reaction was carried out as follows. 10 .mu.l
of a mixture of 20 .mu.M of the primer, about 20 ng of the template
and 0.01% propylenediamine was denatured at 98.degree. C. for 2
minutes, and then cooled to 55.degree. C. Thereafter, 34 mM Tricine
buffer (pH 8.7), 10 mM potassium chloride, 10 mM ammonium sulfate,
0.01% BSA, 1% DMSO, 4 mM magnesium acetate, 0.5 mM each of dNTPs,
4, 8, 12 or 16 U of Bst DNA polymerase and 30 U of RNase H were
added thereto to make the final reaction volume to 50 .mu.l. As a
control, a reaction mixture having a composition identical with the
above-mentioned one was prepared, except that 11 U of Bca BEST DNA
polymerase was used. The reaction mixture was incubated at
55.degree. C. for 1 hour. After the completion of the reaction, the
mixture was cooled to 4.degree. C., and then 5 .mu.l of a 0.5 M
EDTA solution was added thereto to terminate the reaction. 3 .mu.l
of the reaction mixture was subjected to electrophoresis on 3%
NuSieve 3:1 agarose (Takara Shuzo) gel. As a result, an amplified
fragment of interest was obtained using each of the various units
of Bst DNA polymerase. Thus, it was confirmed that heat-resistant
DNA polymerases can be preferably used in the method of the present
invention.
[0750] (2) Use of a mesophilic DNA polymerase in the method of the
present invention was examined. 5'3'exo activity (-) Klenow
fragment (Takara Shuzo) was used as a mesophilic DNA polymerase.
The DNA prepared in (1) above was used a template DNA for the
method of the present invention.
[0751] M13RV-2N 16mer primer having a sequence as shown in SEQ ID
NO:82 of the Sequence Listing was used as a primer in this Example.
In the primer, the first and second bases from the 3'-terminus are
ribonucleotides. The reaction was carried out as follows. 10 .mu.l
of a mixture of 20 .mu.M of the primer, about 20 ng of the template
and 0.01% propylenediamine was denatured at 98.degree. C. for 2
minutes, and then cooled to 40.degree. C. Thereafter, 34 mM Tricine
buffer (pH 8.7), 10 mM potassium chloride, 10 mM ammonium sulfate,
0.01% BSA, 1% DMSO, 4 mM magnesium acetate, 0.5 mM each of dNTPs,
0, 2, 4, 6 or 8 U of Klenow fragment and 30 U of RNase H were added
thereto to make the final reaction volume to 50 .mu.l. The reaction
mixture was incubated at 40.degree. C. for 1 hour. After the
completion of the reaction, the mixture was cooled to 4.degree. C.,
and then 5 .mu.l of a 0.5 M EDTA solution was added thereto to
terminate the reaction. 3 .mu.l of the reaction mixture was
subjected to electrophoresis on 3% NuSieve 3:1 agarose (Takara
Shuzo) gel. As a result, an amplified fragment of interest was
obtained in cases where the various units of Klenow fragment were
used excluding the case where no Klenow fragment was added. Thus,
it was confirmed that mesophilic DNA polymerases can be preferably
used in the method of the present invention.
Example 14
[0752] Chimeric oligonucleotide primers to be used in the method of
the present invention were examined. A DNA as a template and
primers were synthesized as described in Example 1 (1). The
structures of the primers used in this Examples are described below
in detail:
[0753] Primer Pair 1: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:2 or 3 of the Sequence Listing and
wholly composed of deoxyribonucleotides;
[0754] Primer Pair 2: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:83 or 84 of the Sequence Listing in
which the sixth and seventh deoxyribonucleotides from the
3'-terminus are ribonucleotides;
[0755] Primer Pair 3: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:85 or 86 of the Sequence Listing in
which the fifth and sixth deoxyribonucleotides from the 3'-terminus
are ribonucleotides;
[0756] Primer Pair 4: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:87 or 88 of the Sequence Listing in
which the fourth and fifth deoxyribonucleotides from the
3'-terminus are ribonucleotides;
[0757] Primer Pair 5: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:89 or 90 of the Sequence Listing in
which the third and fourth deoxyribonucleotides from the
3'-terminus are ribonucleotides;
[0758] Primer Pair 6: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO: 91 or 92 of the Sequence Listing in
which the second and third deoxyribonucleotides from the
3'-terminus are ribonucleotides;
[0759] Primer Pair 7: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:93 or 94 of the Sequence Listing in
which the first and second deoxyribonucleotides from the
3'-terminus are ribonucleotides; and
[0760] Primer Pair 8: A combination of primers having a nucleotide
sequence as shown in SEQ ID NO:91 or 92 of the Sequence Listing in
which the second and third deoxyribonucleotides from the
3'-terminus are ribonucleotides and the phosphate bond on the
5'-terminal side of the third ribonucleotide from the 3'-terminus
is replaced by a phosphorothioate bond.
[0761] Amplification conditions and detection method were as
described in Example 1 (2) and (3). As a result, an amplified
fragment having a length of interest was observed for each of the
Primer Pairs 2-8. For the Primer Pairs 2-7, the amount of the
amplification product increased as the number of
deoxyribonucleotides at the 3'-terminus decreased. Particularly,
the most abundant amplification product was observed for the Primer
Pair 7 having no deoxyribonucleotide at the 3'-terminus. On the
other hand, no amplified fragment was observed for the Primer Pair
1. Furthermore, the fact that amplified fragments of interest were
observed for both of the Primer Pairs 6 and 8 confirms that both of
a modified ribonucleotide and a unmodified ribonucleotide can be
preferably used as a ribonucleotide contained in a primer in the
method of the present invention.
Example 15
[0762] (1) The effect of the type of the buffer used in the method
of the present invention was examined. Primers for amplifying
.lambda. DNA having sequences represented by SEQ ID NOS:128 and 129
were used in this Example. The reaction was carried out as follows.
Briefly, 10 .mu.l of a mixture containing 120 pmol each of the
primers, 0.01% aqueous solution of propylenediamine and 10 ng or 1
ng of a DNA as a template was heat-denatured at 98 C for 2 minutes,
and then cooled on ice to anneal the primers to the template DNA.
An amplified product (1005 bp) obtained by a PCR using .lambda. DNA
(Takara Shuzo) as a template and primers represented by SEQ ID
NOS:130 and 131, which was then purified using Suprec02 (Takara
Shuzo), was used as the template.
[0763] After annealing, 40 .mu.l of one of three types of buffers
for reaction (42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
42.5 mM Bicine-potassium hydroxide buffer (pH 8.3) and 42.5 mM
HEPES-potassium hydroxide buffer (pH 7.8)) each containing 0.625 mM
each of dNTPs, 5.0 mM magnesium acetate, 0.0125% bovine serum
albumin (BSA), 1.25% dimethyl sulfoxide (DMSO), 30 U of E. coli
RNase H and 11 U of BcaBEST DNA polymerase was added to the mixture
to make the final volume to 50 .mu.l. The reaction mixtures were
incubated at 60 C for 1 hour. After reaction, 3 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3.0% agarose
gel for confirmation. Then, the amplified fragments of interest
were observed for both of the amounts of the template. In
particular, a greater amount of amplification product was obtained
for the reaction system containing Bicine-potassium hydroxide
buffer (pH 8.5).
[0764] (2) Improvement of reactivity by the use of HEPES-potassium
hydroxide buffer was examined. PUC19 plasmid DNA with a DNA
fragment of about 150 bp being inserted into the multi-cloning site
was used as a template. This template was prepared as follows.
[0765] A PCR was carried out using pUC19 upper 150 PCR primer and
pUC19 lower PCR primer having sequences represented by SEQ ID
NOS:223 and 224, and 100 .mu.g of pUC19 plasmid DNA as a template.
The resulting amplified fragment was purified using Microcon-100,
blunt-ended using DNA blunting kit (Takara Shuzo) and subcloned
into a HincII site of the plasmid pUC19. The plasmid with the
amplified fragment being inserted was used to transform Escherichia
coli JM109. The transformant was cultured. The plasmid having the
inserted DNA was purified from the cells using QIAGEN plasmid mini
kit (Qiagen) and used as a template.
[0766] A DNA fragment PCR-amplified using the pUC19-150 plasmid DNA
prepared as described above as a template, and primers MCS-F and
MCS-R having nucleotide sequences represented by SEQ ID NOS:124 and
125 was used as a template. Primers MF2N3(24) and MR1N3(24) having
nucleotide sequences represented by SEQ ID NOS:126 and 127 were
used as chimeric oligonucleotide primers. The expected size of the
amplified fragment obtained using the combination of these primers
was about 350 bp.
[0767] An HEPES-potassium hydoxide buffer system was selected as a
buffer to be examined. A potassium phosphate buffer system and a
Tricine buffer system were used as controls. The compositions of
the reaction mixtures are shown below.
[0768] Reaction mixture A: 10 ng of the PCR-amplified fragment, 50
pmol each of the primers MF2N3(24) and MR1N3(24), 0.01% aqueous
solution of propylenediamine and sterile distilled water to a
reaction volume of 10 .mu.l.
[0769] Reaction mixtures B: The following three types were
prepared.
[0770] Potassium phosphate buffer system: 40 .mu.l of a reaction
mixture containing, at final concentrations, 35 mM potassium
phosphate buffer (pH 7.5), 1.25% DMSO, 0.0125% BSA, 5 mM magnesium
acetate, 0.625 mM each of dNTPs, 60 U of E. coli RNase H and 5.5 U
of BcaBEST DNA polymerase was prepared.
[0771] Tricine buffer system: 40 .mu.l of a reaction mixture
containing, at final concentrations, 42.5 mM Tricine buffer (pH
8.7), 12.5 mM potassium chloride, 12.5 mM ammonium sulfate, 1.25%
DMSO, 0.0125% BSA, 5 mM magnesium acetate, 0.625 mM each of dNTPs,
30 U of E. coli RNase H and 5.5 U of BcaBEST DNA polymerase was
prepared.
[0772] HEPES-potassium hydroxide buffer system: 40 .mu.l of a
reaction mixture containing, at final concentrations, 25 mM
HEPES-potassium hydroxide buffer (pH 7.8), 125 mM potassium
acetate, 1.25% DMSO, 0.0125% BSA, 5 mM magnesium acetate, 0.625 mM
each of dNTPs, 30 U of E. coli RNase H and 5.5 U of BcaBEST DNA
polymerase was prepared.
[0773] The reaction mixture A was heat-denatured at 98 C for 2
minutes, cooled to 60 C or 65 C and then allowed to stand on ice.
One of the reaction mixtures B was added to the reaction mixture A
on ice and mixed to make the reaction volume to 50 .mu.l. The
reaction mixtures were incubated at 60 C or 65 C for 1 hour. After
reaction, they were cooled to 4 C, and {fraction (1/10)} volume of
0.5 M EDTA was added to each of the mixtures to terminate the
reaction. 3 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3% NuSieve 3:1 agarose gel. As a result, the
amplified fragments of interest were observed for the three buffer
systems regardless of the reaction temperature used. In particular,
the largest amount of the amplification product and the highest
reactivity were observed for the HEPES-potassium hydroxide buffer
system in this Example.
Example 16
[0774] (1) Conditions used in the method of the present invention
for annealing primers to a template were examined. Primers having
nucleotide sequences represented by SEQ ID NOS:132 and 133 based on
the partial nucleotide sequence of a bacterium Flavobacterium sp.
SA-0082 as described in WO 97/32010 (deposited at the International
Patent Organism Depositary, National Institute of Advanced
Industrial Science and Technology, AIST Tsukuba Central 6, 1-1,
Higashi 1-chome, Tsukuba-shi, Ibaraki-ken 305-8566, Japan on Mar.
29, 1995 under accession number FERM P-14872, and deposited at the
International Patent Organism Depositary, National Institute of
Advanced Industrial Science and Technology under accession number
FERM BP-5402 (date of request for transmission to international
depositary authority: Feb. 15, 1996)) were used. An amplified
product (573 bp) obtained by a PCR using a genomic DNA from
Flavobacterium sp. SA-0082 as a template and a combination of
primers represented by SEQ ID NOS:134 and 135, which was then
purified using Suprec02 (Takara Shuzo), was used as the DNA as the
template in this Example. The reaction was carried out as follows.
Briefly, 2 .mu.l of one of two annealing solutions (500 mM
potassium chloride and 8 .mu.M spermidine, or 0.05%
propylenediamine) was added to 120 pmol each of the primers. A
final volume of 10 .mu.l of each of the mixtures further containing
10 ng or 1 ng of the PCR-amplified fragment was heat-denatured at
98 C for 2 minute. After denaturation, the mixtures were rapidly
cooled on ice to anneal the primers to the template.
[0775] After annealing, 40 .mu.l of one of three types of buffers
(42.5 mM Tricine-potassium hydroxide buffer (pH 8.5), 42.5 mM
Bicine-potassium hydroxide buffer (pH 8.3) and 42.5 mM
HEPES-potassium hydroxide buffer (pH 7.8)) each containing 0.625 mM
each of dNTPs, 5.0 mM magnesium acetate, 0.0125% bovine serum
albumin (BSA), 1.25% dimethyl sulfoxide (DMSO), 30 U of E. coli
RNase H and 11 U of BcaBEST DNA polymerase was added to the mixture
to make the final volume to 50 .mu.l. The reaction mixtures were
incubated at 52 C for 1 hour. After reaction, 3 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3.0% agarose
gel. The results are shown in FIG. 1. FIG. 1 is a photograph of
electrophoresis of reactions using the respective combinations of
the annealing solutions and the buffers. Lane 1: molecular weight
marker (100 bp ladder, Takara Shuzo); lane 2:
propylenediamine/Tricine (template: 10 ng); lane 3:
propylenediamine/HEPES (template: 10 ng); lane 4:
propylenediamine/HEPES (template: 1 ng); lane 5:
propylenediamine/Bicine (template: 10 ng); lane 6:
propylenediamine/Bicine (template: 1 ng); lane 7: 500 mM potassium
chloride and 8 .mu.M spermidine/Bicine (template: 10 ng); lane 8:
500 mM potassium chloride and 8 .mu.M spermidine/Bicine (template:
1 ng); lane 9: molecular weight marker (100 bp ladder); lane 10:
propylenediamine/Tricine (template: 1 ng); lane 11: 500 mM
potassium chloride and 8 .mu.M spermidine/Tricine (template: 1 ng);
lane 12: propylenediamine/HEPES (template 1 ng); lane 13: 500 mM
potassium chloride and 8 .mu.M spermidine/HEPES (template: 1 ng);
lane 14: propylenediamine/Bicine (template: 1 ng); and lane 15: 500
mM potassium chloride and 8 .mu.M spermidine/Bicine (template: 1
ng).
[0776] As shown in FIG. 1, a greater amount of the amplification
product of interest was obtained when the annealing solution
containing 500 mM potassium chloride+8 .mu.M spermidine was used
for the annealing of the primers to the template DNA for either of
the three buffers regardless of the amount of the DNA as the
template. In particular, the combination of the annealing solution
containing 500 mM potassium chloride+8 .mu.M spermidine and the
Bicine-potassium hydroxide buffer yielded good results in this
EXAMPLE
[0777] (2) The effect of an annealing solution in case where a
PCR-amplified fragment from .lambda. DNA was used as a template was
examined. The chimeric oligonucleotide primers as described in
Example 15(1) were used in this Example. The PCR-amplified fragment
as prepared in Example 15(1) or .lambda. DNA was used as a template
DNA. The reaction was carried out as follows. Briefly, 2 .mu.l of
one of three types of annealing solutions (500 mM potassium
chloride and 8 .mu.M spermidine, 0.05% propylenediamine, or sterile
water) was added to 120 pmol each of the primers. 10 .mu.l of the
mixtures further containing 10 ng or 1 ng of the PCR-amplified
fragment were prepared. The mixtures were heat-denatured at 98 C
for 2 minutes, and then rapidly cooled on ice to anneal the primers
to the template.
[0778] After annealing, 40 .mu.l of one of three types of buffers
(42.5 mM Tricine-potassium hydroxide buffer (pH 8.5), 42.5 mM
Bicine-potassium hydroxide buffer (pH 8.3) and 42.5 mM
HEPES-potassium hydroxide buffer (pH 7.8)) each containing 0.625 mM
each of dNTPs, 5.0 mM magnesium acetate, 0.0125% BSA, 1.25% DMSO,
30 U of E. coli RNase H and 11 U of BcaBEST DNA polymerase was
added to the mixture to make the final volume to 50 .mu.l. The
reaction mixtures were incubated at 60 C for 1 hour. After
reaction, 3 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel. The results are shown in FIG.
2. FIG. 2 is a photograph of electrophoresis showing the results
for the examination of combinations of the amounts of the template,
the reaction buffers and the annealing solutions. Lane 1: marker
(100 bp ladder); lane 2: 10 ng of the template, a combination of
Tricine/500 mM potassium chloride and 8 .mu.M spermidine; lane 3: 1
ng of the template, a combination of Tricine/500 mM potassium
chloride and 8 .mu.M spermidine; lane 4: 10 ng of the template, a
combination of Bicine/500 mM potassium chloride and 8 .mu.M
spermidine; lane 5: 1 ng of the template, a combination of
Bicine/500 mM potassium chloride and 8 .mu.M spermidine; lane 6: 10
ng of the template, a combination of HEPES/500 mM potassium
chloride and 8 .mu.M spermidine; lane 7: 1 ng of the template, a
combination of HEPES/500 mM potassium chloride and 8 .mu.M
spermidine; lane 8: molecular weight marker (100 bp ladder); lane
9: 10 ng of the template, a combination of
Tricine/propylenediamine; lane 10: 1 ng of the template, a
combination of Tricine/propylenediamine; lane 11: 10 ng of the
template, a combination of Bicine/propylenediamine; lane 12: 1 ng
of the template, a combination of Bicine/propylenediamine; lane 13:
10 ng of the template, a combination of HEPES/propylenediamine;
lane 14: 1 ng of the template, a combination of
HEPES/propylenediamine; lane 15: molecular weight marker (100 bp
ladder); lane 16: 10 ng of the template, a combination of
Tricine/water; lane 17: 1 ng of the template, a combination of
Tricine/water; lane 18: 10 ng of the template, a combination of
Bicine/water; lane 19: 1 ng of the template, a combination of
Bicine/water; lane 20: 10 ng of the template, a combination of
HEPES/water; and lane 21: 1 ng of the template, a combination of
HEPES/water.
[0779] As shown in FIG. 2, the amplified fragments of interest were
observed for the respective combinations of the three buffers and
the three annealing solutions regardless of the amount of the
template DNA. In particular, it was confirmed that a greater amount
of the amplified fragment was obtained using the combination of the
Bicine buffer and the annealing solution containing 500 mM
potassium chloride and 8 .mu.M spermidine.
Example 17
[0780] The effect of the presence of an inhibitor of reverse
transcriptase (RTase) on the method of the present invention was
examined. Phosphonoformic acid (PFA) was used as an inhibitor of
RTase. Primers represented by SEQ ID NOS:136 and 137 were used in
this Example. An amplified product (576 bp) obtained by a PCR using
a genomic DNA from enterohemorrhagic Escherichia coli O-157 as a
template and primers represented by SEQ ID NOS:138 and 139, which
was then purified using Suprec02 (Takara Shuzo), was used as the
template DNA. The reaction was carried out as follows. Briefly, 10
.mu.l of a mixture prepared by adding 1 ng of the PCR-amplified
fragment to 120 pmol each of the primers and 2 .mu.l of an
annealing solutions containing 500 mM potassium chloride and 8
.mu.M spermidine was heat-denatured at 98 C for 2 minutes, and then
rapidly cooled on ice to anneal the primers to the template.
[0781] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% bovine serum albumin (BSA), 1.25%
dimethyl sulfoxide (DMSO), 30 U of E. coli RNase H and 11 U of
BcaBEST DNA polymerase as well as PFA to a concentration of 500
.mu.g/ml or 50 .mu.g/ml were added to the annealing mixture to make
the final volume to 50 .mu.l. The reaction mixtures were incubated
at 55 C for 1 hour. A system without the addition of PFA was also
prepared as a control. After reaction, 9 .mu.l each of the reaction
mixtures was subjected to electrophoresis on 3.0% agarose gel. The
results are shown in FIG. 3. FIG. 3 is a photograph of
electrophoresis which shows the effect of the inhibitor of RTase.
Lane 1: molecular weight marker (100 bp ladder); lane 2: without
the addition of PFA; lane 3: with the addition of PFA at a
concentration of 500 .mu.g/ml; lane 4: with the addition of PFA at
a concentration of 50 .mu.g/ml.
[0782] As shown in FIG. 3, when PFA was added, non-specific
amplification was suppressed and the amplified fragment of interest
was observed. In particular, it was confirmed that the non-specific
amplification products which were observed in the system without
the addition of PFA was not observed and the amplified fragment of
interest was clearly amplified in the system to which PFA was added
at a concentration of 500 .mu.g/ml.
Example 18
[0783] The relationship between the length of a fragment to be
amplified and the detection sensitivity in the method of the
present invention was examined.
[0784] (1) Primers for amplifying Escherichia coli O-157 vero toxin
represented by SEQ ID NOS:140-142 were synthesized. The chimeric
oligonucleotide primers used in Example 17 were also used. The
length of a fragment to be amplified using each of the combinations
of primers was as follows: 247 bp (SEQ ID NOS:140 and 137); 168 bp
(SEQ ID NOS:141 and 142); 206 bp (SEQ ID NOS:141 and 137); 135 bp
(SEQ ID NOS:136 and 142); and 173 bp (SEQ ID NOS:136 and 137). The
purified PCR-amplified 576-bp fragment prepared in Example 17 was
used as a template DNA in this Example. The reaction was carried
out as follows. Briefly, 10 .mu.l of a mixture containing 60 pmol
each of the primers, 2 .mu.l of 0.05% aqueous solution of
propylenediamine and 10 fg to 10 ng of the PCR-amplified fragment
was heat-denatured at 98 C for 2 minutes and then cooled to 55 C in
Thermal Cycler Personal (Takara Shuzo) to anneal the primers to the
template.
[0785] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% bovine serum albumin (BSA), 1.25%
dimethyl sulfoxide (DMSO), 30 U of E. coli RNase H, 5.5 U of
BcaBEST DNA polymerase and sterile water was added to the mixture
to make the final volume to 50 .mu.l. The reaction mixtures were
incubated at 55 C for 1 hour. After reaction, 5 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3.0% agarose
gel. As a control, detection of 10 fg to 1 pg of the PCR-amplified
fragment was carried out using primers represented by SEQ ID
NOS:143 and 144. A 135-bp fragment is amplified using the
combination of these primers. 50 .mu.l of a PCR solution containing
60 pmol each of the primers, 5 .mu.l of 10.times.Ex Taq buffer
(Takara Shuzo), 1.25 U of TaKaRa Ex Taq DNA polymerase (Takara
Shuzo) and 0.2 mM each of dNTPs was prepared. The PCR was carried
out as follows: 25 or 30 cycles of 94 C for 30 seconds, 55 C for 30
seconds and 72 C for 30 seconds (2 min. 38 sec./cycle). After
reaction, 1 .mu.l (ICAN) or 5 .mu.l (PCR) each of the reaction
mixtures was subjected to electrophoresis on 3.0% agarose gel. The
results are shown in FIG. 4 and Table 4.
4 TABLE 4 Amplification size (bp) Detection limit ICAN (total time:
70 minutes) 247 100 pg 168 100 fg 206 100 pg 135 10 fg 173 100 fg
PCR (25 cycles; total time: about 66 minutes) 135 100 fg PCR (30
cycles; total time: about 80 minutes) 135 10 fg
[0786] FIG. 4 is a photograph of electrophoresis which shows the
detection limits for amplifying a chain length of 135 bp
accomplished by the ICAN ({fraction (1/50)} of the reaction mixture
was loaded) and the PCR ({fraction (1/10)} of the reaction mixture
was loaded). Lane 1: molecular weight marker (100 bp ladder); lane
2: ICAN using 1 pg of the template; lane 3: ICAN using 100 fg of
the template; lane 4: ICAN using 10 fg of the template; lane 5: PCR
(25 cycles) using 1 pg of the template; lane 6: PCR (25 cycles)
using 100 fg of the template; lane 7: PCR (25 cycles) using 10 fg
of the template; lane 8: PCR (30 cycles) using 1 pg of the
template; lane 9: PCR (30 cycles) using 100 fg of the template; and
lane 10: PCR (30 cycles) using 10 fg of the template.
[0787] As shown in Table 4, it was confirmed that almost the same
detection sensitivity as that of the PCR was accomplished by the
ICAN. Furthermore, the total reaction time for the PCR was about 80
minutes, whereas the reaction time required for accomplishing the
same detection sensitivity using the method of the present
invention was 70 minutes, confirming that the reaction time can be
shortened by using the method of the present invention.
[0788] (2) Primers for amplifying .lambda. DNA having nucleotide
sequences represented by SEQ ID NOS:128, 129 and 145 were
synthesized. The length of a fragment to be amplified using each of
the combinations of primers was as follows: 151 bp (SEQ ID NOS:128
and 129); and 125 bp (SEQ ID NOS:145 and 129). The template DNA
prepared in Example 15(1) was used in this Example. The reaction
was carried out as follows. Briefly, 2 .mu.l of an annealing
solution (500 mM potassium chloride and 8 .mu.M spermidine), 1 fg
to 1 ng of the template were added to 120 pmol each of the primers
and fill up to 10 .mu.l by sterile water. The mixture was
heat-denatured at 98 C for 2 minutes, and then rapidly cooled on
ice to anneal the primers to the template.
[0789] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% BSA, 1.25% DMSO, 30 U of E. coli
RNase H and 11 U of BcaBEST DNA polymerase was added to the mixture
to make the final volume to 50 .mu.l. The reaction mixtures were
incubated at 60 C for 1 hour. After reaction, 3 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3.0% agarose
gel. The results are shown in Table 5.
5 TABLE 5 Amplification size (bp) Detection limit 125 10 fg 151 100
fg
[0790] As shown in Table 5, it was confirmed that, when .lambda.
DNA was used as a template, a detection sensitivity of as low as 10
fg could be also accomplished by examining the optimal region.
[0791] (3) A plasmid was prepared by inserting an amplified
fragment (length: 340 bp) into a plasmid T7Blue T-Vector (Takara
Shuzo). The fragment was prepared as described in JP-A 9-140383
using synthetic primers for amplifying a chrysanthemum viroid gene
having nucleotide sequences represented by SEQ ID NOS:146 and 147,
and an RNA from chrysanthemum infected with the viroid as a
template. The plasmid was used to transform Escherichia coli JM109
competent cells (Takara Shuzo). The transformant was cultured in 5
ml of LB medium at 37 C for 16 hour. The plasmid was purified from
the collected cells using QIAGEN Plasmid Mini Kit (Qiagen)
according to the manual. Dilutions containing 0 fg, 1 fg, 10 fg,
100 fg, 1 pg, 10 pg, 100 pg or 1 ng of the plasmid in 1 .mu.l of
sterile water were prepared based on the concentration of the
plasmid as measured using Beckman DU-600 (Beckman). 1 .mu.l of one
of the thus prepared plasmid solutions was used as a template for
50 .mu.l each of ICAN reaction systems. Primers CSVD-F2 and CSVD-R6
having nucleotide sequences represented by SEQ ID NOS:148 and 149
were used in this Example. The reaction was carried out as follows.
Briefly, 10 .mu.l of a mixture containing 50 pmol each of the
primers, 1 .mu.l of the prepared plasmid solution and
propylenediamine at a final concentration of 0.01% was prepared.
The mixture was heated at 98 C for 2 minutes, cooled to 60 C,
incubated at the temperature for 1 minute in Thermal Cycler
Personal (Takara Shuzo), and then placed on ice.
[0792] After annealing, at final concentrations, 20 mM
HEPES-potassium hydroxide buffer (pH 7.8), 100 mM potassium
acetate, 1% DMSO, 0.01% BSA, 4 mM magnesium acetate, 500 .mu.M each
of dNTPs, 30 U of E. coli RNase H and 5.5 U of BcaBEST DNA
polymerase were added to the mixture to make the final volume to 50
.mu.l with sterile water. The reaction mixtures were placed in
Thermal Cycler Personal which had been set at 60 C and reacted for
60 minutes. After reaction, 3 .mu.l each of the reaction mixtures
was subjected to electrophoresis on 3% NuSieve 3:1 agarose. As a
result, the amplification products of interest (about 90 bp, about
70 bp and about 50 bp) were observed using a template at a
concentration of 10 fg.
Example 19
[0793] Primers to be used in the method of the present invention
were examined.
[0794] (1) The Tm value of a primer and the reaction temperature
were examined. Primers for amplifying Flavobacterium sp. SA-0082
having nucleotide sequences represented by SEQ ID NOS:132 and
150-152 were synthesized. These primers were constructed such that
a region of 160 bp or shorter having a GC content of about 20% was
amplified. The length of a fragment to be amplified using each of
the combinations of primers was as follows: 126 bp (SEQ ID NOS:132
and 151); 158 bp (SEQ ID NOS:132 and 152); 91 bp (SEQ ID NOS:150
and 151); and 123 bp (SEQ ID NOS:150 and 152). The
PCR-amplification product as prepared in Example 16(1) was used as
a DNA as the template in this Example. The reaction was carried out
as follows. Briefly, 10 .mu.l of a mixture containing 120 pmol each
of the primers, 2 .mu.l of one of three types of annealing
solutions (500 mM potassium chloride and 8 .mu.M spermidine, 0.05%
propylenediamine, or water) and 1 fg to 10 ng of the template was
prepared. The mixture was heat-denatured at 98 C for 2 minutes, and
then cooled on ice to anneal the primers to the template.
[0795] After annealing, 40 .mu.l of one of three types of buffers
(17 mM Tricine-potassium hydroxide buffer (pH 8.5), 17 mM
Bicine-potassium hydroxide buffer (pH 8.3) and 20 mM
HEPES-potassium hydroxide buffer (pH 7.8)) containing 0.625 mM each
of dNTPs, 5.0 mM magnesium acetate, 0.0125% bovine serum albumin
(BSA), 1.25% dimethyl sulfoxide (DMSO), 30 U of E. coli RNase H and
11 U of BcaBEST DNA polymerase was added to the mixture to make the
final volume to 50 .mu.l. The reaction mixtures were incubated at
52, 55 or 60 C for 1 hour. After reaction, 3 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3.0% agarose
gel. As a result, the amplified fragment of interest was observed
using the reaction temperature of 52 C. In particular, a greater
amount of amplified fragment of interest was obtained using the
combination of the annealing solution containing 500 mM potassium
chloride and 8 .mu.M spermidine and Tricine or Bicine buffer. The
primer pair, the length of the amplified fragment and the detection
sensitivity for the reaction temperature of 52 C are shown in FIG.
5 and Table 6.
6 TABLE 6 Amplification size (bp) Detection limit 126 100 fg 158 1
pg 91 1 fg 123 100 fg
[0796] FIG. 5 is a photograph of electrophoresis which shows the
relationship between the length of the amplified fragment and the
amount of the DNA as the template when an AT-rich region was
amplified. Lane 1: molecular weight marker (100 bp ladder); lane 2:
amplification of a fragment of 91 bp in length using 1 pg of the
template; lane 3: amplification of a fragment of 91 bp in length
using 100 fg of the template; lane 4: amplification of a fragment
of 91 bp in length using 10 fg of the template; lane 5:
amplification of a fragment of 91 bp in length using 1 fg of the
template; lane 6: amplification of a fragment of 123 bp in length
using 1 pg of the template; lane 7: amplification of a fragment of
123 bp in length using 100 fg of the template; lane 8:
amplification of a fragment of 123 bp in length using 10 fg of the
template; lane 9: amplification of a fragment of 126 bp in length
using 1 pg of the template; lane 10: amplification of a fragment of
126 bp in length using 100 fg of the template; lane 11:
amplification of a fragment of 126 bp in length using 10 fg of the
template; lane 12: amplification of a fragment of 158 bp in length
using 1 pg of the template; lane 13: amplification of a fragment of
158 bp in length using 100 fg of the template; and lane 14:
amplification of a fragment of 158 bp in length using 10 fg of the
template.
[0797] As shown in FIG. 5 and Table 6, it was demonstrated that
good results were yielded by lower the reaction temperature
depending on the Tm value of the primer when the method of the
present invention was carried out using an AT-rich template and a
set of AT-rich primers.
[0798] (2) The higher-order structure of the primer may influence
the reactivity in the method of the present invention. Then,
modification of the primer for avoiding the formation of the
higher-order structure of the primer and for making the primer
readily anneal to the objective template was examined. Primers
represented by SEQ ID NOS:136, 137 and 153-158 were used.
Specifically, a primer having a nucleotide sequence represented by
SEQ ID NOS:136, primers 120I4, 121I5 and 122I6 which are primers
having nucleotide sequences represented by SEQ ID NOS:153 to 155
and having an inosine deoxynucleotide at the fourth, fifth or sixth
base from the 3'-terminus, a primer having a nucleotide sequence
represented by SEQ ID NO:193, and primers 123I4, 124I5 and 125I6
which are primers having nucleotide sequences represented by SEQ ID
NOS:156 to 158 and having an inosine deoxynucleotide at the fourth,
fifth or sixth base from the 3'-terminus were used. The DNA as the
template as prepared in Example 17 was used in this Example. The
reaction was carried out as follows. Briefly, 10 .mu.l of a mixture
containing 50 pmol each of the primers, 2 .mu.l of 0.05% aqueous
solution of propylenediamine, 1 ng to 10 ng of the DNA as the
template and sterile distilled water was heated at 98 C for 2
minutes, cooled to 55 C, and incubated at the temperature for 1
minute using a thermal cycler (GeneAmp PCR System 9600, Applied
Biosystems).
[0799] After annealing, 0.625 mM each of dNTPs, 42.5 mM
Tricine-potassium hydroxide buffer (pH 8.5), 5.0 mM magnesium
acetate, 0.0125% BSA, 1.25% DMSO, 30 U of E. coli RNase H or 5 U of
a heat-resistant RNase H from Thermus thermophilus (Tth) (Toyobo,
hereinafter referred to as Tth RNase H) and 5.5 U of BcaBEST DNA
polymerase were added to the mixture to make the final volume to 50
.mu.l with sterile water. The reaction mixtures were incubated at
55 C for 1 hour. After reaction, 5 .mu.l each of the reaction
mixtures was subjected to electrophoresis on 3.0% agarose gel. The
results are shown in FIG. 6.
[0800] FIG. 6 is a photograph of electrophoresis which shows the
effects on chimeric oligonucleotide primers containing inosine
deoxynucleotides when E. coli RNase H and Tth RNase H were used.
Lanes 2 to 9 represent the results obtained using E. coli RNase H.
Lanes 10 to 17 represent the results obtained using Tth RNase H.
Lane 1: molecular weight marker (100 bp ladder); lane 2: a pair of
primers represented by SEQ ID NOS:136 and 137, 1 ng of the
template; lane 3: a pair of primers 120I4 and 123I4, 1 ng of the
template; lane 4: a pair of primers 121I5 and 124I5, 1 ng of the
template; lane 5: a pair of primers 122I6 and 125I6, 1 ng of the
template; lane 6: a pair of primers represented by SEQ ID NOS:136
and 137, 10 ng of the template; lane 7: a pair of primers 120I4 and
123I4, 10 ng of the template; lane 8: a pair of primers 121I5 and
124I5, 10 ng of the template; lane 9: a pair of primers 122I6 and
125I6, 10 ng of the template; lane 10: a pair of primers
represented by SEQ ID NOS:136 and 137, 1 ng of the template; lane
11: a pair of primers 120I4 and 123I4, 1 ng of the template; lane
12: a pair of primers 121I5 and 124I5, 1 ng of the template; lane
13: a pair of primers 122I6 and 125I6, 1 ng of the template; lane
14: a pair of primers represented by SEQ ID NOS:136 and 137, 10 ng
of the template; lane 15: a pair of primers 120I4 and 123I4, 10 ng
of the template; lane 16: a pair of primers 121I5 and 124I5, 10 ng
of the template; and lane 17: a pair of primers 122I6 and 125I6, 10
ng of the template.
[0801] As shown in FIG. 6, when primers having inosines being
incorporated at fourth or fifth base from the 3'-termini of the
primers were used, the amplification products of interest were
observed using either of E. coli RNase H and the heat-resistant
RNase H from Thermus thermophilus regardless of the amount of the
template. These results demonstrate that the reactivity of the ICAN
is improved by incorporating inosine at an appropriate
position.
[0802] (3) Primers were examined for the same purpose as that in
(2) above. Oligonucleotide primers 1S and 4S having nucleotide
sequences represented by SEQ ID NOS:173 and 174 in which the three
bases at the 3'-terminus were .alpha.-S (or alpha-thio)
ribonucleotides, i.e., which had 5'-phosphothioate bonds in the RNA
moieties, were synthesized. In addition, oligonucleotide primers
1N3N3 and 4N3N3 having nucleotide sequences represented by SEQ ID
NOS:159 and 160 and having ribonucleotides at the three bases from
the 3'-terminus and in a portion of the sequence of the
deoxyribonucleotide moiety, i.e., ribonucleotides at eleventh to
thirteenth bases from the 3'-terminus of the primer, were
synthesized. The template DNA as prepared in Example 17 was used.
The reaction was carried out as follows. Briefly, 10 .mu.l of a
mixture containing 50 pmol each of the primers, 2 .mu.l of 0.05%
aqueous solution of propylenediamine, 10 ng of the DNA as the
template and sterile water was heated at 98 C for 2 minutes using a
thermal cycler, and then placed on ice for cooling.
[0803] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% BSA, 1.25% DMSO, 30 U of E. coli
RNase H or 5 U of Tth RNase H and 5.5 U of BcaBEST DNA polymerase
was added to the mixture to make the final volume to 50 .mu.l with
sterile water. The reaction mixtures were incubated at 55 C for 1
hour in a thermal cycler.
[0804] After reaction, 5 .mu.l each of the reaction mixtures was
subjected to electrophoresis on 3.0% agarose gel. As a result, the
amplification product was clearly observed at the expected position
using the combination of primers 1S and 4S or 1N3N3 and 4N3N3
regardless of the type of the RNase H used. These results confirmed
that modification of a primer at its 3'-terminus with
5'-phophothioate was effective for the method of the present
invention. Additionally, it was confirmed that substitution with a
ribonucleotide at an appropriate internal position in addition to
the 3'-terminus of a primer was effective for improving the
reactivity of the method of the present invention.
Example 20
[0805] Use of a DNA polymerase having RNase H activity in the
presence of a specific metal ion in the method of the present
invention was examined. 10 .mu.l of a mixture containing 120 pmol
each of the chimeric oligonucleotide primers used in Example 15(1),
2 .mu.l of an annealing solution containing 500 mM potassium
chloride and 8 .mu.M spermidine, 1 ng of the DNA as the template
used in Example 15(1) and sterile water was heat-denatured at 98 C
for 2 minutes, and then rapidly cooled on ice to anneal the primers
to the template. After annealing, 40 .mu.l of a mixture containing
0.625 mM each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer
(pH 8.5), 5.0 mM magnesium acetate, 0.0125% bovine serum albumin
(BSA), 1.0% dimethyl sulfoxide (DMSO) and 11 U of BcaBEST DNA
polymerase, and manganese chloride (Nacalai Tesque) at a final
concentration of 0.5, 2.5, 5.0 or 10 mM were added to the mixture
to make the final volume to 50 .mu.l with sterile water. The
reaction mixtures were incubated at 60 C for 1 hour. In addition, a
mixture without the addition of manganese chloride, and a mixture
to which 30 U of E. coli RNase H was added but manganese chloride
was not added were prepared as controls. After reaction, 3 .mu.l
each of the reaction mixtures was subjected to electrophoresis on
3.0% agarose gel. The results are shown in FIG. 7.
[0806] FIG. 7 is a photograph of electrophoresis which shows the
results of the ICAN utilizing the RNase H activity of BcaBEST DNA
polymerase. Lane 1: molecular weight marker (100 bp ladder); lane
2: without the addition of manganese chloride/with the addition of
E. coli RNase H; lane 3: without the addition of manganese
chloride/without the addition of E. coli RNase H; lane 4: with the
addition of 0.5 mM manganese chloride/without the addition of E.
coli RNase H; lane 5: with the addition of 2.5 mM manganese
chloride/without the addition of E. coli RNase H; lane 6: with the
addition of 5.0 mM manganese chloride/without the addition of E.
coli RNase H; and lane 7: with the addition of 10.0 mM manganese
chloride/without the addition of E. coli RNase H.
[0807] As shown in FIG. 7, the amplification product of interest
was observed for a reaction system to which manganese chloride was
added at a concentration of 2.5 mM in the absence of E. coli RNase
H.
Example 21
[0808] The method of the present invention was examined using a
practical biological sample.
[0809] (1) Detection was carried out using a hot water-extract
prepared from a culture of enterohemorrhagic Escherichia coli O-157
(ATCC accession number 43895) as a template. Enterohemorrhagic
Escherichia coli O-157 was cultured in mEC medium containing
novobiocin at 42 C for 18 hours, and then heated at 95 C for 10
minutes. Hot water-extracts of O-157 corresponding to 0, 1, 10,
10.sup.2, 10.sup.3, 10.sup.4 or 10.sup.5 cells were prepared by
diluting the extract with sterile water. Vero toxin 2 (VT2) gene
was amplified using one of these hot water-extracts of O-157 under
the same conditions as those in Example 18(1). In addition, a PCR
was carried out using the same template under the conditions as
described in Example 18(1) as a control. After reaction, 1 .mu.l
(ICAN) or 5 .mu.l (PCR) each of the reaction mixtures was subjected
to electrophoresis on 3.0% agarose gel. The results are shown in
Table 7 and FIG. 8.
7 TABLE 7 Amplification size (bp) Detection limit (cells) ICAN
(total time: 70 minutes) 135 10.sup.2 173 10.sup.3 PCR (25 cycles;
total time: about 66 minutes) 135 10.sup.3 PCR (30 cycles; total
time: about 80 minutes) 135 10.sup.2
[0810] FIG. 8 is a photograph of electrophoresis which shows the
detection of Escherichia coli O157 using ICAN or PCR. The chain
length to be amplified was 135 bp. Lane 1: molecular weight marker
(100 bp ladder); lane 2: ICAN for 10.sup.4 cells; lane 3: ICAN for
10.sup.3 cells; lane 4: ICAN for 10.sup.2 cells; lane 5: PCR of 25
cycles for 10.sup.4 cells; lane 6: PCR of 25 cycles for 10.sup.3
cells; lane 7: PCR of 25 cycles for 10.sup.2 cells; lane 8: PCR of
30 cycles for 10.sup.4 cells; lane 9: PCR of 30 cycles for 10.sup.3
cells; and lane 10: PCR of 30 cycles for 10.sup.2 cells.
[0811] As shown in Table 7 and FIG. 8, it was confirmed that the
detection sensitivity of the detection method of the present
invention was equivalent to that of the PCR, and that the method of
the present invention required shorter time for detection as
compared with that required for the PCR.
[0812] (2) .lambda. DNA was detected using the primers represented
by SEQ ID NOS:129 and 145 used in Examples 15 and 17. The reaction
was carried out as follows. Briefly, 10 .mu.l of a mixture
containing 120 pmol each of the primers, 2 .mu.l of an annealing
solution containing 500 mM potassium chloride and 8 .mu.M
spermidine, 10 fg to 1 ng of .lambda. DNA (Takara Shuzo) and
sterile water was prepared. The mixture was heat-denatured at 98 C
for 2 minutes, and then rapidly cooled on ice to anneal the primers
to the template.
[0813] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% bovine serum albumin (BSA), 1.25%
dimethyl sulfoxide (DMSO), 30 U of E. coli RNase H and 11 U of
BcaBEST DNA polymerase was added to the mixture to make the final
volume to 50 .mu.l with sterile water. The reaction mixtures were
incubated at 60 C for 1 hour. After reaction, 3 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3.0% agarose
gel. The results are shown in Table 8.
8 TABLE 8 Amplification size (bp) Detection limit 125 1 pg
[0814] As shown in Table 8, it was confirmed that the method of the
present invention was effective in detecting .lambda. DNA.
[0815] (3) Detection was carried out using a genomic DNA from a
bacterium Flavobacterium sp. SA-0082 as a template and the primers
represented by SEQ ID NOS:150 and 151 used in Example 19(1). The
genomic DNA as a template was prepared according to a conventional
method from the bacterium of genus Flavobacterium cultured as
described in WO 97/32010. The reaction was carried out as follows.
Briefly, 10 .mu.l of a mixture containing 120 pmol each of the
primers, 2 .mu.l of an annealing solution containing 500 mM
potassium chloride and 8 .mu.M spermidine, 10 fg to 1 ng of the
genomic DNA and sterile water was prepared. The mixture was
heat-denatured at 98 C for 2 minutes, and then rapidly cooled on
ice to anneal the primers to the template.
[0816] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% BSA, 1.25% DMSO, 30 U of E. coli
RNase H and 11 U of BcaBEST DNA polymerase was added to the mixture
to make the final volume to 50 .mu.l with sterile water. The
reaction mixtures were incubated at 52 C for 1 hour. After
reaction, 3 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel. The results are shown in Table
9 and FIG. 9.
9 TABLE 9 Amplification size (bp) Detection limit 91 100 fg
[0817] FIG. 9 is a photograph of electrophoresis which shows the
detection of a bacterium of genus Flavobacterium. Lane 1: molecular
weight marker (100 bp ladder); lane 2: 1 ng of the template; lane
3: 10 pg of the template; lane 4: 1 pg of the template; lane 5: 100
fg of the template; and lane 6: 10 fg of the template.
[0818] As shown in Table 9 and FIG. 9, it was confirmed that the
method of the present invention was effective in detecting a
bacterium.
Example 22
[0819] A method for detecting a target nucleic acid in which the
amplification method of the present invention and a hybridization
method were combined was examined. Enterohemorrhagic Escherichia
coli O-157 was selected as a target. The DNA as the template was
prepared as described in Example 21(1). A region of about 100 bp
having a GC content of about 40% was selected as a fragment to be
amplified. Primers VT2-IF20 and VT2-IR20-2 having nucleotide
sequences represented by SEQ ID NOS:140 and 161 were used as
primers. The reaction was carried out as follows. Briefly, 10 .mu.l
of a mixture containing 50 pmol each of the primers VT2-IF20 and
VT2-IR20-2, an annealing solution containing propylenediamine at a
final concentration of 0.01%, one of the hot water-extracts
corresponding to 0 to 10.sup.4 cells and sterile water was
prepared. The mixture was heat-denatured at 98 C for 2 minutes,
cooled to 55 C and incubated at the temperature for 1 minute in
Thermal Cycler Personal (Takara Shuzo), and then placed on ice for
annealing.
[0820] After annealing, at final concentrations, 20 mM
HEPES-potassium hydroxide buffer (pH 7.8), 100 mM potassium
acetate, 1% dimethyl sulfoxide (DMSO), 0.01% bovine serum albumin
(BSA), 4 mM magnesium acetate, 500 .mu.M each of dNTPs, 30 U of E.
coli RNase H and 5.5 U of BcaBEST DNA polymerase was added to the
mixture to make the final volume to 50 .mu.l with sterile water.
The reaction mixtures were placed on Thermal Cycler Personal which
had been set at 55 C and incubated at the temperature for 60
minutes. As a control, a PCR was carried out using O-157 Typing Set
(Takara Shuzo) according to the manual using Thermal Cycler
Personal. The PCR was carried out as follows: 35 cycles of 94 C for
1 minute, 55 C for 1 minute and 72 C for 1 minute. This reaction
required about 4 minutes per cycle and a total time of about 145
minutes. The expected size of the amplification product was 404 bp.
After reaction, 3 .mu.l each of the reaction mixtures was subjected
to electrophoresis on 3% NuSieve 3:1 agarose. The results are shown
in FIG. 28A. FIG. 28A shows the results of electrophoresis for the
detection of enterohemorrhagic Escherichia coli O157 vero toxin II
gene using the ICAN or the PCR. Lane M1: molecular weight marker
(50-2000 bp); lane M2: molecular weight marker (100 bp ladder);
lane N: negative control; lane 1: the template corresponding to 1
cell; lane 2: the template corresponding to 10 cells; lane 3: the
template corresponding to 10.sup.2 cells; lane 4: the template
corresponding to 10.sup.3 cells; and lane 5: the template
corresponding to 10.sup.4 cells. Furthermore, results of comparison
between the amplification levels accomplished by the ICAN and the
PCR for 1 cell or 10 cells are shown in Table 10.
10 TABLE 10 Number of E. coli O-157 cells 0 1 10 ICAN - + +++ PCR -
+ ++ -: no amplification; + to +++ indicate the degree of
amplification in three grades.
[0821] As shown in FIG. 28A and Table 10, the amplification
products of interest were obtained for the reaction systems using a
hot water-extract corresponding to 1 cell according to both the
detection method of the present invention and the PCR. Dot blot
hybridization was further carried out for the amplification product
obtained according to the ICAN using an oligonucleotide VT2 having
a nucleotide sequence represented by SEQ ID NO:162 labeled with
biotin at the 5'-terminus as a probe. Hybridization was carried out
under as follows. Briefly, 1 .mu.l of a reaction mixture was
denatured at 98 C for 5 minutes, rapidly cooled on ice, and spotted
onto Hybond-N membrane (Amersham Pharmacia Biotech). After exposure
to UV, the membrane was placed in a hybridization bag. 10 ml of a
hybridization solution containing 0.5 M disodium hydrogenphosphate
(pH 7.2), 1 mM ethylenediaminetetraacetic acid and 7% sodium lauryl
sulfate was added thereto. Pre-hybridization was then carried out
at 42 C for 30 minutes. 10 .mu.l of the solution of the VT2 probe
at a concentration of 100 ng/.mu.l was heat-denatured and added to
the pre-hybridization reaction system. After hybridization at 42 C
for 60 minutes, the membrane was washed twice in a solution
containing 66.6 mM sodium chloride, 66.6 mM sodium citrate and 0.1%
sodium lauryl sulfate at room temperature for 5 minutes, incubated
in 6 ml of a washing buffer (0.3 M sodium chloride, 17.3 mM
disodium hydrogenphosphate dihydrate, 2.5 mM EDTA, 0.1% sodium
lauryl sulfate) to which 2 .mu.l of 5 mg/ml horseradish peroxidase
streptoavidin conjugate (PIERCE) was added at 42 C for 12 minutes,
and then washed twice in the washing buffer at room temperature.
The membrane was then washed in 10 ml of 0.1 M citrate buffer (pH
5.0) at room temperature and reacted in a mixture of 5 ml of 0.1 M
citrate buffer, 5 .mu.l of 3% hydrogen peroxide and 250 .mu.l of a
solution of 2 mg/ml tetramethylbenzidine (TMB, Nacalai Tesque) in
ethanol in the dark for about 10 minutes. After color development,
the reaction was terminated with deionized water. The results are
shown in FIG. 28B. FIG. 28B shows the results of dot blot
hybridization for detecting a gene for vero toxin II from
enterohemorrhagic Escherichia coli O-157 by the ICAN. The results
were consistent with those obtained for the above-mentioned
electrophoresis. Thus, the detection sensitivity of the method of
the present invention was equivalent to that of the PCR. The total
time required for the amplification reaction using the ICAN of the
present invention was 1/2 or shorter as compared with that required
for the PCR. Thus, the ICAN of the present invention was confirmed
to be effective as a method for detecting a pathogen and the
like.
Example 23
[0822] (1) Combination of a reverse transcription reaction and the
method of the preset invention was examined using an RNA from
cultured cells as a template. The reaction was carried out as
follows. Briefly, RAW264.7 cells (ATCC TIB 71) were suspended in
Dulbecco's modified Eagle's medium (Bio Whittaker, 12-604F)
containing 10% fetal calf serum (Gibco) at a concentration of
1.5.times.10.sup.5 cells/ml. 5 ml of the suspension was added to
each well of a 6-well microtiter plate and the plate was incubated
at 37 C overnight in the presence of 5% CO.sub.2. 50 .mu.l of a 100
.mu.g/ml solution of lipopolysaccharide (LPS, Sigma) in water and
50 .mu.l of a 1000 U/.mu.l solution of interferon-.gamma.
(IFN-.gamma., Genzyme Techne) in water were added to the well. The
plate was incubated for additional 4 hours. An RNA was then
prepared from the cells using RNeasy Mini Kit (Qiagen) according to
the instructions attached to the kit. As a negative control, a
group to which LPS or IFN-.gamma. was not added was provided.
[0823] A cDNA was prepared by incubating 60 .mu.l of a mixture
containing 3 .mu.g of the thus prepared RNA, 10 mM
tris-hydrochloride buffer (pH 8.3), 50 mM KCl, 5 mM MgCl.sub.2, 1
mM each of dNTPs, 150 pmol of random 6mers primer, 60 U of
ribonuclease inhibitor (Takara Shuzo) and 15 U of Reverse
Transcriptase XL (AMV) (Takara Shuzo, 2620A) at 30 C for 10
minutes, 42 C for 1 hour and then 99 C for 5 minutes for
inactivating the enzyme using a thermal cycler (GeneAmp PCR System
9600, Applied Biosystems).
[0824] Primers having nucleotide sequences represented by SEQ ID
NOS:163 and 164 were synthesized based on the nucleotide sequence
of the mRNA for mouse inducible NO synthase (iNOS) (GeneBank
accession no. NM-010927). As a control, primers for PCR represented
by SEQ ID NOS:165 and 166 were also synthesized.
[0825] 10 .mu.l of a mixture containing 50 pmol each of the
primers, 2 .mu.l of an aqueous solution of propylenediamine at a
concentration of 0.05%, 1 .mu.l of the cDNA as a template
(corresponding to 50 ng of the RNA) and sterile water was prepared.
The mixture was heat-denatured at 98 C for 2 minutes, cooled to 55
C and incubated at the temperature for 1 minute in a thermal cycler
to anneal the primers to the template.
[0826] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% bovine serum albumin (BSA), 1.25%
dimethyl sulfoxide (DMSO), 15 U of E. coli RNase H and 11 U of
BcaBEST DNA polymerase was added to the mixture to make the final
volume to 50 .mu.l with sterile water. The reaction mixtures were
incubated at 55 C for 1 hour in a thermal cycler. The reacted
samples were stored by freezing at -20 C until being analyzed. The
PCR as a control was carried out as follows. Briefly, 50 .mu.l of a
reaction mixture containing 50 pmol each of the primers, 1 .mu.l of
the cDNA (corresponding to 50 ng of the RNA), 5 .mu.l of
10.times.Ex Taq buffer (Takara Shuzo), 1.25 U of TaKaRa Ex Taq DNA
polymerase (Takara Shuzo) and 0.2 mM each of dNTPs was reacted in a
thermal cycler. The program was as follows: 1 cycle of 94 C for 2
minutes; 30 cycles of 94 C for 30 seconds, 55 C for 30 seconds and
72 C for 30 seconds; and 1 cycle of 72 C for 5 minutes. The reacted
samples were stored by freezing at -20 C until being analyzed.
After reaction, 5 .mu.l each of the reaction mixtures was subjected
to electrophoresis on 3.0% agarose gel. The results are shown in
FIG. 10.
[0827] FIG. 10 is a photograph of electrophoresis which shows the
comparison between the RT-ICAN and the RT-PCR. Lane 1: molecular
weight marker (100 bp ladder); lane 2: negative control group; and
lane 3: a group treated with LPS and IFN-.gamma..
[0828] As shown in FIG. 10, the amplification products were
observed for both of the method of the present invention and the
PCR only when the cDNA prepared from cells treated with LPS and
IFN-.gamma. was used as a template. Thus, it was confirmed that,
since the method of the present invention required a shorter period
of time for reaction as compared with the PCR, the method of the
present invention was more effective as a DNA amplification method
after reverse transcription.
Example 24
[0829] E. coli RNase H of which the optimal temperature is 37 C may
become inactivated during amplification reaction of the present
invention. Then, the effect of addition of E. coli RNase H to the
reaction mixture during the amplification reaction was examined. An
amplified fragment (1071 bp) obtained by a PCR using primers
GMO-PCR-F and GMO-PCR-R represented by SEQ ID NOS:167 and 168 from
a genomic DNA extracted from recombinant soybeans into which
cauliflower mosaic virus .sup.35S promoter and EPSPS gene had been
introduced was used as a template DNA. In addition, primers GMO-S1,
S2, A1 and A2 having nucleotide sequences represented by SEQ ID
NOS:169 to 172 were used. The reaction was carried out as follows.
Briefly, 10 .mu.l of a mixture containing 50 pmol each of the
primers, propylenediamine at a final concentration of 0.01%, 1 pg
to 10 ng of the DNA as the template and sterile water was prepared.
The mixture was heat-denatured at 98 C for 2 minutes and cooled to
55 C for annealing.
[0830] After annealing, at final concentrations, 500 .mu.M each of
dNTPs, 34 mM Tricine-potassium hydroxide buffer (pH 8.7), 4.0 mM
magnesium acetate, 0.01% bovine serum albumin (BSA), 1% dimethyl
sulfoxide (DMSO), 30 U of E. coli RNase H and 5.5 U of BcaBEST DNA
polymerase were added to the mixture to make the final volume to 50
.mu.l with sterile water. The reaction mixtures were incubated at
55 C for 25 minutes in a thermal cycler. 30 U of E. coli RNase H
was further added thereto 25 minutes after the initiation of the
reaction. The mixture was incubated at 55 C for 30 minutes. As a
control, a reaction was carried out by incubating the mixture at 55
C for 55 minutes. After reaction, 3 .mu.l each of the reaction
mixtures was subjected to electrophoresis on 3% agarose. As a
result, it was confirmed that the amplification efficiency was
improved by the addition of E. coli RNase H during the reaction
regardless of the concentration of the template DNA for either of
the combinations of the primers, S1/A1, S1/A2, S2/A1 and S2/A2.
Example 25
[0831] The combination of a method for amplifying or duplicating a
nucleic acid to be used as a template in the present invention and
the method of the present invention was examined. The reaction was
carried out as follows. Briefly, in vitro transcription was carried
out using a plasmid containing the chrysanthemum viroid gene as
prepared in Example 18(3) which was duplicated in Escherichia coli
as a template and T7 RNA polymerase (Takara Shuzo) to obtain a
fragment duplicated from an RNA. A cDNA was synthesized using
primers having nucleotide sequences represented by SEQ ID NOS:146
and 147 and cDNA synthesis kit (Takara Shuzo). An amplification
reaction was carried out as described in Example 18(3) using the
cDNA fragment or the duplicated plasmid as a template. As a result,
it was confirmed that both a nucleic acid duplicated in a form of a
plasmid and a nucleic acid in a form of a cDNA duplicated from an
RNA using an RNA polymerase can be used as templates for the method
of the present invention.
Example 26
[0832] (1) Synthesis of Primer
[0833] Oligonucleotide primers NS1 and NS2 represented by SEQ ID
NOS:175 and 176 were synthesized on the basis of the nucleotide
sequence of the mRNA for mouse inducible NO synthase (iNOS).
[0834] (2) Amplification of DNA Fragment According to ICAN Using
PCR Product as Template
[0835] 10 .mu.l of a mixture containing 50 pmol each of the
synthetic oligonucleotide primers, 2 .mu.l of a 0.05% aqueous
solution of propylenediamine and 10 fg to 10 pg of the template was
heated at 98 C for 2 minutes and then 60 C for 2 minutes using a
thermal cycler (GeneAmp PCR System 9600, Applied Biosystems) to
anneal the primers to the template. iNOS cDNA (741 bp) amplified
using primers NS-PCR1 and NS-PCR2 represented by SEQ ID NOS:221 and
222, which was then purified using Suprec02 (Takara Shuzo), was
used as the DNA as the template. 40 .mu.l of a reaction mixture
containing 0.625 mM each of dNTPs, 40 mM HEPES-potassium hydroxide
buffer (pH 7.8), 125 mM potassium acetate, 5.0 mM magnesium
acetate, 0.0125% bovine serum albumin, 1.25% dimethyl sulfoxide,
0.0156 pg of Pfu RNase H and 0.66 U of BcaBEST DNA polymerase was
added to the heated solution. The mixtures were at incubated at 60
C for 1 hour in a thermal cycler. 5 .mu.l each of the reaction
mixtures was analyzed by electrophoresis on 3.0% agarose gel. The
results are shown in FIG. 11. FIG. 11 represents the results of the
ICAN using Pfu RNase H. Lane 1: molecular weight marker (100 bp);
lane 2: 10 fg of the template; lane 3: 100 fg of the template; lane
4: 1 pg of the template; and lane 5: 10 pg of the template.
[0836] As shown in FIG. 11, the amplification product of interest
was observed using 100 fg of the template.
Example 27
[0837] (1) Preparation of RNA
[0838] RAW264.7 cells (ATCC TIB 71) were suspended in Dulbecco's
modified Eagle's medium (Bio Whittaker) containing 10% fetal calf
serum (Gibco) at a concentration of 1.5.times.10.sup.5 cells/ml. 5
ml of the suspension was added to each well of a 6-well microtiter
plate and the plate was incubated at 37 C overnight in the presence
of 5% CO.sub.2. 50 .mu.l of a 100 .mu.g/ml solution of
lipopolysaccharide (LPS, Sigma) in water and 50 .mu.l of a 1000
U/ml solution of interferon-.gamma. (IFN-.gamma., Genzyme Techne)
in water were added to the well. The plate was incubated for
additional 4 hours. An RNA was then prepared from the cells using
RNeasy Mini Kit (Qiagen, 74104) according to the instructions
attached to the kit. As a negative control, a group to which LPS or
IFN-.gamma. was not added was provided.
[0839] A cDNA was prepared by incubating 60 .mu.l of a mixture
containing 3 .mu.g of the thus prepared RNA, 10 mM
tris-hydrochloride buffer (pH 8.3), 50 mM KCl, 5 mM MgCl.sub.2, 1
mM each of dNTPs, 150 pmol of random 6mers, 60 U of Ribonuclease
Inhibitor (Takara Shuzo) and 15 U of Reverse Transcriptase XL (AMV)
(Takara Shuzo) at 30 C for 10 minutes, 42 C for 1 hour and then 99
C for 5 minutes for inactivating the enzyme using a thermal cycler
(GeneAmp PCR System 9600, Applied Biosystems).
[0840] Primers NS5 and NS6 having nucleotide sequences represented
by SEQ ID NOS:181 and 182 were synthesized based on the nucleotide
sequence of the mRNA for mouse inducible NO synthase (iNOS).
Furthermore, primers NS3 and NS4 for PCR represented by SEQ ID
NOS:177 and 178 were also synthesized.
[0841] 50 .mu.l of a mixture containing 50 pmol each of the primers
NS5 and NS6, 1 .mu.l of the cDNA solution synthesized as described
above (corresponding to 50 ng of the RNA) or a 10-, 100-, 1000- or
10000-fold dilution with water thereof as a template, 0.5 mM each
of dNTPs, 32 mM HEPES-potassium hydroxide buffer (pH 7.8), 100 mM
potassium acetate, 4.0 mM magnesium acetate, 0.01% bovine serum
albumin, 1% dimethyl sulfoxide, 0.0156 pg of Pfu RNase H and 0.66 U
of BcaBEST DNA polymerase was incubated at 60 C for 1 hour in a
thermal cycler. The reacted samples were stored by freezing at -20
C until being analyzed.
[0842] On the other hand, a PCR was carried out as a control. 50
.mu.l of a reaction system containing 50 pmol each of the primers
NS3 and NS4, 1 .mu.l of the cDNA solution (corresponding to 50 ng
of the RNA) or a 10-, 100-, 1000- or 10000-fold dilution with water
thereof, 5 .mu.l of 10.times.Ex Taq buffer (Takara Shuzo), 1.25 U
of TaKaRa Ex Taq polymerase (Takara Shuzo) and 0.2 mM each of dNTPs
was reacted using a thermal cycler. The program was as follows: 1
cycle of 94 C for 2 minutes; 35 cycles of 94 C for 30 seconds, 55 C
for 30 seconds and 72 C for 30 seconds; and 1 cycle of 72 C for 5
minutes. The reacted samples were stored by freezing at -20 C until
being analyzed.
[0843] 5 .mu.l each of the reaction mixtures (ICAN or PCR) was
analyzed by electrophoresis on 3.0% agarose gel. The results are
shown in FIG. 12. FIG. 12 shows the results of the detection of
iNOS gene according to the ICAN using Pfu RNase H or the PCR. Lane
1: a lane for 100 bp DNA ladder marker; lane 2: the 10000-fold
dilution of the negative control cDNA; lane 3: the 1000-fold
dilution of the negative control cDNA; lane 4: the 100-fold
dilution of the negative control cDNA; lane 5: the 10-fold dilution
of the negative control cDNA; lane 6: the original solution of the
negative control cDNA; lane 7: the 10000-fold dilution of the cDNA
from the group with the addition of LPS and IFN-.gamma.; lane 8:
the 1000-fold dilution of the cDNA from the group with the addition
of LPS and IFN-.gamma.; lane 9: the 100-fold dilution of the cDNA
from the group with the addition of LPS and IFN-.gamma.; lane 10:
the 10-fold dilution of the cDNA from the group with the addition
of LPS and IFN-.gamma.; and lane 11: the original solution of the
cDNA from the group with the addition of LPS and IFN-.gamma..
[0844] As shown in FIG. 12, the amplification products were
observed for both of the ICAN and the PCR only when the cDNA
prepared from cells treated with LPS and IFN-.gamma. was used as a
template. For the ICAN, the increase in amplification product was
observed using the 1000-fold dilution of the cDNA. For the PCR, the
increase in amplification product was observed using the 100-fold
dilution of the cDNA.
Example 28
[0845] (1) Oligonucleotide primers 4 and 5 represented by SEQ ID
NOS:179 and 180 were synthesized based on the nucleotide sequence
of .lambda. DNA. The oligonucleotide primer 4 is a sense primer
having 75% of a GC content. The oligonucleotide primer 5 is an
antisense primer having 80% of a GC content.
[0846] 10 .mu.l of a reaction system containing 120 pmol each of
the primers 4 and 5, 2 .mu.l of a 0.05% propylenediamine solution
and 10 ng of a template was heat-denatured at 98 C for 2 minutes,
and then rapidly cooled on ice to anneal the primers to the
template. The PCR product (1005 bp) purified using Suprec02 as
described in Example 15 was used as the template.
[0847] (2) After annealing, 40 .mu.l of a mixture containing 0.625
mM each of dNTPs, 42.5 mM Bicine-potassium hydroxide buffer (pH
8.3), 5.0 mM magnesium acetate, 0.0125% bovine serum albumin, 1.25%
dimethyl sulfoxide, 0.5 .mu.l of Thermotoga maritima RNase HII
(0.58 .mu.g/ml) and 2.2 U of BcaBEST DNA polymerase was added to
the mixture to carry out the ICAN at 60, 65 or 70 C for 1 hour. 3
.mu.l each of the reaction mixtures after the ICAN was confirmed by
electrophoresis on 3.0% agarose gel. The results are shown in FIG.
13. FIG. 13 shows the results of the ICAN using Thermotoga maritima
RNase HII. Lane 1: molecular weight marker (100 bp); lane 2:
reaction temperature of 60 C; lane 3: reaction temperature of 65 C;
and lane 4: reaction temperature of 70 C.
[0848] As shown in FIG. 13, the amplification products of interest
were observed for the respective reaction temperatures.
Example 29
[0849] (1) Amplification of a DNA fragment according to the ICAN
using a PCR product as a template (alkali-denatured) was examined.
1 .mu.l of a solution containing 10 fg to 10 pg of a template and 1
.mu.l of 0.4 N NaOH were mixed together. The mixture was incubated
at 37 C for 5 minutes to denature the template. The PCR-amplified
iNOS cDNA (741 bp) purified using Suprec02 (Takara Shuzo) as
described in Example 26 was used as a template. Each of the
denatured templates was neutralized using 1 .mu.l of 0.4 N HCl. 47
.mu.l of a reaction mixture containing 50 pmol each of the primers
NS1 and NS2, 0.5 mM each of dNTPs, 32 mM HEPES-potassium hydroxide
buffer (pH 7.8), 100 mM potassium acetate, 4.0 mM magnesium
acetate, 0.01% bovine serum albumin, 1.0% dimethyl sulfoxide,
0.0156 pg of Pfu RNase H and 0.66 U of BcaBEST DNA polymerase was
then added thereto. The mixture was incubated at 60 C for 1 hour in
a thermal cycler. 5 .mu.l each of the reaction mixtures was
analyzed by electrophoresis on 3.0% agarose gel. The results are
shown in FIG. 14. FIG. 14 shows the results of the ICAN using an
alkali-denatured template. Lane 1: molecular weight marker (100
bp); lane 2: 10 fg of the template; lane 3: 100 fg of the template;
lane 4: 1 pg of the template; and lane 5: 10 pg of the
template.
[0850] As shown in FIG. 14, the amplification product was clearly
increased using 1 pg of the template.
Example 30
[0851] (1) Amplification of a DNA fragment according to the ICAN
without denaturing a template was examined. Primers NS5 and NS6
represented by SEQ ID NOS:181 and 182 were used as primers. The
template as prepared in Example 26 was used as a template DNA.
[0852] 50 .mu.l of a reaction mixture containing 10 fg to 100 pg of
the template or water for a negative control, 50 pmol each of the
primers NS5 and NS6, 0.5 mM each of dNTPs, 32 mM HEPES-potassium
hydroxide buffer (pH 7.8), 100 mM potassium acetate, 4.0 mM
magnesium acetate, 0.01% bovine serum albumin, 1.0% dimethyl
sulfoxide, 0.0156 pg of Pfu RNase H and 1 U of BcaBEST DNA
polymerase (Takara Shuzo) was incubated at 60 C for 1 hour in a
thermal cycler. After reaction, 5 .mu.l each of the reaction
mixture was analyzed by electrophoresis on 3.0% agarose gel. A
photograph of the electrophoresis is shown in FIG. 15. FIG. 15 is a
photograph of electrophoresis for the amplification method of the
present invention without denaturing a template DNA. Lane 1: 100 bp
DNA ladder marker; lane 2: negative control (water); lane 3: 10 fg
of the template; lane 4: 100 fg of the template; lane 5: 1 pg of
the template; lane 6: 10 pg of the template; and lane 7: 100 pg of
the template.
[0853] As shown in FIG. 15, the amplification product of interest
was observed using 1 pg of the template.
Example 31
[0854] (1) Primers pDON-AI-1 and pDON-AI-2 represented by SEQ ID
NOS:183 and 184 were synthesized based the nucleotide sequence of
the packaging region in a vector plasmid pDON-AI DNA (Takara
Shuzo).
[0855] (2) Amplification of DNA Fragment According to ICAN Without
Denaturing Template
[0856] 50 .mu.l of a reaction mixture containing 1 .mu.l of a
solution containing 10 fg to 1 ng of pDON-AI DNA or water for a
negative control, 50 pmol each of the primers, 0.5 mM each of
dNTPs, 32 mM HEPES-potassium hydroxide buffer (pH 7.8), 100 mM
potassium acetate, 4.0 mM magnesium acetate, 0.01% bovine serum
albumin, 1.0% dimethyl sulfoxide, 0.0156 pg of Pfu RNase H as
prepared in Referential Example 4 and 1 U of BcaBEST DNA polymerase
was incubated at 60 C for 1 hour in a thermal cycler. 5 .mu.l each
of the reaction mixtures was analyzed by electrophoresis on 3.0%
agarose gel. The results are shown in FIG. 16. FIG. 16 is a
photograph of electrophoresis for the method of the present
invention using a circular double-stranded DNA as a template
without denaturation. Lane 1: 100 bp DNA ladder marker; lane 2:
negative control (water); lane 3: 10 fg of the template; lane 4:
100 fg of the template; lane 5: 1 pg of the template; lane 6: 10 pg
of the template; lane 7: 100 pg of the template; and lane 8: 1 ng
of the template.
[0857] As shown in FIG. 16, it was confirmed that the amplification
product of interest was obtained using 10 fg of the template.
Example 32
[0858] Detection of human papilloma virus 16 gene utilizing the
method of the present invention was examined. A DNA from cells
infected with human papilloma virus 16, CaSki cells (Dainippon
Pharmaceutical; containing 500 copies of human papilloma virus 16
in a cell), was used as a template. Primers HPV16 S3 and HPV16 A2
having nucleotide sequences represented by SEQ ID NOS:185 and 186
were used as primers for detecting HPV16. The expected size of the
amplification product obtained using the primer pair was about 120
bp. The reaction was carried out as follows.
[0859] 10 .mu.l of a mixture containing 1 pg, 3 pg, 30 pg, 100 pg,
300 pg, 1 ng, 3 ng or 10 ng of the template DNA, 50 pmol each of
the primers HPV16 S3 and HPV16 A2 and propylenediamine at a final
concentration of 0.01% was prepared. The mixtures were incubated at
98 C for 2 minutes and at 55 C for 1 minute in Thermal Cycler
Personal, and then placed on ice. At final concentrations, 20 mM
HEPES-potassium hydroxide buffer (pH 7.8), 100 mM potassium
acetate, 1% dimethyl sulfoxide, 0.01% bovine serum albumin, 4 mM
magnesium acetate, 500 .mu.M each of dNTPs, 30 U of E. coli RNase H
and 5.5 U of BcaBEST DNA polymerase were added to the mixture to
make the final volume to 50 .mu.l. The reaction mixtures were
placed in a thermal cycler which had been set at 55 C and reacted
for 60 minutes. As a control, a PCR was carried out using Human
Papillomavirus Primers HPVp16 (forward, reverse) (Takara Shuzo)
according to the manual in Thermal Cycler Personal. The expected
size of the amplification product was 140 bp.
[0860] After reaction, 3 .mu.l each of the reaction mixtures was
subjected to electrophoresis on 4% NuSieve 3:1 agarose. The results
are shown in FIG. 17A. FIG. 17A shows the results of the detection
of HPV16 gene utilizing the ICAN and the PCR. Lane M1: molecular
weight marker (100 bp ladder); lane M2: molecular weight marker
(50-2000 bp); lane 1: no template; lane 2: 1 pg of the template;
lane 3: 3 pg of the template; lane 4: 30 pg of the template; lane
5: 100 pg of the template; lane 6: 300 pg of the template; lane 7:
1 ng of the template; lane 8: 3 ng of the template; and lane 9: 10
ng of the template.
[0861] As shown in FIG. 17A, it was confirmed that the
amplification products of interest were obtained using 3 pg of the
template DNA for the ICAN and 1 pg of the template DNA for the PCR,
respectively.
[0862] Furthermore, dot blot hybridization for the reaction
products was carried out using an oligonucleotide HPV16 probe
having a nucleotide sequence represented by SEQ ID NO:187.
Hybridization was carried out as described in Example 22. The
results are shown in FIG. 17B. FIG. 17B shows the results of dot
blot hybridization detection of HPV16 gene according to the PCR and
the ICAN. Lane 1: no template; lane 2: 1 pg of the template; lane
3: 3 pg of the template; lane 4: 30 pg of the template; lane 5: 100
pg of the template; lane 6: 300 pg of the template; lane 7: 1 ng of
the template; lane 8: 3 ng of the template; and lane 9: 10 ng of
the template.
[0863] As shown in FIG. 17B, the detection sensitivities of the
ICAN and the PCR were almost equivalent. Thus, it was confirmed
that these methods were effective for detecting a virus or the
like.
Example 33
[0864] Detection of human papilloma virus 16 gene from a clinical
specimen DNA sample was examined. DNAs prepared according to a
conventional method from 6 clinical specimens obtained with
informed consent were used as templates. The types of the infecting
HPVs in the samples prepared from these clinical specimens had been
proved by the PCR. The primers HPV16 S3 and HPV16 A2 as described
in Example 32 were used as primers for detection. The
concentrations of the DNA samples from the clinical specimens to be
used as templates were adjusted to 100 ng/.mu.l with TE buffer. The
composition of the reaction mixture and the reaction conditions as
described in Example 32 were used except for the amount of the
template. In addition, similar reactions were carried out using a
reaction mixture without the addition of the template DNA as a
negative control and a reaction mixture containing 500 pg of the
DNA from CaSki cells infected with HPV 16 as a positive control.
After reaction, 3 .mu.l each of the reaction mixtures was subjected
to electrophoresis on 4% NuSieve 3:1 agarose. The results are shown
in FIG. 18A. FIG. 18A shows the results of the detection of HPV16
gene from clinical specimens. Lane M: molecular weight marker;
lanes 1 to 6: clinical specimens; lane 7: negative control; and
lane 8: positive control.
[0865] As shown in FIG. 18A, the amplification products of about
120 bp were observed according to the ICAN for the samples which
had been proved to be infected with HPV16 by the conventional PCR.
No amplification was observed for samples infected with other types
of HPVs or non-infected samples.
[0866] Furthermore, dot blot hybridization for the amplification
products was carried out as described in Example 22. The results
are shown in FIG. 18B and Table 11. FIG. 18B shows the results of
dot blot hybridization detection of HPV16 gene from the clinical
specimens. Lanes 1 to 6: clinical specimens; lane 7: negative
control; and lane 8: positive control.
[0867] As shown in FIG. 18B, results consistent with those obtained
by the electrophoresis were obtained, confirming that similar
results with those of the PCR could be obtained by using
electrophoresis as well as dot blot hybridization. Thus, it was
confirmed that HPV16 could be detected from practical clinical
specimens according to the method of the present invention and that
the method was effective for detecting a virus or the like.
11TABLE 11 No Positive Sample No. 3 No. 4 No. 6 No. 7 No. 8 No. 9
template control Typing by non- non- Type Type Type Type * * PCR
infected infected 18 16 67 16 ICAN - - - + - + - + amplification
using HPV16 detection primer -: no amplification; +: amplification
observed.
Example 34
[0868] Detection of HCV from clinical specimens was examined.
Specimen samples were prepared from 300 .mu.l each of 5 serum
specimens from patients with HCV obtained with informed consent
using TRIzol reagent (Life Technologies) according to the
instructions attached to the reagent and finally dissolved in 6
.mu.l of injectable water (Otsuka Pharmaceutical) to obtain RNA
samples. An RNA similarly extracted from 300 .mu.l of a serum from
a healthy individual was used as a negative control. First, 4 .mu.l
of a reaction mixture for reverse transcription containing
1.times.RNA PCR Buffer, 5 mM MgCl.sub.2, 1 mM dNTPs, 1 U of AMV
Reverse Transcriptase XL, 10 pmol each of primers HCV-F and HCV-R
represented by SEQ ID NOS:188 and 189, and 2 .mu.l of one the RNA
samples was prepared using RNA PCR kit (AMW) ver 2.1 (Takara
Shuzo). The mixtures were warmed at 30 C for 10 minutes and then
reacted at 50 C for 30 minutes. After reverse transcription, the
ICAN was carried out. Primers HCV-F2 and HCV-R1 having nucleotide
sequences represented by SEQ ID NOS:190 and 191 were used for the
ICAN. The reaction was carried as follows.
[0869] 10 .mu.l of a mixture containing 50 pmol each of the
primers, 3 .mu.l one of the reverse transcription reaction mixtures
and propylenediamine at a final concentration of 0.01% was
prepared. 3 .mu.l of sterile water was used for a blank. The
mixtures were heated at 98 C for 2 minutes, rapidly cooled to 60 C
and incubated at the temperature for 1 minute in Thermal Cycler
Personal, and stored on ice.
[0870] After annealing, at final concentrations, 20 mM
HEPES-potassium hydroxide buffer (pH 7.8), 100 mM potassium
acetate, 1% dimethyl sulfoxide, 0.01% bovine serum albumin, 4 mM
magnesium acetate, 500 .mu.M each of dNTPs, 30 U of E. coli RNase H
and 5.5 U of BcaBEST DNA polymerase were added to the mixture to
make the final volume to 50 .mu.l with sterile water. The reaction
mixtures were placed in Thermal Cycler MP which had been set at 60
C and reacted for 60 minutes. After reaction, 3 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3% NuSieve
3:1 agarose. The results are shown in FIG. 19A. FIG. 19A shows the
results of HCV detection from clinical specimens. Lane B: sterile
water as a template; lane 1: a sample from a healthy individual;
lanes 2 to 6: samples from patients with HCV; and lane M: molecular
weight marker (50-2000 bp).
[0871] As shown in FIG. 19A, the amplification products of about
107 bp expected from the nucleotide sequence of HCV genome were
observed only for the RNA samples from patients with HCV, whereas
such an amplification product was not observed for the serum from
the healthy individual and the blank. Furthermore, dot blot
hybridization for the ICAN-amplified products was carried out as
described in Example 22 using a probe for HCV represented by SEQ ID
NO:192 biotinated at 5'-terminus. The results are shown in FIG.
19B. The lanes for the samples in FIG. 19B are as those indicated
for the photograph of electrophoresis.
[0872] As shown in FIG. 19, it was confirmed that the results from
the electrophoresis were consistent with those from the dot blot
hybridization. These results confirms that the method of the
present invention can be used to detect HCV from practical clinical
specimens and is effective for detecting a virus or the like.
Example 35
[0873] A method for detecting adenovirus was examined.
[0874] Primers for amplifying E1A (tumor gene), E1A-1 (sense),
E1A-2 (antisense) and E1A-3 (antisense), represented by SEQ ID
NOS:193 to 195 were constructed based on the nucleotide sequence of
adenovirus (GenBank accession no. J01917). Adenovirus (ATCC
accession no. VR-5) was used. A template was prepared as follows.
100 .mu.l of a solution containing adenovirus at a concentration of
8.73.times.10.sup.10 PFU/ml was incubated in the presence of SDS at
a final concentration of 0.1% and proteinase K at a final
concentration of 0.2 mg/ml at 37 C for 1 hour. The DNA was purified
by affinity to silica gel. Adenoviral DNAs corresponding to
10.sup.3, 10.sup.4, 105 or 10.sup.6 PFU prepared by diluting the
purified DNA with sterile water were used. The reaction was carried
out as follows. Briefly, 10 .mu.l of a reaction system containing
60 pmol each of the primers E1A-1 and E1A-2 (chain length to be
amplified: 112 bp) or E1A-1 and E1A-3 (chain length to be
amplified: 91 bp), 2 .mu.l of 0.05% propylenediamine and the
template was heat-denature at 98 C for 2 minutes and then rapidly
cooled on ice to anneal the primers to the template.
[0875] After annealing, 40 .mu.l of a mixture containing 0.625 mM
each of dNTPs, 42.5 mM Tricine-potassium hydroxide buffer (pH 8.5),
5.0 mM magnesium acetate, 0.0125% bovine serum albumin, 1.25%
dimethyl sulfoxide, 30 U of E. coli RNase H and 5.5 U of BcaBEST
DNA polymerase was added to the mixture to make the final volume to
50 .mu.l. The reaction mixtures were incubated at 60 C for 1 hour.
As a control, a detection by a PCR was carried out using the same
template as the above and primers constructed for PCR-amplifying
E1A (tumor gene), E1A-1P (sense), E1A-2P (antisense) and E1A-3P
(antisense) having nucleotide sequences represented by SEQ ID
NOS:196, 197 and 231. The PCR was carried out as follows. Brief ly,
50 .mu.l of a PCR solution containing 60 pmol each of the primers
E1A-1P and E1A-2P (chain length to be amplified: 112 bp) or E1A-1P
and E1A-3P (chain length to be amplified: 91 bp), 5 .mu.l of
10.times.Ex Taq buffer (Takara Shuzo), 1.25 U of TaKaRa Ex Taq DNA
polymerase (Takara Shuzo) and 0.2 mM each of dNTPs was prepared.
The conditions for the PCR were as follows: 30 cycles of 94 C for
30 seconds, 55 C for 30 seconds and 72 C for 30 seconds.
[0876] After reaction, 3 .mu.l each of the reaction mixtures of the
ICAN and the PCR was subjected to electrophoresis on 3.0% agarose
gel. The results are shown in FIG. 20 and Table 12. FIG. 20 shows
the results of the detection of viral E1A gene from adenoviral
particles. Lanes 1 to 10 show the results obtained using the
combination of the primers E1A-1 and E1A-2. Lanes 11 to 20 show the
results obtained using the combination of the primers E1A-1 and
E1A-3. Lane 1: molecular weight marker (100 bp ladder); lane 2:
ICAN using DNA corresponding to 10.sup.6 PFU; lane 3: ICAN using
DNA corresponding to 10.sup.5 PFU; lane 4: ICAN using DNA
corresponding to 104 PFU; lane 5: ICAN using DNA corresponding to
10.sup.3 PFU; lane 6: molecular weight marker (100 bp ladder); lane
7: PCR using DNA corresponding to 10.sup.6 PFU; lane 8: PCR using
DNA corresponding to 10.sup.5 PFU; lane 9: PCR using DNA
corresponding to 10.sup.4 PFU; and lane 10: PCR using DNA
corresponding to 10.sup.3 PFU. In addition, lane 11: molecular
weight marker (100 bp ladder); lane 12: ICAN using DNA
corresponding to 10.sup.6 PFU; lane 13: ICAN using DNA
corresponding to 10.sup.5 PFU; lane 14: ICAN using DNA
corresponding to 10.sup.4 PFU; lane 15: ICAN using DNA
corresponding to 10.sup.3 PFU; lane 16: molecular weight marker
(100 bp ladder); lane 17: PCR using DNA corresponding to 10.sup.6
PFU; lane 18: PCR using DNA corresponding to 10.sup.5 PFU; lane 19:
PCR using DNA corresponding to 104 PFU; and lane 20: PCR using DNA
corresponding to 10.sup.3 PFU.
12TABLE 12 Amplification size Detection limit (bp) ICAN PCR 112
10.sup.4 10.sup.4 91 10.sup.4 10.sup.4
[0877] As shown in FIG. 20 and Table 12, it was confirmed that the
detection sensitivity for the detection of adenovirus E1A gene by
the ICAN was equivalent to that by the PCR.
Example 36
[0878] Detection of an integrated viral gene from cells infected
with a retrovirus vector was examined. Cells infected with a
retrovirus and a genomic DNA were prepared as follows. Briefly, a
vector plasmid pDON-AI (Takara Shuzo) was introduced into packaging
cells GPE+86 according to the calcium phosphate method. An
ecotropic vector was prepared from the culture supernatant of the
introduced cells. Cells infected with a virus vector were prepared
by infecting NIH/3T3 cells with the ecotropic vector and culturing
the infected cells for 14 days in a medium containing G418. 27
.mu.g of a genomic DNA was obtained according to a conventional
method from 4.times.10.sup.4 of the prepared cells infected with
the retrovirus. The primers pDON-AI-1 and pDON-AI-2 as described in
Example 31(1) were used as primers. The reaction was carried out as
follows. Briefly, 10 .mu.l of a reaction system containing 60 pmol
each of the primers, 2 .mu.l of a 0.25% aqueous solution of
propylenediamine and 0.1 ng to 1000 ng of the genomic DNA as a
template was heated at 98 C for 2 minutes and then at 60 C in a
thermal cycler (Takara Shuzo) to anneal the primers to the
template.
[0879] After annealing, 40 .mu.l of a reaction mixture containing
0.625 mM each of dNTPs, 40 mM HEPES-potassium hydroxide buffer (pH
7.8), 125 mM potassium acetate, 5 mM magnesium acetate, 0.0125%
bovine serum albumin, 1.25% dimethyl sulfoxide, 30 U of E. coli
RNase H and 5.5 U of BcaBEST DNA polymerase was added to the
mixture to make the final volume to 50 .mu.l. The reaction mixtures
were incubated at 60 C for 1 hour in a thermal cycler. After
reaction, 5 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel. In addition, a PCR was carried
out using primers pDON-AI-3 and pDON-AI-4 represented by SEQ ID
NOS:200 and 201 in order to compare the sensitivities of detecting
a DNA by the ICAN and the PCR. The PCR was carried out as follows.
50 .mu.l of a reaction mixture containing 0.1 ng to 100 ng of the
template, 60 pmol each of the primers, 5 .mu.l of 10.times.Ex Taq
buffer, 1.25 U of TaKaRa Ex Taq polymerase and 0.2 mM each of dNTPs
was prepared. The mixtures were subjected to reactions using
Thermal Cycler Personal as follows: 35 cycles of 94 C for 30
seconds, 55 C for 30 seconds and 72 C for 30 seconds. After
reaction, 5 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel. The results are shown in FIG.
21. FIG. 21 shows the results of the detection of an integrated
viral gene from cells infected with a retrovirus vector according
to the ICAN and the PCR. Lane 1: molecular weight marker (100 bp
ladder); lane 2: 1000 ng of the template; lane 3: 100 ng of the
template; lane 4: 10 ng of the template; lane 5: 1 ng of the
template; and lane 6: 0.1 ng of the template.
[0880] As shown in FIG. 21, the amplification products of interest
were observed for the ICAN using 1 ng of the template DNA and for
the PCR of 35 cycles using 1 ng of the template.
Example 37
[0881] A method for detecting a target nucleic acid in which the
amplification method of the present invention and a hybridization
method were combined was examined for the detection of Escherichia
coli O-157 vero toxin I gene. Vero toxin I gene from
enterohemorrhagic Escherichia coli O-157 was selected as a target.
The template DNA was prepared as described in Example 21(1). A
region of about 80 bp having a GC content of about 40% was selected
as a region to be amplified. Primers VT1-IF4 and VT1-IR1 having
nucleotide sequences represented by SEQ ID NOS:202 and 203 were
used as primers. The reaction was carried out as follows. Briefly,
5 .mu.l of a mixture containing 60 pmol each of the primers VT1-IF4
and VT1-IR1, propylenediamine at a final concentration of 0.01%,
one of hot water-extracts corresponding to 0 to 10.sup.5 cells and
sterile water was prepared. The mixtures were heat-denatured at 98
C for 2 minutes, rapidly cooled to 55 C and incubated at the
temperature for 1 minute in Thermal Cycler Personal, and then
placed on ice for annealing.
[0882] After annealing, at final concentrations, 20 mM
HEPES-potassium hydroxide buffer (pH 7.8), 100 mM potassium
acetate, 1% dimethyl sulfoxide, 0.01% bovine serum albumin, 4 mM
magnesium acetate, 500 .mu.M each of dNTPs, 15 U of E. coli RNase H
and 2.75 U of BcaBEST DNA polymerase were added to the mixture to
make the final volume to 25 .mu.l with sterile water. The reaction
mixtures were placed in Thermal Cycler Personal which had been set
at 55 C and incubated at the temperature for 60 minutes. As a
control, a PCR for the hot water-extract was carried out using
O-157 Typing Set (Takara Shuzo) according to the manual in Thermal
Cycler Personal. The PCR was carried out as follows: 35 cycles of
94 C for 1 minute, 55 C for 1 minute and 72 C for 1 minute. The
total time required for the reaction was about 145 minutes. The
expected size of the amplification product was 349 bp. After
reaction, 3 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3% NuSieve 3:1 agarose. The results for the ICAN
are shown in FIG. 22. FIG. 22 shows the results of the detection of
O-157 vero toxin I gene. Lane M: molecular weight marker (50-2000
bp); lane N: sterile water as template; lane 1: the template
corresponding to 1 cell; lane 2: the template corresponding to 10
cells; lane 3: the template corresponding to 10.sup.2 cells; and
lane 4: the template corresponding to 10.sup.3 cells. Furthermore,
the results of the detection by the ICAN and the PCR are shown in
Table 13.
13 TABLE 13 Number of Escherichia coli O-157 cells 0 1 10 ICAN - +
+++ PCR - + ++ -: no amplification; + to +++ indicate the degree of
amplification in three grades.
[0883] As shown in Table 13, the amplification products of interest
were obtained for the reaction systems in which the hot
water-extract corresponding to 1 cell was used for both of the ICAN
and the PCR. Furthermore, dot blot hybridization for the
amplification products was carried out using an oligonucleotide
probe VT1 having a nucleotide sequence represented by SEQ ID NO:204
labeled with biotin at the 5'-terminus. The hybridization was
carried out as described in Example 32. The results were consistent
with those obtained by the electrophoresis. Thus, it was confirmed
that the detection sensitivities of the ICAN and the PCR were
equivalent. In addition, the total time required for the
amplification reaction using the ICAN of the present invention was
1/2 or shorter as compared with that required for the PCR. Thus,
the ICAN of the present invention was confirmed to be effective as
a method for detecting a pathogenic bacterium and the like.
Example 38
[0884] A method for detecting a gene for botulinum toxin type A was
examined. A DNA prepared from Clostridium botulinum, a strain from
a food poisoning case, type A-190 was used as a template. This
strain is preserved in Department of Hygiene, Kagawa Nutrition
University. Primers BotA S2 and BotA A2 having nucleotide sequences
represented by SEQ IOD NOS:205 and 206 were synthesized as primers
for detection. The expected size of the amplification product
obtained using the primer pair was about 150 bp. Solutions
containing 100 fg, 1 pg, 10 pg or 100 pg of the DNA from type A
toxin-producing Clostridium botulinum in 1 .mu.l of sterile water
to be used as templates were prepared. The reaction was carried out
as follows.
[0885] 10 .mu.l of a mixture containing 50 pmol each of the
primers, propylenediamine at a final concentration of 0.01% and 1
.mu.l of one of the DNA solutions as a template was prepared. The
mixtures were subjected to the ICAN using the composition of the
reaction mixture and the reaction conditions as described in
Example 32. As a control, a PCR was carried out in using a primer
set for detecting botulinum toxin type A gene, BAS-1 and BAS-2
(Takara Shuzo), according to the manual in Thermal Cycler Personal.
The expected size of the amplification product was 284 bp.
[0886] After reaction, 3 .mu.l each of the reaction mixtures was
subjected to electrophoresis on 4% NuSieve 3:1 agarose. The results
are shown in FIG. 23A. FIG. 23A shows the results of the detection
of the gene for botulinum toxin type A according to the ICAN and
the PCR. Lane M1: molecular weight marker (100 bp ladder); lane M2:
molecular weight marker (50-2000 bp marker); lane 1: no template;
lane 2: 100 fg of the template; lane 3: 10 pg of the template; and
lane 4: 100 pg of the template.
[0887] As shown in FIG. 23A, the amplification product of interest
was observed for the reaction in which 100 fg of the template DNA
was used according to the ICAN. On the other hand, the
amplification product of interest was not observed for the reaction
in which 100 fg of the template DNA was used according to the PCR.
Furthermore, dot blot hybridization for the reaction products was
carried out using BotA probe having a nucleotide sequence
represented by SEQ ID NO:207. Dot blot hybridization was carried
out as described in Example 22. The results are shown in FIG. 23B.
As shown in FIG. 23B, the signals were observed using 100 fg of the
template for the ICAN and 10 pg of the template for the PCR,
respectively. These results were consistent with those of the
electrophoresis.
Example 39
[0888] Detection of chrysanthemum viroid was examined. 10-fold
serial dilutions of low molecular weight RNA obtained according to
the method for extracting low molecular weight RNAs from
chrysanthemum infected with chrysanthemum stunt viroid (CSVd) as
described in Example 1 of JP-A 9-140383 were prepared. A reverse
transcription reaction was carried out using RNA PCR kit (AMW) ver
2.1 (Takara Shuzo). Specifically, 20 .mu.l of a reaction mixture
for reverse transcription containing 1.times.RNA PCR Buffer, 5 mM
MgCl.sub.2, 1 mM each of dNTPs, 20 U of RNase Inhibitor, 5 U of AMV
Reverse Transcriptase XL, 50 pmol of Random 9mers, 1 .mu.l of one
of the serial dilutions of the RNA was prepared. The mixtures were
warmed at 30 C for 10 minutes, reacted at 55 C for 30 minutes and
then heated at 99 C for 5 minutes for inactivating the reverse
transcriptase. After cooling, the ICAN was carried out. 1 .mu.l of
the reverse transcription reaction mixture was used as a template
for 50 .mu.l of a reaction mixture for the ICAN. Primers CSVD-F4
and CSVD-R3 having nucleotide sequences represented by SEQ ID
NOS:208 and 209 were used as primers in this Example. The reaction
was carried out as described in Example 32 except that reaction
temperature was 60 C and that Thermal Cycler MP was used. After
reaction, 3 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3% NuSieve 3:1 agarose.
[0889] On the other hand, PCR amplification was carried out in a
reaction system of 50 .mu.l using 1 .mu.l of the same reverse
transcription reaction mixture as a template. Primers F94 and R264
represented by SEQ ID NOS:198 and 199 were used as primers. The
reaction was carried out as follows. Briefly, a reaction mixture
was prepared using TaKaRa PCR Amplification kit according to the
protocol. 10 pmol each of the primers and 1 .mu.l of one of the
reverse transcription reaction mixture were added thereto to make
the total volume to 50 .mu.l. An amplification reaction was carried
out using Thermal Cycler MP. The reaction was carried out as
follows: 30 cycles of 94 C for 30 seconds, 55 C for 30 seconds and
72 C for 30 seconds. After reaction, 5 .mu.l each of the reaction
mixtures was subjected to electrophoresis on 3% NuSieve 3:1
agarose. The results are shown in Table 14.
14 TABLE 14 Dilution rate of RNA as template 10.sup.2 10.sup.3
RT-ICAN ++ + RT-PCR + - -: not amplified; +: amplified; ++:
amplified well.
[0890] As shown in Table 14, the amplification product was observed
for the reaction in which the 10.sup.3-fold-diluted RNA sample was
used as a template according to the ICAN. On the other hand, the
amplification product was observed for the reaction in which the
10.sup.2-fold-diluted RNA sample was used as a template according
to the PCR.
[0891] Furthermore, the ICAN-amplified products and the
PCR-amplified products were confirmed to be the products of
interest by dot blot hybridization. Dot blot hybridization was
carried out using CSVD probe having a nucleotide sequence
represented by SEQ ID NO:210 labeled with biotin at the
5'-terminus. Hybridization was carried out as described in Example
22. The results were consistent with those of the electrophoresis.
The signals were observed using the 10.sup.3-fold-diluted RNA
sample for the ICAN and the 10.sup.2-fold-diluted RNA sample for
the PCR, respectively, demonstrating that the ICAN was more
sensitive than the PCR.
Example 40
[0892] Detection of a viroid gene from chrysanthemum infected with
chrysanthemum dwarfing viroid (CSVd) using Pfu RNase H was
examined. 60 .mu.l of a mixture containing 3 .mu.l of one of the
10-fold serial dilutions of the RNA as prepared in Example 39, 10
mM tris-hydrochloride buffer (pH 8.3), 50 mM potassium chloride, 5
mM magnesium chloride, 1 mM each of dNTPs, 150 pmol of Random
6mers, 60 U of Ribonuclease Inhibitor (Takara Shuzo) and 15 U of
Reverse Transcriptase XL (AMV) (Takara Shuzo) was incubated at 30 C
for 10 minutes and at 42 C for 1 hour and then heated at 99 C for 5
minutes for inactivating the enzyme using a thermal cycler (GeneAmp
PCR System 9600, Applied Biosystems) to prepare a cDNA. Primers
Vd1, Vd2, Vd3 and Vd4 represented by SEQ ID NOS:211 to 214 were
synthesized based on the nucleotide sequence of the mRNA for the
viroid.
[0893] 50 .mu.l of a mixture containing 50 pmol each of the primers
Vd1 and Vd2, 1 .mu.l of the cDNA solution synthesized as described
above, a 10-, 100-, 1000- or 10000-fold dilution thereof with water
or water for a negative control as a template, 0.5 mM each of
dNTPs, 32 mM HEPES-potassium hydroxide buffer (pH 7.8), 100 mM
potassium acetate, 4.0 mM magnesium acetate, 0.01% bovine serum
albumin, 1% dimethyl sulfoxide, 0.0156 .mu.g of Pfu RNase H and 1 U
of BcaBEST DNA polymerase was incubated at 57 C for 1 hour in a
thermal cycler. The reacted samples were stored by freezing at -20
C until being analyzed.
[0894] A PCR was carried out as a control. Briefly, 50 .mu.l of a
reaction system containing 50 pmol each of the primers Vd3 and Vd4,
1 .mu.l of the cDNA solution, a 10-, 100-, 1000- or 10000-fold
dilution thereof with water or water for a negative control, 5
.mu.l of 10.times.Ex Taq buffer, 1.25 U of TaKaRa Ex Taq polymerase
and 0.2 mM each of dNTPs was subjected to a reaction in a thermal
cycler. The program was as follows: 1 cycle of 94 C for 2 minute;
35 cycles of 94 C for 30 seconds, 55 C for 30 seconds and 72 C for
30 seconds; and 1 cycle of 72 C for 5 minutes. The reacted samples
were stored by freezing at -20 C until being analyzed.
[0895] 5 .mu.l each of the reaction mixtures of the ICAN and the
PCR was subjected to electrophoresis on 3.0% agarose gel. The
results are shown in FIG. 24. FIG. 24 shows the results of the
detection of a viroid according to the ICAN using Pfu RNase H and
the PCR. Lane 1: 100 bp DNA ladder marker; lane 2: negative
control; lane 3: 10000-fold dilution of the cDNA; lane 4: 1000-fold
dilution of the cDNA; lane 5: 100-fold dilution of the cDNA; lane
6: 10-fold dilution of the cDNA; and lane 7: the original solution
of the cDNA.
[0896] As shown in FIG. 24, the amplification products of interest
were observed using the 100-fold dilution of the cDNA for both of
the ICAN and the PCR.
Example 41
[0897] Detection of K-ras gene was examined.
[0898] (1) Detection from Genomic DNA
[0899] Primers c-Ki-ras-1 and c-Ki-ras-2 represented by SEQ ID
NOS:215 and 216 were constructed based on the nucleotide sequence
of human c-Ki-ras.
[0900] 10 .mu.l of a mixture containing 60 pmol each of the
primers, 2 .mu.l of a 0.25% aqueous solution of propylenediamine
and 1 ng to 100 ng of human genomic DNA (Clontech) as a template
was prepared. The mixtures were heated at 98 C for 2 minutes and
then 53 C in Thermal Cycler Personal to anneal the primers to the
template.
[0901] After annealing, 40 .mu.l of a reaction mixture containing
0.625 mM each of dNTPs, 40 mM HEPES-potassium hydroxide buffer (pH
7.8), 125 mM potassium acetate, 5 mM magnesium acetate, 0.0125%
bovine serum albumin, 1.25% dimethyl sulfoxide, 30 U of E. coli
RNase H and 5.5 U of BcaBEST DNA polymerase was added to the
mixture to make the final volume to 50 .mu.l. The reaction mixtures
were incubated at 53 C for 1 hour. After reaction, 5 .mu.l each of
the reaction mixtures was subjected to electrophoresis on 3.0%
agarose gel.
[0902] On the other hand, a PCR was carried out as a control.
Primers c-Ki-ras-3 and c-Ki-ras-4 represented by SEQ ID NOS:217 and
218 were used as primers. 50 .mu.l of a solution containing 60 pmol
each of the primers, 0.1 ng to 100 ng of the template, 5 .mu.l of
10.times.Ex Taq buffer, 1.25 U of TaKaRa Ex Taq polymerase and 0.2
mM each of dNTPs was prepared. The mixtures were subjected to
reactions using Thermal Cycler Personal as follows: 30 or 35 cycles
of 94 C for 30 seconds, 55 C for 30 seconds and 72 C for 30
seconds. After reaction, 5 .mu.l each of the reaction mixtures was
subjected to electrophoresis on 3.0% agarose gel. The results are
shown in FIG. 25. FIG. 25 shows the results of the detection of
c-Ki-ras gene from human genomic DNA according to the ICAN and the
PCR. For the ICAN, lane 1: molecular weight marker; lane 2: 100 ng
of the template; lane 3: 10 ng of the template; lane 4: 1 ng of the
template; and lane 5: no template. For the PCR, lane 1: 100 ng of
the template; lane 2: 10 ng of the template; lane 3: 1 ng of the
template; and lane 4: no template.
[0903] As shown in FIG. 25, the amplification products of interest
were observed using 1 ng of the template for the ICAN and 10 ng of
the template for the PCR of 30 cycles. The comparative results for
the amounts of the amplification products obtained by the ICAN and
the PCR using 1 ng to 100 ng of the template are shown in FIG. 30.
As shown in FIG. 30, it was confirmed that the amount of the
amplification product obtained by the ICAN was greater than that by
the PCR.
[0904] (2) Detection from Blood Sample
[0905] Genomic DNAs were prepared using Dr. GenTLE.TM. (for Whole
Blood) (Takara Shuzo) from 100 .mu.l each of blood samples
collected from a healthy individual using sodium citrate or heparin
as an anticoagulating agent. Detection of c-Ki-ras gene by the ICAN
was carried out as described in (1) above using the prepared DNA
corresponding to 0.04 to 5 .mu.l of the blood. Furthermore,
detection by PCR using the DNA from 0.04 to 5 .mu.l of the blood
sample was carried out as described in (1) above in order to
compare the sensitivities for detecting a DNA by the ICAN and the
PCR. The results are shown in FIG. 26. FIG. 26 shows the results of
the detection of c-Ki-ras gene from blood samples according to the
ICAN and the PCR. For the ICAN, lane 1: molecular weight marker;
lane 2: 5 .mu.l of citrated blood; lane 3: 1 .mu.l of citrated
blood; lane 4: 0.2 .mu.l of citrated blood; lane 5: 0.04 .mu.l of
citrated blood; lane 6: 5 .mu.l of heparinized blood; lane 7: 1
.mu.l of heparinized blood; lane 8: 0.2 .mu.l of heparinized blood;
and lane 9: 0.04 .mu.l of heparinized blood. For the PCR, lane 1:
molecular weight marker; lane 2: 5 .mu.l of citrated blood, 30
cycles; lane 3: 1 .mu.l of citrated blood, 30 cycles; lane 4: 0.2
.mu.l of citrated blood, 30 cycles; lane 5: 0.04 .mu.l of citrated
blood, 30 cycles; lane 6: 5 .mu.l of citrated blood, 35 cycles;
lane 7: 1 .mu.l of citrated blood, 35 cycles; lane 8: 0.2 .mu.l of
citrated blood, 35 cycles; lane 9: 0.04 .mu.l of citrated blood, 35
cycles; lane 10: 5 .mu.l of heparinized blood, 30 cycles; lane 11:
1 .mu.l of heparinized blood, 30 cycles; lane 12: 0.2 .mu.l of
heparinized blood, 30 cycles; lane 13: 0.04 .mu.l of heparinized
blood, 30 cycles; lane 14: 5 .mu.l of heparinized blood, 35 cycles;
lane 15: 1 .mu.l of heparinized blood, 35 cycles; lane 16: 0.2
.mu.l of heparinized blood, 35 cycles; and lane 17: 0.04 .mu.l of
heparinized blood, 35 cycles.
[0906] As shown in FIG. 26, the amplification products of interest
were observed using the genomic DNA corresponding to 0.2 .mu.l of
either of the blood samples for the ICAN, and the genomic DNA
corresponding to 0.2 .mu.l of either of the blood samples (citrated
or heparinized) for the PCR of 30 cycles, respectively.
Example 42
[0907] Detection of Escherichia coli O-157 vero toxin 2 (VT-2) gene
using Bca RNase HIII was examined. Enterohemorrhagic Escherichia
coli O-157 was cultured in mEC medium containing novobiocin at 42 C
for 18 hours, and then heated at 95 C for 10 minutes. Dilutions
corresponding to 0, 1, 10, 10.sup.2 or 10.sup.3 cells in sterile
water were prepared and used as templates. Primers VT-2 IF4 and
VT-2 IR3 having nucleotide sequences represented by SEQ ID NOS:219
and 220 were synthesized as primers for detection. The expected
size of the amplification product obtained using the primer pair
was about 146 bp. The reaction was carried out as follows. Briefly,
10 .mu.l of a mixture containing 50 pmol each of the primers,
propylenediamine at a final concentration of 0.01% and one of the
hot water-extracts was prepared. The mixtures were heated at 98 C
for 2 minutes and incubated at 55 C for 1 minute in Thermal Cycler
Personal, and then placed on ice. At final concentrations, 34 mM
Tricine buffer (pH 8.7), 10 mM potassium chloride, 10 mM ammonium
sulfate, 1% dimethyl sulfoxide, 0.01% bovine serum albumin, 4 mM
magnesium acetate, 500 .mu.M each of dNTPs, 32 U of Bca RNase HIII
as prepared in Referential Example 3(5) and 5.5 U of BcaBEST DNA
polymerase were added to the mixture to make the final volume to 50
.mu.l. The reaction mixtures were placed in a thermal cycler which
had been set at 55 C and reacted at the temperature for 60 minutes.
After reaction, 3 .mu.l each of the reaction mixtures was subjected
to electrophoresis on 4% NuSieve 3:1 agarose. The results are shown
in FIG. 27. FIG. 27 shows the results of the detection of
Escherichia coli O-157 vero toxin II (VT2) gene using Bca RNase
HIII. Lane M: molecular weight marker (100 bp ladder); lane N:
sterile water as template; lane 1: the template corresponding to 1
cell; lane 2: the template corresponding to 10 cells; lane 3: the
template corresponding to 10.sup.2 cells; and lane 4: the template
corresponding to 10.sup.3 cells.
[0908] As shown in FIG. 27, VT2 gene was detected using the hot
water-extract corresponding to 1 cell according to the ICAN. These
results were equivalent to those of the detection reactions
according to the ICAN using E. coli RNase H and the PCR as
described in Example 22. Thus, it was confirmed that the ICAN using
a heat-resistant RNase H, Bca RNase HIII, was also effective in
detecting a virus, a bacterium and the like.
Example 43
[0909] Detection of Staphylococcus aureus enterotoxin A gene was
examined. Primers SEA-1 and SEA-2 represented by SEQ ID NOS:225 and
226 were synthesized based on the nucleotide sequence of the
enterotoxin A gene region of Staphylococcus aureus. 50 .mu.l of a
reaction mixture containing 1 .mu.l of a solution containing 115 pg
or 1.15 ng of a genomic DNA from Staphylococcus aureus (ATCC
accession no. 13565) or 1 .mu.l of water for a negative control, 50
pmol each of the primers, 0.5 mM each of dNTPs, 32 mM
HEPES-potassium hydroxide buffer (pH 7.8), 100 mM potassium
acetate, 4.0 mM magnesium acetate, 0.01% bovine serum albumin, 1.0%
dimethyl sulfoxide, 0.0156 pg of Pfu RNase H and 1 U of BcaBEST DNA
polymerase was incubated at 58 C for 1 hour in a thermal cycler.
After reaction, 5 .mu.l each of the reaction mixtures was analyzed
by electrophoresis on 3.0% agarose gel. The results are shown in
FIG. 29. FIG. 29 shows the results of electrophoresis for the
detection of Staphylococcus aureus enterotoxin A gene. Lane 1:
molecular weight marker (100 bp ladder); lane 2: negative control
(sterile water); lane 3: 115 pg of the template; and lane 4: 1.15
ng of the template.
[0910] As shown in FIG. 29, the amplification product of interest
was observed using about 1.15 ng of the template.
Example 44
[0911] Detection of hepatitis C virus (HCV) was examined. Primers
HCV-F3 and HCV-R1 having nucleotide sequences represented by SEQ ID
NOS:227 and 228 were synthesized based on the nucleotide sequence
of HCV. A template DNA was prepared as follows. Briefly, 4 .mu.l of
a mixture containing RNA prepared as described in Example 34 from
100 .mu.l of a serum from a healthy individual or a patient with
HCV, 10 mM tris-hydrochloride buffer (pH 8.3), 5 mM MgCl.sub.2, 1
mM each of dNTPs, 10 pmol of Random 6mers primer and 10 U of
Reverse Transcriptase XL (Takara Shuzo) was incubated at 30 C for
10 minutes and at 42 C for 1 hour and then heated at 99 C for 5
minutes for inactivating the enzyme using a thermal cycler (Gene
Amp PCR System 9600, Applied Biosystems) to prepare a cDNA.
[0912] An ICAN was carried out at 55 C for 1 hour as described in
Example 26 except that 1 .mu.l of the cDNA reaction mixture and 100
pmol each of the primers HCV-F3 and HCV-R1 were used. After
reaction, 2.5 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel. The results are shown in FIG.
31. FIG. 31 shows the results of electrophoresis for the detection
of hepatitis C virus. Lane 1: molecular weight marker (100 bp);
lane 2: the template prepared from a serum from a healthy
individual; and lanes 3 to 6: the templates prepared from sera from
patients infected with HCV.
[0913] As shown in FIG. 31, it was confirmed that HCV could be
specifically detected from the serum samples from patients infected
with HCV.
Example 45
[0914] The amplification method of the present invention was
examined.
[0915] (1) A PCR was carried out using the pUC19-150 plasmid DNA as
prepared in Example 15(2) as a template and primers MCS-F and MCS-R
represented by SEQ ID NOS:124 and 125. A PCR-amplified fragment of
534 bp was obtained by purifying the reaction mixture using
Microcon-100 (Millipore). A reaction mixture containing 15 ng of
the PCR fragment and 30 pmol of a primer MR1 having a nucleotide
sequence represented by SEQ ID NO:229 labeled with
[.gamma.-.sup.32P]ATP by phosphorylation at the 5'-terminus and
sterile distilled water to 5 .mu.l and a reaction mixture further
containing 30 pmol of a primer MR2 having a nucleotide sequence
represented by SEQ ID NO:230 were prepared. The reaction mixtures
were heat-denatured at 98 C for 2 minutes and then cooled to 55 C.
20 .mu.l of a reaction mixture (42.5 mM Tricine buffer (pH 8.7),
12.5 mM potassium chloride, 12.5 mM ammonium sulfate, 0.0125% BSA,
1.25% DMSO, 5 mM magnesium acetate, 0.625 mM each of dNTPs)
containing 1 U of BcaBEST DNA polymerase was added to the reaction
mixture. The resulting mixture was reacted at 55 C for 15 minutes.
After reaction, 2.5 .mu.l of a reaction termination solution (95%
formamide, 20 mM EDTA, 0.05% Bromophenol Blue, 0.5% xylene cyanol)
was added to 5 .mu.l of the reaction mixture. The mixture was
heat-denatured at 94 C for 3 minutes. 1.6 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 6%
polyacrylamide gel containing 8 M urea and the signals were read
using BAS2000 (Fujix) to detect products extended from the primer
MR1. The results are shown in FIG. 32A. The sequence ladder in FIG.
32A was prepared by sequencing M13 mp18 single strand DNA (Takara
Shuzo) using the primer MF2 labeled with [.gamma.-.sup.32P]ATP by
phosphorylation and used for the determination of the length of the
extension product. Lane 1: a combination of the primers MF2 and
MR1; and lane 2: MR1.
[0916] As shown in FIG. 32A, a band of 448 bp extended from the
primer MR1 to the end of the template was detected when the
extension reaction was carried out by adding only the primer MR1 to
the template. On the other hand, a band of 373 bp bounded by the
primers MR1 and MF2 was detected in addition to the above-mentioned
band by further adding the primer MF2. Thus, it was confirmed that
the extension from the MR1 primer using the PCR-amplified fragment
as a template by the action of BcaBEST DNA polymerase was switched
due to template switching to the extension using a strand extended
from the primer MF2 as a template. Furthermore, template switching
was observed when Klenow DNA polymerase was used as a mesophilic
DNA polymerase having a strand displacement activity under similar
conditions. On the other hand, template switching was not observed
when TaKaRa Taq DNA polymerase (Takara Shuzo) or PyroBEST DNA
polymerase (Takara Shuzo) without a strand displacement activity
was used.
[0917] (2) The template switching reaction was examined using a
template DNA strand with a primer being annealed thereto. DNA
fragments to which the primers MF2 and MR1 could be annealed were
prepared as follows. PCRs were carried out using the plasmid pUC19
as a template and primers MCSF and RV (Takara Shuzo) or primers M4
(Takara Shuzo) and MCSR. The reaction mixtures were purified using
Microcon-100 to obtain PCR-amplified fragments MSCF-RV (236 bp) and
M4-MCSR (271 bp). The region bounded by the primers M4 and RV was
commonly present in the two PCR-amplified fragments.
[0918] Next, a template-primer (1) in which template DNA strands
with primers being annealed thereto were not annealed each other,
and a template-primer (2) in which template DNA strands with
primers being annealed thereto were annealed each other were
prepared as follows.
[0919] (1) A reaction mixture containing 30 ng of the fragment
MCSF-RV, 40 pmol of the primer MF2 labeled with
[.gamma.-.sup.32P]ATP by phosphorylation at the 5'-terminus,
propylenediamine at a final concentration of 0.01% and sterile
distilled water to 5 .mu.l, and a mixture containing 30 ng of the
fragment M4-MCSR, 40 pmol of the primer MR1, propylenediamine at a
final concentration of 0.01% and sterile distilled water to 5 .mu.l
were separately heat-denatured at 98 C for 2 minutes and then
cooled to 55 C. 2.5 .mu.l each of the reaction mixtures were mixed
together to prepare a template-primer.
[0920] (2) A reaction mixture containing 15 ng of the fragment
MCSF-RV, 15 ng of the fragment M4-MCSR, 20 pmol of the primer MF2
labeled with [.gamma.-.sup.32P]ATP by phosphorylation at the
5'-terminus, 20 pmol of the primer MR1, propylenediamine at a final
concentration of 0.01% and sterile distilled water to 5 .mu.l was
heat-denatured at 98 C for 2 minutes and then cooled to 55 C to
prepare a template-primer.
[0921] 20 .mu.l of a reaction mixture (42.5 mM Tricine buffer (pH
8.7), 12.5 mM potassium chloride, 12.5 mM ammonium sulfate, 0.0125%
BSA, 1.25% DMSO, 5 mM magnesium acetate, 0.625 mM each of dNTPs)
containing 1 U of BcaBEST DNA polymerase was added to 5 .mu.l of
the template-primer reaction mixture. The resulting mixture was
reacted at 55 C for 15 minutes. After reaction, 2.5 .mu.l of a
reaction termination solution (95% formamide, 20 mM EDTA, 0.05%
Bromophenol Blue, 0.5% xylene cyanol) was added to 5 .mu.l of the
reaction mixture. The mixture was heat-denatured at 94 C for 3
minutes. 1.6 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 6% polyacrylamide gel containing 8 M urea and
the signals were read using BAS2000 (Fujix) to detect products
extended from the primer MF2. The results are shown in FIG. 32B.
The sequence ladder in FIG. 32B was prepared by sequencing M13 mp18
single strand DNA using the primer MR1 labeled with
[.gamma.-.sup.32P]ATP by phosphorylation and used for the
determination of the length of the extension product. Lane 1:
template DNA strands not being annealed each other; and lane 2:
template DNA strands being annealed each other.
[0922] As shown in FIG. 32B, only a band of 161 bp extended from
the primer MF2 to the end of the template was detected for the
template-primer in which template DNA strands with primers being
annealed thereto were not annealed each other. On the other hand, a
band of 223 bp bounded by the primers MF2 and MR1 in addition to
the above-mentioned band was detected for the template-primer in
which template DNA strands with primers being annealed thereto were
annealed each other. Thus, it was confirmed that a template
switching reaction took place if template DNA strands with primers
being annealed thereto were annealed each other.
Example 46
[0923] (1) Detection of Mycobacterium tuberculosis was examined
using the RNase H derived from Archaeoglobus fulgidus (Afu)
described in Referential Example 7. Primers MTIS2F (SEQ ID NO:244)
and MTIS2R (SEQ ID NO:245) were synthesized on the basis of the
nucleotide sequence of the Mycobacterium tuberculosis genome
registered in GenBank under accession number AL123456. The length
of the region bordered by the primer pair including the primer
portions is 103 bp. Mycobacterium tuberculosis genomic DNA as a
template was extracted from dried BCG vaccine (Nippon BCG Seizo)
according to a conventional method. Solutions containing 100 pg, 10
pg, 1 pg, 100 fg, 10 fg or 1 fg of the genomic DNA per .mu.l of
sterile water were prepared. Reactions were carried out as follows.
Briefly, at final concentrations, 32 mM HEPES-potassium hydroxide
buffer (pH 7.8), 100 mM potassium acetate, 1% DMSO, 0.01% BSA, 4 mM
magnesium acetate, 500 .mu.M each of dNTPs, 50 pmol each of the
primers MTIS2F and MTIS2R, 8.75 U of RNase H from Afu, 8 U of
BcaBEST DNA polymerase and 1 .mu.l of one of the templates were
mixed and the final volume was made to 50 .mu.l with sterile water.
The reaction mixtures were placed in Thermal Cycler Personal which
had been set at 60 C and incubated for 60 minutes. After reaction,
3 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel.
[0924] On the other hand, a PCR was carried out as a control.
Primers MTIS PCR-F and MTIS PCR-R as described in Rinsho Byori (the
Japanese Journal of Clinical Pathology), 43(9):941-947 (1995) were
used as primers. An amplification product of 276 bp is obtained
using the primer pair. A reaction mixture of 50 .mu.l was prepared
using 10 pmol each of the primers according to the instruction
manual attached to Ex Taq DNA polymerase (Takara Shuzo). The
reaction mixture was placed in Thermal Cycler and subjected to a
reaction of 40 cycles each cycle consisting of 94 C for 30 seconds,
50 C for 30 seconds and 72 C for 30 seconds. After reaction, 3
.mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel.
[0925] As a result, the amplification products of interest were
observed in either case using 100 fg of the template.
[0926] (2) Detection of Chlamydia trachomatis was examined using
RNase H from Afu or RNase H from Pyrococcus horikoshii (Pho).
Primers CT2F (SEQ ID NO:246) and CT2R (SEQ ID NO:247) were
synthesized on the basis of the nucleotide sequence of the
Chlamydia trachomatis plasmid registered in GenBank under accession
number X06707. The length of the region bordered by the primer pair
including the primer portions is 109 bp. A samples as a template
DNA was prepared by subjecting a clinical specimen obtained from a
patient agreed with the informed concent to phenol-chloroform
treatment and ethanol precipitation, and collecting a DNA.
Reactions were carried out as follows. Briefly, at final
concentrations, 32 mM HEPES-potassium hydroxide buffer (pH 7.8),
100 mM potassium acetate, 1% DMSO, 0.01% BSA, 4 mM magnesium
acetate, 500 .mu.M each of dNTPs, 50 pmol each of the primers CT2F
and CT2R, 46.4 U of RNase H from Pho or 8.75 U of RNase H from Afu,
8 U of BcaBEST DNA polymerase and 1 .mu.l of the sample were mixed
and the final volume was made to 50 .mu.l with sterile water. The
reaction mixtures were placed in Thermal Cycler Personal which had
been set at 55 C and incubated for 60 minutes. After reaction, 3
.mu.l each of the reaction mixtures was subjected to
electrophoresis on 3.0% agarose gel. As a result, the amplification
products of interest was observed. These results demonstrate that
Chlamydia trachomatis can be detected using RNase H from Afu or Pho
in the method of the present invention.
[0927] (3) Furthermore, detection using magnetic beads in a
commercially available detection instrument was examined. Briefly,
an amplification reaction was carried out as described in (1) above
using the primer MTIS2R used in (1) above labeled at its
5'-terminus with biotin as a primer and 100 ng of the Mycobacterium
tuberculosis genomic DNA as a template. The resulting amplified
fragment was diluted 30-fold, 300-fold or 3000-fold and subjected
to detection using streptoavidin-coated magnetic beads (Pierce) in
an automated detection instrument Lumipuls (Fujirebio). Magnetic
beads having streptoavidin capable of binding 100 pmol of biotin
being immobilized was reacted with the biotinylated amplified
fragment for 5 minutes on the first layer of a cuvette. 0.1 N NaOH
was then added thereto. Hybridization with a FITC-labeled probe
MTISBF was carried out for 5 minutes. After washing, a POD-labeled
anti-FITC antibody was added thereto. After reacting for 5 minutes
and washing, a luminescent substrate was added thereto. As a
result, it was shown that detection can be carried out
semi-quantitatively in a short time (20 minutes) using magnetic
beads in a conventional automated detection instrument. The
detection was carried out by measuring the luminescence level by
photocounting. The results are shown in Table 15.
15 TABLE 15 Mycobacterium tuberculosis amplicon Photocounting S/N
ratio .times.30 3.55 .times. 10.sup.7 29.6 .times.300 1.21 .times.
10.sup.7 10.0 .times.3000 0.21 .times. 10.sup.7 1.75 0 0.12 .times.
10.sup.7 --
[0928] The results in Table 15 demonstrate that detection can be
carried out with sensitivity equivalent to that of the conventional
plate luminescence method.
[0929] (4) A hybrid chromatography method was examined as a method
for detecting the above-mentioned amplified fragment. Streptoavidin
(Nacalai Tesque) was immobilized onto a nitrocellulose membrane. A
water-absorptive pad was connected therewith to construct a hybrid
chromatography strip. This strip was used to detect the amplified
fragment used in (3) above according to a hybrid chromatography
method. Detection was carried out by color development using 1-step
TMB-Blotting (Pierce). Specifically, a reaction mixture containing
the amplified fragment was developed on the nitrocellulose
membrane. Then, 0.1 N NaOH solution, FITC-labeled probe, washing
solution and color development solution were developed in this
order. As a result, a blue band was detected for the amplified
fragment derived from a Mycobacterium tuberculosis-positive sample.
It was demonstrated that this method is useful as a rapid gene
examination method because, using this method, results are obtained
with naked eyes in 5 to 10 minutes by the method of the present
invention.
Example 47
[0930] (1) Southern Hybridization Analysis of Amplified Products
Containing Laddered Bands
[0931] In some cases, plural high molecular weight laddered bands
other than three bands of interest may be observed in the
amplification method of the present invention. The laddered bands
were examined. Enterohemorrhagic E. coli O-157 was selected as a
target. A template DNA, chimeric primers and reaction conditions
for ICAN were as described in Example 22. After reaction, 5 .mu.l
of the reaction mixture was subjected to electrophoresis on 3%
NuSieve 3:1 agarose gel. The results are shown in FIG. 37. In FIG.
37, the lanes represent results for the following: lane M: 100 bp
DNA ladder marker; lane 1: negative control; lane 2: the heated
extract corresponding to 1 cell; lane 3: the heated extract
corresponding to 10 cells; lane 4: the heated extract corresponding
to 10.sup.2 cells; lane 5: the heated extract corresponding to
10.sup.3 cells; lane 6: the heated extract corresponding to
10.sup.4 cells; and lane 7: the heated extract corresponding to
10.sup.5 cells. Ladder bands were observed as shown in FIG. 37.
[0932] (2) Analysis of Laddered Amplified Fragments
[0933] The nucleotide sequences of the laddered bands obtained in
(1) above were analyzed. Briefly, 50 .mu.l of the reaction mixture
prepared in (1) was subjected to electrophoresis on 3% agarose gel.
After electrophoresis, the laddered bands were excised from the
gel. The amplified DNA fragments were then recovered from the gel
using EASYTRAP Ver.2 (Takara Shuzo). The recovered amplified
fragments were blunt-ended using DNA Blunting kit (Takara
Shuzo).
[0934] The blunt-ended DNA fragments were ligated with a vector
pGEM-3Z (Promega) digested with a restriction enzyme HincII (Takara
Shuzo) using DNA ligation Kit (Takara Shuzo). The ligation mixtures
were used to transform competent cells of JM109 (Takara Shuzo).
After transformatin, the cells were cultured on LB agar plate
containing 0.1 mM ampicillin, 1 mM IPTG and 0.02% X-gal at 37 C
overnight.
[0935] After cultivation, several white colonies were selected from
the plates. Colony PCRs were carried out using primers M13-M4 and
M13-RV (both from Takara Shuzo) to determine the presence of an
insert. Colonies having inserts were cultured with shaking in LB
liquid medium containing 0.1 mM ampicillin at 37 C overnight. After
cultivation, plasmids were purified from cells using QIAGEN plasmid
mini Kit (Qiagen). The sequences of fragments cloned at the HincII
sites of the plasmids were analyzed in both directions using
primers M13-M4 and M13-RV according to a conventional method.
[0936] As a result, it was demonstrated that the laddered fragment
obtained by the method of the present invention has a structure in
which the region to be amplified is repeated. Furthermore, it was
confirmed that the repetition is in the same direction from 5' to
3'.
[0937] (3) The laddered amplified fragments other than three
amplified fragments of interest formed in the method of the present
invention for detecting Mycobacterium tuberculosis, HCV or
Chlamydia trachomatis were examined. HCV was detected under
conditions as described in Example 44. Mycobacterium tuberculosis
or Chlamydia trachomatis was detected under conditions as described
in Example 46. The resulting laddered amplified fragments were
subcloned and sequenced as described in (2) above. As a result, it
was demonstrated that the laddered fragment obtained by the method
of the present invention has a structure in which the region to be
amplified is repeated. Furthermore, it was confirmed that the
repetition is in the same direction from 5' to 3'.
Example 48
[0938] (1) The detection method of the present invention for
Mycobacterium tuberculosis was examined. First, primers
K-F-1033(60) (SEQ ID NO:248) and K-F-1133(62) (SEQ ID NO:249) were
synthesized for amplifying a region with relatively low GC content
in the Mycobacterium tuberculosis genome. Serial dilutions
containing 100 fg to 10 pg of the Mycobacterium tuberculosis
genomic DNA as described in Example 46(1) were used as templates.
The reaction was carried our as follows. Briefly, at final
concentrations, 32 mM HEPES-potassium hydroxide buffer (pH 7.8),
100 mM potassium acetate, 1% DMSO, 0.01% BSA, 4 mM magnesium
acetate, 500 .mu.M each of dNTPs, 50 pmol each of the primers
K-F-1033(60) and K-F-1133(62), 9.375 U of RNase HII from Pfu or
4.375 U of RNase H from Afu, 2.75 U of BcaBEST DNA polymerase and 1
.mu.l of one of the templates were mixed and the final volume was
made to 25 .mu.l with sterile water. The reaction mixtures were
placed in Thermal Cycler Personal which had been set at 62 C and
incubated for 60 minutes. After reaction, 3 .mu.l each of the
reaction mixtures was subjected to electrophoresis on 3.0% agarose
gel. As a result, it was demonstrated that the amplification
products could be detected using 100 fg to 10 pg of the genomic DNA
as a template and either RNase H.
[0939] (2) The method as described in (1) above was examined using
primers having higher Tm values. First, primers K-F-1033(68) (SEQ
ID NO:250) and K-F-1133(68) (SEQ ID NO:251) were synthesized. The
amplification reaction was carried out under the same conditions as
those described in (1) above except that the reaction temperature
was 63 C. After reaction, 3 .mu.l each of the reaction mixtures was
subjected to electrophoresis on 3.0% agarose gel. The results are
shown in FIG. 38. FIG. 38 illustrates results of electrophoresis of
Mycobacterium tuberculosis genome amplified using RNase H from Pfu
or RNase H from Afu. Lanes 1 to 4 represent results obtained using
RNase HII from Pfu and the following amount of template DNA: lane
1: 10 pg; lane 2: 1 pg; lane 3: 100 fg; and lane 4: negative
control. Lanes 5 to 8 represent results obtained using RNase HII
from Afu and the following amount of template DNA: lane 5: 10 pg;
lane 6: 1 pg; lane 7: 100 fg; and lane 8: negative control. Lane M
represents 100 bp DNA ladder marker.
[0940] As shown in FIG. 38, it was demonstrated that the
amplification fragment of interest could be detected using 100 fg
of the template DNA and either RNase H. It was shown that more
amplification product is obtained when RNase H from Afu is used. In
addition, it was shown that more stable detection sensitivity is
accomplished when RNase H from Afu is used.
[0941] (3) Amplification using a combination of the primers
K-F-1033(68) and K-F-1133(68) and a plasmid containing a region to
be amplified as a template was examined. First, primers F26 (SEQ ID
NO:252) and R1310 (SEQ ID NO:253) were synthesized in order to
prepare a plasmid containing a region to be amplified. A PCR was
carried out using these primers and BCG vaccine strain. The
resulting amplification product was then introduced into pT7-Blue-T
vector (Takara Shuzo) to prepare the plasmid. The composition of
the reaction mixture was las described in (2) above except that 4 U
of Bca DNA polymerase was used. As a result, it was confirmed that
detection can be carried out using 1 fg of the template.
[0942] (4) The detection sensitivity accomplished when a
combination of primers MTIS2F and MTIS2R, which results in the
formation of laddered amplified fragments containing the three
amplified fragments of interest, was used was compared with that
accomplished when a combination of primers K-F-1033(68) and
K-F-1133(68), which results in the three amplified fragments of
interest, was used. Mycobacterium tuberculosis was selected as a
target. Reactions were carried out as described in Example 46(2)
when the combination of the primers MTIS2F and MTIS2R was used or
in (2) above when the combination of the primers K-F-1033(68) and
K-F-1133(68) was used. As a result, the same detection sensitivity
was observed in either case.
Example 49
[0943] The amplification method of the present invention that does
not comprise denaturation of a genomic DNA as a template was
examined.
[0944] (1) Primers pDON-AI-68-1 (SEQ ID NO:254) and pDON-AI-68-2
(SEQ ID NO:255) were synthesized in accordance with the nucleotide
sequence of the packaging region in a plasmid pDON-AI (Takara
Shuzo).
[0945] (2) A reaction mixture of a total volume of 50 .mu.l
containing 1 .mu.l of a solution containing 10 fg or 1 pg of
pDON-AI, 1 .mu.l of a solution containing 1 ng, 10 ng or 100 ng of
the genomic DNA derived from NIH/3T3 cells having pDON-AI being
incorporated prepared in Example 36, or 1 p.sup.1 of water as a
negative control, 50 pmol each of the primers as described in (1)
above, 0.5 mM each of dNTPs, 32 mM HEPES-potassium hydroxide buffer
(pH 7.8), 100 mM potassium acetate, 4 mM magnesium acetate, 0.01%
BSA, 1% DMSO, 18.5 U of RNase HII from Pfu and 4 U of BcaBEST DNA
polymerase was prepared. The reaction mixtures were placed in
Thermal Cycler Personal and incubated at 64 C for 1 hour. After
reaction, 5 .mu.l each of the reaction mixtures was subjected to
electrophoresis on 3% agarose gel to observe amplification
products. The results are shown in FIG. 39. In FIG. 39, the lanes
represent results for the following templates: lane M: 100 bp DNA
ladder marker; lane 1: negative control; lane 2: 1 ng of genomic
DNA having pDON-AI being incorporated; lane 3: 10 ng of genomic DNA
having pDON-AI being incorporated; lane 4: 100 ng of genomic DNA
having pDON-AI being incorporated; lane 5: 10 fg of pDNA-AI DNA;
and lane 6: 1 pg of pDON-AI DNA.
[0946] As shown in FIG. 39, amplification of specific DNA fragments
was observed for either pDON-AI or the genomic DNA having pDON-AI
being incorporated. Thus, it was confirmed that a DNA fragment of
interest can be amplified without denaturing the DNA as a template
prior to the reaction even if a genomic DNA is used as a
template.
Example 50
[0947] The fidelity (accuracy) of the present invention was
compared with that of a PCR utilizing LA technology in which TaKaRa
Ex Taq polymerase (Takara Shuzo) was used. First, a plasmid as a
template was prepared as follows.
[0948] Specifically, the regions each consisting of 300 bp
represented by SEQ ID NOS:256 to 259 were amplified by PCR from
human proto-oncogene, Wnt-5a gene (GenBank accession no. L20861),
ribosomal protein S5 gene (GenBank accession no. XM.sub.--009371),
human NADH gene (GenBank accession no. NM.sub.--000903) and human
protocadherin 43 gene (GenBank accession no. AU077347). In this
case, the PCRs were carried out using specific primers each having
a site for a restriction enzyme SfiI at the 5'-terminus of the
primer. After reaction, the amplified fragments were digested with
a restriction enzyme SfiI (Takara Shuzo). pUC19 (Takara Shuzo) was
digested with restriction enzymes AflIII (NEB) and NdeI (Takara
Shuzo) and subjected to agarose gel electrophoresis. A fragment of
about 2 kbp was excised from the gel and recovered using EASYTRAP
(Takara Shuzo). A DNA having the sequence of SEQ ID NO:260 and a
DNA complementary thereto were synthesized using a DNA synthesizer.
These DNAs were heat-denatured and then annealed each other to form
a double-stranded DNA. This double-stranded DNA has cohesive ends
for restriction enzymes AflIII and NdeI at its termini. The
double-stranded synthetic DNA was inserted into the fragment
obtained by digesting pUC19 with restriction enzymes AflIII and
NdeI using DNA Ligation kit ver. 2 (Takara Shuzo). The resulting
plasmid was designated as pIC62. pIC62 has sequences to which
primers ICAN2 (SEQ ID NO:261) and ICAN6 (SEQ ID NO:262) anneal as
well as a site for a restriction enzyme SfiI. The plasmid pIC62 was
digested with the restriction enzyme SfiI. The above-mentioned
PCR-amplified fragment digested with the restriction enzyme SfiI
was ligated with the plasmid using Ligation kit ver. 2 (Takara
Shuzo). The ligation mixture was used to transform Escherichia coli
JM109 (Takara Shuzo). The resulting transformants were cultured,
plasmids having the about 300-bp DNAs being inserted were obtained,
and the sequences of the inserted DNAs were determined. The
plasmids were then used as templates in this Example.
[0949] (2) ICAN amplification products were prepared as follows.
Briefly, a solution of 10 .mu.l containing 10 ng of one of the
plasmids as a template, 50 pmol each of chimeric primers ICAN2 (SEQ
ID NO:261) and ICAN6 (SEQ ID NO:262) and 0.01% propylenediamine was
prepared. The solution was denatured at 98 C for 2 minutes and
incubated at 60 C for 1 minute in Thermal Cycler Personal, and then
transferred onto ice. Next, at final concentrations, 20 mM
HEPES-potassium hydroxide buffer (pH 7.8), 100 mM potassium
acetate, 1% DMSO, 0.01% BSA, 4 mM magnesium acetate, 500 .mu.M each
of dNTPs, 30 U of RNase H from E. coli and 5.5 U of BcaBEST DNA
polymerase were added thereto and the final volume was made to 50
.mu.l with sterile water. The reaction mixtures were placed in
Thermal Cycler Personal which had been set at 60 C and incubated
for 60 minutes. After reaction, the reaction mixtures were
subjected to electrophoresis on 2% SeaKem GTG agarose gel (Takara
Shuzo). After electrophoresis, bands for the amplification products
of interest were recovered by excision from the agarose gel,
recovery using SUPREC-10 (Takara Shuzo), treatment with
phenol-chloroform and ethanol precipitation.
[0950] (3) PCR amplification products were prepared as follows
using TaKaRa Ex Taq DNA polymerase. Briefly, a reaction mixture was
prepared using 10 ng of the above-mentioned plasmid as a template
as well as 10 pmol each of DNA primers ICAN2 (SEQ ID NO:263) and
ICAN6 (SEQ ID NO:264) according to the instruction manual attached
to TaKaRa Ex Taq DNA polymerase (Takara Shuzo). The reaction
mixture was placed in Thermal Cycler and subjected to a reaction of
30 cycles, each cycle consisting of 94 C for 30 seconds, 55 C for
30 seconds and 72 C for 30 seconds. After reaction, the reaction
mixture was subjected to agarose gel electrophoresis as described
in (2) above. The amplification products of interest were recovered
by excision from the agarose gel, recovery using Microcon-100
(Takara Shuzo), treatment with phenol-chloroform and ethanol
precipitation.
[0951] (4) The amplification products obtained in (2) and (3) above
were subcloned as follows. Briefly, the ICAN amplification products
and the PCR amplification products were introduced into a vector
pT7 Blue (Takara Shuzo) using Perfectly Blunt Cloning kit (Takara
Shuzo) according to the instruction manual. The ligation mixture
was used to transform NovaBlue Singles Competent Cell (Takara
Shuzo). For each clone, 10 colonies were selected from the
resulting transformants and cultured to obtain plasmids each having
about 0.4-kb DNA being inserted. The fragments inserted in the
plasmids were sequenced using T7 promoter primer (Takara Shuzo) and
M3 primer (Takara Shuzo).
[0952] A total of about 16,000 bases were analyzed by sequencing as
described above. As a result, one mutation was found in about
25,000 bases for both of the fragments amplified according to the
method of the present invention and the fragments amplified by PCR
using TaKaRa Ex Taq DNA polymerase. Thus, it was confirmed that the
fidelity (accuracy) of the method of the present invention is
equivalent to that of LA-PCR whose fidelity is high.
Example 51
[0953] (1) Preparation of Template for ICAN Reaction by PCR
[0954] A double-stranded cDNA was prepared from polyA+ RNA derived
from mouse brain (OriGene) using cDNA synthesis kit (Takara Shuzo).
PCR fragments were amplified using the double-stranded cDNA as a
template and combinations of the primers having nucleotide
sequences of SEQ ID NOS:265-278. The fragments were introduced into
pT7 Blue T-vector (Takara Shuzo) by TA cloning to obtain plasmid
clones. A reaction mixture of total volume of 50 .mu.l containing 1
.mu.l (1 ng) of one the plasmid clones, 10 pmol each of primers
MCS-F (SEQ ID NO:279) and MCS-R (SEQ ID NO:280), 1.25 U of Ex Taq
(Takara Shuzo), 5 .mu.l of 10.times.Ex Taq buffer (Takara Shuzo)
and 0.2 mM each of dNTPs was subjected to the following reaction
using TaKaRa PCR Thermal Cycler Personal (Takara Shuzo): 94 C for 2
minutes; 30 cycles of 94 C for 30 seconds, 55 C for 30 seconds and
72 C for 1 minute. The resulting amplified DNA fragment was used as
a template for an ICAN reaction.
[0955] (2) Amplification of DNA Fragment by ICAN Using PCR Product
as Template
[0956] An ICAN reaction was carried out using Aminoallyl dUTP
(Sigma) in order to introduce an amino group into an ICAN
amplification product. The ratio of amino group introduced into an
ICAN amplification product was examined by changing the ratio of
the amount of dTTP to the amount of Aminoallyl dUTP in the ICAN
reaction as follows: 10:0, 9:1, 8:2, 7:3 and 6:4. The reaction was
carried out as follows.
[0957] First, a solution of total volume of 10 .mu.l containing 1
.mu.l of the PCR reaction mixture prepared in (1) above, 50 pmol
each of primers MF2N3(24) (SEQ ID NO:281) and MR1N3(24) (SEQ ID
NO:282) and 2 .mu.l of 0.05% aqueous solution of propylenediamine
was heated at 98 C for 2 minutes followed by 65 C for 30 seconds in
TaKaRa PCR Thermal Cycler Personal and rapidly cooled on ice to
anneal the primers to the template. A reaction mixture of total
volume of 40 .mu.l containing 0.625 mM each of DATP, dCTP and dGTP,
0.625 mM of a dTTP+Aminoallyl dUTP mixture, 32 mM HEPES-potassium
hydroxide buffer (pH 7.8), 5.0 mM magnesium acetate, 0.6 U of RNase
H from E. coli (Takara Shuzo) and 2.75 U of BcaBEST DNA polymerase
was added to the heated solution. The resulting mixture was
incubated in Thermal Cycler at 65 C for 1 hour.
[0958] 50 .mu.l of isopropanol and 5 .mu.l of 3 M sodium acetate
solution (pH 5.2) were added to the reaction mixture of 50 .mu.l.
The resulting mixture was cooled at -80 C for 20 minutes and then
centrifuged to remove a supernatant. 200 .mu.l of 70% ethanol
solution was added thereto. The supernatant was removed by
centrifugation. The precipitate was air-dried. The resulting DNA
was re-dissolve in water. OD.sub.260/280 was measured to determined
the amount of the product.
[0959] (3) Confirmation of Introduction of Aminoallyl dUTP into
ICAN Amplification Product
[0960] Introduction of an amino group into an ICAN product was
confirmed by fluorescence-label the amino group in the ICAN product
using 5-carboxyfluorecein succinimidil ester (Molecular Probe). The
above-mentioned DNA solution was diluted to make the concentration
to 2 .mu.g/50 .mu.l. 20 .mu.l of 1 M sodium carbonate buffer (pH
9.0) was added thereto. Then, 4 .mu.l of a solution of FITC
(Nacalai Tesque) in N,N-dimethylformamide at a concentration of 10
mM was further added. The resulting mixture was reacted at 20 C for
16 hours. After removing excess FITC using a commercially available
spin column, 10 .mu.l of the reaction mixture was applied onto 2.0%
agarose gel and electrophoresed. After electrophoresis, fluorescent
dye was detected using FM-BIO. Furthermore, the ICAN-amplified
fragment was detected by staining with EtBr. As a result, it was
confirmed that an amino group can be introduced into an ICAN
amplification product by conducting an ICAN using Aminoallyl dUTP.
It was also confirmed that the detection sensitivity can be further
increased by using a modified nucleotide having a functional group
and fluorescent label for an amplification product in
combination.
[0961] (4) The amplification method of the present invention was
examined using deoxyUTP. Mycobacterium tuberculosis was selected as
a target. First, primers MTIS2F-16 (SEQ ID NO:283) and MTIS2R-ACC
(SEQ ID NO:284) were synthesized in accordance with the nucleotide
sequence of Mycobacterium tuberculosis genome registered in GenBank
under accession no. AL123456. The length of the region to be
amplified using this primer pair including the primer portions is
98 bp. A template was prepared as follows. Briefly, a product
obtained by PCR-amplifying the Mycobacterium tuberculosis genome
using primers MTIS-PCR-F-2 (SEQ ID NO:285) and MTIS-PCR-R-2 (SEQ ID
NO:286) was inserted into pT7 Blue T-Vector (Takara Shuzo) using
DNA Ligation kit Ver. 2. The ligated plasmid was used to transform
Escherichia coli JM109. The resulting transformants were cultured
to obtain a plasmid having an about 400-bp DNA being introduced. A
solution containing 10.sup.3 copies of the plasmid per .mu.l was
prepared based on the concentration determined by measuring
OD260.
[0962] At final concentrations, 32 mM HEPES-potassium hydroxide
buffer (pH 7.8), 100 mM potassium acetate, 1% DMSO, 0.01% BSA, 4 mM
magnesium acetate, 500 .mu.M each of DATP, dCTP, dGTP and a
dTTP/dUTP mixture (500/0, 400/100, 300/200, 200/300, 100/400 or
0/500 .mu.M), 50 pmol each of the primers MTIS 2F-16 and MTIS
2R-AAC, 8.75 U of RNase H from Afu, 8 U of BcaBEST DNA polymerase
and 1 .mu.l of the template (10.sup.3 copies) were mixed and the
final volume was made to 50 .mu.l with sterile water. The reaction
mixtures were placed in Thermal Cycler Personal which had been set
at 60 C and incubated for 60 minutes. After reaction, 3 .mu.l each
of the reaction mixtures was subjected to electrophoresis on 3%
agarose gel.
[0963] As a result, the amplification product of interest was
observed for each of the dTTP/dUTP ratios. Based on these results,
it was confirmed that a modified nucleotide can be used as a
substrate in the method of the present invention.
Example 52
[0964] Application of the method of the present invention to a
one-step amplification method was examined. HCV was selected as a
target.
[0965] (1) Preparation of Transcript RNA
[0966] A transcript RNA as a template was prepared. At first, HCV
RNA was prepared from 300 .mu.l of a serum derived from a patient
with hepatitis C virus agreed with the informed concent using
TRIzol reagent (Life Technologies) according to the instructions
attached to the reagent and finally dissolved in 20 .mu.l of
injectable water (Otsuka Pharmaceutical) to obtain an RNA sample.
An RT-PCR was carried out using the RNA sample above as a template.
The reaction was carried out as follows. A reaction mixture of 50
.mu.l was prepared using 2 .mu.l of the RNA sample and 20 pmol each
of primers SP6--HCV-F (SEQ ID NO:287) and T7-HCV-R (SEQ ID NO:288)
according to a manual attached to One-Step RNA PCR kit (Takara
Shuzo). The reaction mixture was placed in Thermal Cycler Personal
and subjected to the following reaction: 50 C for 15 minutes; 94 C
for 2 minutes; and 40 cycles of 94 C for 30 seconds, 60 C for 30
seconds and 72 C for 30 seconds. After reaction, the reaction
mixture was subjected to electrophoresis on 2% SeaPlaque GTG
agarose gel. A 350-bp amplification product of interest was excised
from the gel. The DNA was then recovered using EASYTRAP Ver. 2
according to the instructions attached to the kit. A transcript RNA
was synthesized using the recovered DNA as a template and
Competitive RNA Transcription kit (Takara Shuzo) according to the
instructions attached to the kit. The transcript RNA was used as a
template for examination of a one-step RT-ICAN.
[0967] (2) Examination of One-Step RT-ICAN
[0968] The concentration of the transcript RNA prepared in (1)
above was determined based on the OD.sub.260 value and dilutions
containing 10.sup.4, 10.sup.5, 10.sup.6 or 10.sup.7 copies per
.mu.l were prepared. A reaction mixture of 50 .mu.l was prepared by
adding thereto, at final concentrations, 32 mM HEPES-potassium
hydroxide buffer (pH 7.8), 100 mM potassium acetate, 1% DMSO, 0.01%
BSA, 4 mM magnesium acetate, 500 .mu.M each of dNTPs, 50 pmol each
of the primers HCV-A S (SEQ ID NO:289) and HCV-A A (SEQ ID NO:290),
30 U of RNase H from Pfu, 8 U of BcaBEST DNA polymerase, 20 U of
RNase inhibitor, 0, 1, 2.5, 3 or 5 U of AMV RTase XL (Takara Shuzo)
and 1 .mu.l of one of the dilutions containing varying copies of
the transcript RNA. The reaction mixtures were placed in Thermal
Cycler Personal which had been set at 60 C and incubated for 60
minutes. After reaction, 2 .mu.l each of the reaction mixtures was
subjected to electrophoresis on 3% agarose gel.
[0969] As a result, no amplification product of interest was
observed using each of the dilutions of the template when AMV RTase
was not added. On the other hand, the amplification product of
interest was observed using the dilution containing 10.sup.7 copies
(1 U of AMV RTase XL added), 10.sup.6 copies (2.5 U of AMV RTase XL
added), 10.sup.6 copies (3 U of AMV RTase XL added) or 10.sup.6
copies (5 U of AMV RTase XL added). When the reaction was carried
out at a temperature of 57 C, the amplification product of interest
was observed using the dilution containing 10.sup.5 copies and 2.5
U of AMV RTase XL. Furthermore, when 1 U of BcaBEST DNA polymenrase
and 10 U of RNase H from Pfu were used, the amplification product
of interest was observed using the dilution containing 10.sup.6
copies even if no AMV RTase was added.
[0970] Sequence Listing Free Text
[0971] SEQ ID No:1: Synthetic DNA corresponding to a portion of
human transferrin receptor-encoding sequence used as a template
[0972] SEQ ID NO:2: Designed oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence
[0973] SEQ ID NO:3: Designed oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence
[0974] SEQ ID No:4: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotide 21 is ribonucleotide--other nucleotides are
deoxyribonucleotides"
[0975] SEQ ID No:5: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotide 21 is ribonucleotide--other nucleotides are
deoxyribonucleotides"
[0976] SEQ ID No:6: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotide 22 is ribonucleotide--other nucleotides are
deoxyribonucleotides"
[0977] SEQ ID No:7: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotide 22 is ribonucleotide--other nucleotides are
deoxyribonucleotides"
[0978] SEQ ID No:8: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0979] SEQ ID No:9: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0980] SEQ ID No:10: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 19 to 20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0981] SEQ ID No: 11: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 19 to 20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0982] SEQ ID No:12: Designed oligonucleotide used as a probe for
detecting an amplified portion of human transferrin
receptor-encoding sequence
[0983] SEQ ID No: 13: Designed chimeric oligonucleotide primer
designated as pUC19 upper(2)NN to amplify a portion of plasmid
PUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[0984] SEQ ID No: 14: Designed chimeric oligonucleotide primer
designated as pUC19 lower NN to amplify a portion of plasmid pUC19.
"nucleotides 24 to 25 are ribonucleotides-other nucleotides are
deoxyribonucleotides"
[0985] SEQ ID No:15: Designed chimeric oligonucleotide primer to
amplify a portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[0986] SEQ ID No:16: Designed chimeric oligonucleotide primer
designated as pUC19 lower 542 to amplify a portion of plasmid
PUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[0987] SEQ ID No:17: Designed chimeric oligonucleotide primer to
amplify a portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[0988] SEQ ID No:18: Designed oligonucleotide primer designated as
pUC19 upper 150 to amplify a portion of plasmid pUC19. "nucleotides
23 to 25 are ribonucleotides-other nucleotides are
deoxyribonucleotides"
[0989] SEQ ID No:19: Designed chimeric oligonucleotide primer
designated as pUC19 lower NN to amplify a portion of plasmid pUC19.
"nucleotides 23 to 25 are ribonucleotides-other nucleotides are
deoxyribonucleotides"
[0990] SEQ ID No:20: Designed chimeric oligonucleotide primer
designated as pUC19 upper 249 to amplify a portion of plasmid
PUC19. "nucleotides 23 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[0991] SEQ ID No: 21: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 20 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0992] SEQ ID No:22: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0993] SEQ ID No:23: Designed chimeric oligonucleotide primer
designated as pUC19 upper(2)NN to amplify a portion of plasmid
pUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[0994] SEQ ID No: 24: Designed chimeric oligonucleotide primer
designated as pUC19 upper(2)NN to amplify a portion of plasmid
pUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[0995] SEQ ID No:25: Designed chimeric oligonucleotide primer
designated as pUC19 upper(2)NN to amplify a portion of plasmid
pUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[0996] SEQ ID No:26: Designed chimeric oligonucleotide primer
designated as pUC19 upper(2)NN to amplify a portion of plasmid
PUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[0997] SEQ ID No:27: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0998] SEQ ID No:28: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[0999] SEQ ID No:29: Designed chimeric oligonucleotide primer
designated as MF2N3(24) to amplify a portion of plasmid pUC19-249
or plasmid pUC19-911. "nucleotides 22 to 24 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1000] SEQ ID No:30: Designed oligonucleotide primer designated as
MR1N3(24) to amplify a portion of plasmid pUC19-249 or plasmid
pUC19-911. "nucleotides 22 to 24 are ribonucleotides--other
nucleotides are deoxyribonucleotides"
[1001] SEQ ID No:31: Designed chimeric oligonucleotide primer
designated as pUC19 upper 249 to amplify a portion of plasmid
pUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[1002] SEQ ID No:32: Designed oligonucleotide primer designated as
pUC19 upper 150 to amplify a portion of plasmid pUC19
[1003] SEQ ID No:33: Designed oligonucleotide primer designated as
pUC19 upper 249 to amplify a portion of plasmid pUC19
[1004] SEQ ID No:34: Designed oligonucleotide primer designated as
pUC19 lower NN to amplify a portion of plasmid pUC19
[1005] SEQ ID No:35: Designed chimeric oligonucleotide primer to
amplify a portion of plasmid pUC19. "nucleotides 28 to 30 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1006] SEQ ID No:36: Designed chimeric oligonucleotide primer
designated as MR1N3 to amplify a portion of plasmid pUC19.
"nucleotides 28 to 30 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1007] SEQ ID No:37: Designed oligonucleotide primer to amplify a
portion of plasmid pUC19
[1008] SEQ ID No:38: Designed oligonucleotide primer designated as
MR1N3 to amplify a portion of plasmid pUC19
[1009] SEQ ID No:39: Synthetic RNA used as a probe for detecting an
amplified portion of plasmid pUC19
[1010] SEQ ID No:40: Designed chimeric oligonucleotide primer
designated as pUC19 upper 150 to amplify a portion of plasmid
pUC19. "nucleotides 24 to 25 are ribonucleotides--other nucleotides
are deoxyribonucleotides"
[1011] SEQ ID No:41: Designed chimeric oligonucleotide primer
designated as MR1N3 to amplify a portion of plasmid pUC19.
"nucleotides 28 to 30 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1012] SEQ ID No:42: Designed oligonucleotide primer designated as
M13M4
[1013] SEQ ID No:43: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 1-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 16 to 18 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1014] SEQ ID No:44: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 1-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 15 to 17 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1015] SEQ ID No:45: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 16 to 18 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1016] SEQ ID No:46: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 16 to 18 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1017] SEQ ID No:47: Designed oligonucleotide primer designated as
MCR-F to amplify a long DNA fragment
[1018] SEQ ID No:48: Designed oligonucleotide primer designated as
MCR-R to amplify a long DNA fragment
[1019] SEQ ID No:49: Designed chimeric oligonucleotide primer
designated as MF2N3(24) to amplify a long DNA fragment.
"nucleotides 22 to 24 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1020] SEQ ID No:50: Designed chimeric oligonucleotide primer
designated as MR1N3(24) to amplify a long DNA fragment.
"nucleotides 22 to 24 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1021] SEQ ID No:51: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1022] SEQ ID No:52: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1023] SEQ ID No:53: Designed chimeric oligonucleotide primer to
amplify a portion of bacteriophage lambda DNA. "nucleotides 16 to
17 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1024] SEQ ID No:54: Designed chimeric oligonucleotide primer to
amplify a portion of bacteriophage lambda DNA. "nucleotides 16 to
17 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1025] SEQ ID No:55: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1026] SEQ ID No:56: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1027] SEQ ID No:57: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1028] SEQ ID No:58: Designed oligonucleotide primer designated as
R1-S1 to amplify a portion of bacteriophage lambda DNA
[1029] SEQ ID No:59: Designed oligonucleotide primer designated as
R1-A3 to amplify a portion of bacteriophage lambda DNA
[1030] SEQ ID No:60: Designed oligonucleotide primer designated as
R2-S1 to amplify a portion of bacteriophage lambda DNA
[1031] SEQ ID No:61: Designed oligonucleotide primer designated as
R2-A3 to amplify a portion of bacteriophage lambda DNA
[1032] SEQ ID No:62: Designed oligonucleotide primer designated as
R3-S1 to amplify a portion of bacteriophage lambda DNA
[1033] SEQ ID No:63: Designed oligonucleotide primer designated as
R3-A3 to amplify a portion of bacteriophage lambda DNA
[1034] SEQ ID No:64: Designed chimeric oligonucleotide primer
designated as M13RV-2N 17mer. "nucleotides 16 to 17 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1035] SEQ ID No:65: Designed chimeric oligonucleotide primer
designated as M13RV-2N 20mer. "nucleotides 19 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1036] SEQ ID No:66: Designed oligonucleotide primer to amplify a
portion of CDC2-related protein kinase PISSLRE gene
[1037] SEQ ID No:67: Designed oligonucleotide primer to amplify a
portion of CDC2-related protein kinase PISSLRE gene
[1038] SEQ ID No:68: Designed oligonucleotide primer to amplify a
portion of Type II cytoskeltal 11 keratin gene
[1039] SEQ ID No:69: Designed oligonucleotide primer to amplify a
portion of Type II cytoskeltal 11 keratin gene
[1040] SEQ ID No:70: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1041] SEQ ID No:71: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1042] SEQ ID No:72: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1043] SEQ ID No:73: Designed oligonucleotide primer to amplify a
portion of bacteriophage lambda DNA
[1044] SEQ ID No:74: Designed oligonucleotide primer designated as
MF2N3(24) to amplify a portion of plasmid pUC19-249 or plasmid
pUC19-911
[1045] SEQ ID No:75: Designed oligonucleotide primer designated as
MR1N3(24) to amplify a portion of plasmid pUC19-249 or plasmid
pUC19-911
[1046] SEQ ID No:76: Designed chimeric oligonucleotide primer
designated as M13M4-3N 20mer. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1047] SEQ ID No:77: Designed chimeric oligonucleotide primer
designated as M13RV-3N 20mer. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1048] SEQ ID No:78: Designed chimeric oligonucleotide primer
designated as M13M4-3N 24mer. "nucleotides 22 to 24 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1049] SEQ ID No:79: Designed oligonucleotide primer designated as
M13RV-3N 24mer. "nucleotides 22 to 24 are ribonucleotides--other
nucleotides are deoxyribonucleotides"
[1050] SEQ ID No:80: Designed oligonucleotide primer designated as
5'ID to amplify a portion of cyclin A DNA
[1051] SEQ ID No:81: Designed oligonucleotide primer designated as
3'ID to amplify a portion of cyclin A DNA
[1052] SEQ ID No:82: Designed oligonucleotide primer designated as
M13RV-2N 16mer. "nucleotides 15 to 16 are ribonucleotides--other
nucleotides are deoxyribonucleotides"
[1053] SEQ ID No:83: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1054] SEQ ID No:84: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1055] SEQ ID No:85: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1056] SEQ ID No:86: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1057] SEQ ID No:87: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1058] SEQ ID No:88: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1059] SEQ ID No:89: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1060] SEQ ID No:90: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1061] SEQ ID No:91: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1062] SEQ ID No:92: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1063] SEQ ID No: 93: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1064] SEQ ID No:94: Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1065] SEQ ID No:95: Designed oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence
[1066] SEQ ID No:96: Designed oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence
[1067] SEQ ID NO:97: PCR primer BsuII-3 for cloning a gene encoding
a polypeptide having a RNaseHII activity from Bacillus
caldotenax.
[1068] SEQ ID NO:98: PCR primer BsuII-6 for cloning a gene encoding
a polypeptide having a RNaseHII activity from Bacillus
caldotenax.
[1069] SEQ ID NO:99: PCR primer RNII-S1 for cloning a gene encoding
a polypeptide having a RNaseHII activity from Bacillus
caldotenax.
[1070] SEQ ID NO:100: PCR primer RNII-S2 for cloning a gene
encoding a polypeptide having a RNaseHII activity from Bacillus
caldotenax.
[1071] SEQ ID NO:101: PCR primer RNII-S5 for cloning a gene
encoding a polypeptide having a RNaseHII activity from Bacillus
caldotenax.
[1072] SEQ ID NO:102: PCR primer RNII-S6 for cloning a gene
encoding a polypeptide having a RNaseHII activity from Bacillus
caldotenax.
[1073] SEQ ID NO:103: PCR primer RNII-Nde for cloning a gene
encoding a polypeptide having a RNaseHII activity from Bacillus
caldotenax.
[1074] SEQ ID NO:104: Nucleotide sequence of ORF in RNaseHII gene
from Bucillus caldotenax.
[1075] SEQ ID NO:105: Amino acid sequence of RNaseHII from Bucillus
caldotenax.
[1076] SEQ ID NO:106: PCR primer BsuIII-1 for cloning a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax.
[1077] SEQ ID NO:107: PCR primer BsuIII-3 for cloning a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax.
[1078] SEQ ID NO:108: PCR primer BsuIII-6 for cloning a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax.
[1079] SEQ ID NO:109: PCR primer BsuIII-8 for cloning a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax.
[1080] SEQ ID NO:110: PCR primer RNIII-S3 for cloning a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax.
[1081] SEQ ID NO:111: PCR primer BcaRNIII-3 for cloning a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax.
[1082] SEQ ID NO:112: Nucleotide sequence of ORF in RNaseHIII from
Bacillus caldotenax.
[1083] SEQ ID NO:113: Amino acid sequence of RNaseHIII from
Bacillus caldotenax.
[1084] SEQ ID NO:114: PCR primer BcaRNIIINde for amplifying a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax.
[1085] SEQ ID NO:115: Nucleotide sequence conserving between PH1650
and a portion of Pyrococcus furiosus genome sequence.
[1086] SEQ ID NO:116: PCR primer 1650Nde for cloning a gene
encoding a polypeptide having a RNaseHII activity from Pyrococcus
furiosus.
[1087] SEQ ID NO:117: PCR primer 1650Bam for cloning a gene
encoding a polypeptide having a RNaseHII activity from Pyrococcus
furiosus.
[1088] SEQ ID NO:118: Nucleotide sequence of ORF in RNaseHII from
Pyrococcus furiosus.
[1089] SEQ ID NO:119: Amino acid sequence of RNaseHII from
Pyrococcus furiosus.
[1090] SEQ ID NO:120: PCR primer 915-F1 for cloning a gene encoding
a polypeptide having a RNaseHII activity from Thermotoga
maritima.
[1091] SEQ ID NO:121: PCR primer 915-F2 for cloning a gene encoding
a polypeptide having a RNaseHII activity from Thermotoga
maritima.
[1092] SEQ ID NO:122: PCR primer 915-R1 for cloning a gene encoding
a polypeptide having a RNaseHII activity from Thermotoga
maritima.
[1093] SEQ ID NO:123: PCR primer 915-R2 for cloning a gene encoding
a polypeptide having a RNaseHII activity from Thermotoga
maritima.
[1094] SEQ ID NO:124: Designed oligonucleotide primer designated as
MCR-F to amplify a long DNA fragment
[1095] SEQ ID NO:125: Designed oligonucleotide primer designated as
MCR-R to amplify a long DNA fragment
[1096] SEQ ID NO:126: Designed chimeric oligonucleotide primer
designated as MF2N3(24) to amplify a long DNA fragment.
"nucleotides 22 to 24 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1097] SEQ ID NO:127: Designed chimeric oligonucleotide primer
designated as MR1N3(24) to amplify a long DNA fragment.
"nucleotides 22 to 24 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1098] SEQ ID NO:128: Designed oligonucleotide primer to amplify a
portion of lambda DNA. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1099] SEQ ID NO:129: Designed chimeric oligonucleotide primer to
amplify a portion of lambda DNA. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1100] SEQ ID NO:130: Designed oligonucleotide primer to amplify a
portion of lambda DNA
[1101] SEQ ID NO:131: Designed oligonucleotide primer to amplify a
portion of lambda DNA
[1102] SEQ ID NO:132: Designed chimeric oligonucleotide primer to
amplify a portion of Flavobacterium species DNA. "nucleotides 18 to
20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1103] SEQ ID NO:133: esigned chimeric oligonucleotide primer to
amplify a portion of Flavobacterium species DNA. "nucleotides 18 to
20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1104] SEQ ID NO:134: Designed oligonucleotide primer to amplify a
portion of Flavobacterium species DNA.
[1105] SEQ ID NO:135: Designed oligonucleotide primer to amplify a
portion of Flavobacterium species DNA.
[1106] SEQ ID NO:136: esigned chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1107] SEQ ID NO:137: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1108] SEQ ID NO:138: Designed oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157.
[1109] SEQ ID NO:139: Designed oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157.
[1110] SEQ ID NO:140: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1111] SEQ ID NO:141: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1112] SEQ ID NO:142: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1113] SEQ ID NO:143: Designed oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157.
[1114] SEQ ID NO:144: Designed oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157.
[1115] SEQ ID NO:145: Designed chimeric oligonucleotide primer to
amplify a portion of lambda DNA. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1116] SEQ ID NO:146: Designed oligonucleotide primer to amplify a
portion of viroid CSVd.
[1117] SEQ ID NO:147: Designed oligonucleotide primer to amplify a
portion of viroid CSVd.
[1118] SEQ ID NO:148: Designed chimeric oligonucleotide primer to
amplify a portion of viroid CSVd. "nucleotides 16 to 18 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1119] SEQ ID NO:149: Designed chimeric oligonucleotide primer to
amplify a portion of viroid CSVd. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1120] SEQ ID NO:150: Designed chimeric oligonucleotide primer to
amplify a portion of Flavobacterium species DNA. "nucleotides 18 to
20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1121] SEQ ID NO:151: Designed chimeric oligonucleotide primer to
amplify a portion of Flavobacterium species DNA. "nucleotides 18 to
20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1122] SEQ ID NO:152: Designed chimeric oligonucleotide primer to
amplify a portion of Flavobacterium species DNA. "nucleotides 18 to
20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1123] SEQ ID NO:153: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 19 to 21 are
ribonucleotides-nucloetide 18 is inosine--other nucleotides are
deoxyribonucleotides"
[1124] SEQ ID NO:154: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 19 to 21 are
ribonucleotides-nucleotide 17 is inosine other nucleotides are
deoxyribonucleotides"
[1125] SEQ ID NO:155: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 19 to 21 are
ribonucleotides-nucleotide 16 is inosine--other nucleotides are
deoxyribonucleotides"
[1126] SEQ ID NO:156: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-nucleotide 17 is inosine--other nucleotides are
deoxyribonucleotides"
[1127] SEQ ID NO:157: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-nucleotide 16 is inosine--other nucleotides are
deoxyribonucleotides"
[1128] SEQ ID NO:158: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-nucleotide 15 is inosine--other nucleotides are
deoxyribonucleotides"
[1129] SEQ ID NO:159: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 9 to 11 and 19 to
21 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1130] SEQ ID NO:160: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 8 to 10 and 18 to
20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1131] SEQ ID NO:161: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1132] SEQ ID NO:162: Designed oligonucleotide probe to detect a
DNA fragment amplifing a portion of vero toxin 2-encoding sequence
from hemorrhagic Escherichia coli O-157.
[1133] SEQ ID NO:163: Designed chimeric oligonucleotide primer to
amplify a portion of iNOS-encoding sequence from mouse.
"nucleotides 18 to 20 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1134] SEQ ID NO:164: Designed chimeric oligonucleotide primer to
amplify a portion of iNOS-encoding sequence from mouse.
"nucleotides 17 to 19 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1135] SEQ ID NO:165: Designed oligonucleotide primer to amplify a
portion of iNOS-encoding sequence from mouse.
[1136] SEQ ID NO:166: Designed oligonucleotide primer to amplify a
portion of iNOS-encoding sequence from mouse
[1137] SEQ ID NO:167: Designed oligonucleotide primer designated as
GMO-PCR-F 20mer
[1138] SEQ ID NO:168: Designed oligonucleotide primer designated as
GMO-PCR-R 20mer
[1139] SEQ ID NO:169: Designed chimeric oligonucleotide primer
designated as GMO-S1 20mer. "nucleotides 19 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1140] SEQ ID NO:170: Designed oligonucleotide primer designated as
GMO-S2 20mer. "nucleotides 19 to 20 are ribonucleotides--other
nucleotides are deoxyribonucleotides"
[1141] SEQ ID NO:171: Designed oligonucleotide primer designated as
GMO-A1 20mer. "nucleotides 19 to 20 are ribonucleotides--other
nucleotides are deoxyribonucleotides"
[1142] SEQ ID NO:172: Designed oligonucleotide primer designated as
GMO-A2 20 mer. "nucleotides 19 to 20 are ribonucleotides--other
nucleotides are deoxyribonucleotides"
[1143] SEQ ID NO:173: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
(alpha-thio)ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1144] SEQ ID NO:174: Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
(alpha-thio)ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1145] SEQ ID NO:175: Designed chimeric oligonucleotide primer to
amplify a portion of INOS-encoding sequence from mouse.
"nucleotides 20 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1146] SEQ ID NO:176: Designed chimeric oligonucleotide primer to
amplify a portion of INOS-encoding sequence from mouse.
"nucleotides 20 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1147] SEQ ID NO:177: Designed oligonucleotide primer to amplify a
portion of INOS-encoding sequence from mouse.
[1148] SEQ ID NO:178: Designed oligonucleotide primer to amplify a
portion of INOS-encoding sequence from mouse.
[1149] SEQ ID NO:179: Designed chimeric oligonucleotide primer to
amplify a portion of lambda DNA. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1150] SEQ ID NO:180: Designed chimeric oligonucleotide primer to
amplify a portion of lambda DNA. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1151] SEQ ID NO:181: Designed chimeric oligonucleotide primer to
amplify a portion of INOS-encoding sequence from mouse.
"nucleotides 21 to 23 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1152] SEQ ID NO:182: Designed chimeric oligonucleotide primer to
amplify a portion of INOS-encoding sequence from mouse.
"nucleotides 20 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1153] SEQ ID NO:183: Designed chimeric oligonucleotide primer to
amplify a portion of pDON-AI DNA. "nucleotides 17 to 19 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1154] SEQ ID NO:184: Designed chimeric oligonucleotide primer to
amplify a portion of pDON-AI DNA. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1155] SEQ ID NO:185: Designed chimeric oligonucleotide primer to
amplify a portion of HPV DNA. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1156] SEQ ID NO:186: Designed chimeric oligonucleotide primer to
amplify a portion of HPV DNA. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1157] SEQ ID NO:187: Designed oligonucleotide probe to detect a
DNA fragment amplifing a portion of HPV DNA.
[1158] SEQ ID NO:188: Designed oligonucleotide primer to amplify a
portion of HCV.
[1159] SEQ ID NO:189: Designed oligonucleotide primer to amplify a
portion of HCV.
[1160] SEQ ID NO:190: Designed chimeric oligonucleotide primer to
amplify a portion of HCV. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1161] SEQ ID NO:191: Designed chimeric oligonucleotide primer to
amplify a portion of HCV. "nucleotides 16 to 18 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1162] SEQ ID NO:192: Designed oligonucleotide probe to detect a
DNA fragment amplifing portion of HCV.
[1163] SEQ ID NO:193: Designed chimeric oligonucleotide primer to
amplify a portion of adenovirus. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1164] SEQ ID NO:194: Designed chimeric oligonucleotide primer to
amplify a portion of adenovirus. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1165] SEQ ID NO:195: Designed chimeric oligonucleotide primer to
amplify a portion of adenovirus. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1166] SEQ ID NO:196: Designed oligonucleotide primer to amplify a
portion of adenovirus
[1167] SEQ ID NO:197: Designed oligonucleotide primer to amplify a
portion of adenovirus.
[1168] SEQ ID NO:198: Designed oligonucleotide primer to amplify a
portion of viroid CSVd.
[1169] SEQ ID NO:199: Designed oligonucleotide primer to amplify a
portion of viroid CSVd.
[1170] SEQ ID NO:200: Designed oligonucleotide primer to amplify a
portion of pDON-AI DNA.
[1171] SEQ ID NO:201: Designed oligonucleotide primer to amplify a
portion of pDON-AI DNA.
[1172] SEQ ID NO:202: Designed chimeric oligonucleotide primer to
amplify a portion of verotoxin-1 encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1173] SEQ ID NO:203: Designed chimeric oligonucleotide primer to
amplify a portion of verotoxin-1 encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1174] SEQ ID NO:204: Designed oligonucleotide probe to detect a
DNA fragment amplifying a portion of verotoxin-1 encoding sequence
from hemorrhagic Escherichia coli O-157.
[1175] SEQ ID NO:205: Designed chimeric oligonucleotide primer to
amplify a portion of botulinum toxin A encoding sequence from
Clostridium botulinum. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1176] SEQ ID NO:206: Designed chimeric oligonucleotide primer to
amplify a portion of botulinum toxin A encoding sequence from
Clostridium botulinum. "nucleotides 21 to 23 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1177] SEQ ID NO:207: Designed oligonucleotide probe to detect a
DNA fragment amplifying a portion of botulinum toxin A encoding
sequence from Clostridium botulinum.
[1178] SEQ ID NO:208: Designed chimeric oligonucleotide primer to
amplify a portion of viroid CSVd. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1179] SEQ ID NO:209: Designed chimeric oligonucleotide primer to
amplify a portion of viroid CSVd. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1180] SEQ ID NO:210: Designed oligonucleotide probe to detect a
DNA fragment amplifying a portion of viroid CSVd.
[1181] SEQ ID NO:211: Designed chimeric oligonucleotide primer to
amplify a portion of viroid CSVd. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1182] SEQ ID NO:212: Designed chimeric oligonucleotide primer to
amplify a portion of viroid CSVd. "nucleotides 19 to 21 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1183] SEQ ID NO:213: Designed oligonucleotide primer to amplify a
portion of viroid CSVd.
[1184] SEQ ID NO:214: Designed oligonucleotide primer to amplify a
portion of viroid CSVd.
[1185] SEQ ID NO:215: Designed chimeric oligonucleotide primer to
amplify a portion of c-ki-ras oncogene. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1186] SEQ ID NO:216: Designed chimeric oligonucleotide primer to
amplify a portion of c-ki-ras oncogene. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1187] SEQ ID NO:217: Designed oligonucleotide primer to amplify a
portion of c-ki-ras oncogene.
[1188] SEQ ID NO:218: Designed oligonucleotide primer to amplify a
portion of c-ki-ras oncogene.
[1189] SEQ ID NO:219: Designed chimeric oligonucleotide primer to
amplify a portion of verotoxin-1 encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1190] SEQ ID NO:220: Designed chimeric oligonucleotide primer to
amplify a portion of verotoxin-1 encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides"
[1191] SEQ ID NO:221: Designed oligonucleotide primer to amplify a
portion of INOS-encoding sequence from mouse.
[1192] SEQ ID NO:222: Designed oligonucleotide primer to amplify a
portion of INOS-encoding sequence from mouse.
[1193] SEQ ID NO:223: Designed oligonucleotide primer designated as
pUC19 upper 150 to amplify a portion of plasmid pUC19.
[1194] SEQ ID NO:224: Designed oligonucleotide primer designated as
pUC19 lower NN to amplify a portion of plasmid pUC19.
[1195] SEQ ID NO:225: Designed chimeric oligonucleotide primer
designated as SEA-1 to amplify a portion of Staphylococcus aureus.
"nucleotides 19 to 21 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1196] SEQ ID NO:226: Designed chimeric oligonucleotide primer
designated as SEA-2 to amplify a portion of Staphylococcus aureus.
"nucleotides 19 to 21 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1197] SEQ ID NO:227: Designed chimeric oligonucleotide primer
designated as HCV-F3 to amplify a portion of HCV. "nucleotides 17
to 19 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1198] SEQ ID NO:228: Designed chimeric oligonucleotide primer
designated as HCV-R1 to amplify a portion of HCV. "nucleotides 16
to 18 are ribonucleotides--other nucleotides are
deoxyribonucleotides"
[1199] SEQ ID NO:229: Designed oligonucleotide primer designated as
MF2 to amplify a portion of pUC19 plasmid DNA.
[1200] SEQ ID NO:230: Designed oligonucleotide primer designated as
MR1 to amplify a portion of pUC19 plasmid DNA.
[1201] SEQ ID NO:231: Designed oligonucleotide primer to amplify a
portion of adenovirus.
[1202] SEQ ID NO:232: Nucleotide sequence of ORF in RNaseHII gene
from Thermotoga maritima.
[1203] SEQ ID NO:233: Amino acid sequence of RNaseHII from
Thermotoga maritima.
[1204] SEQ ID NO:234: Nucleotide sequence of PH1650 from Pyrococcus
horikoshii.
[1205] SEQ ID NO:235: PCR primer PhoNde for cloning a gene encoding
a polypeptide having a RNaseHII activity from Pyrococcus
horikoshii
[1206] SEQ ID NO:236: PCR primer PhoBam for cloning a gene encoding
a polypeptide having a RNaseHII activity from Pyrococcus
horikoshii
[1207] SEQ ID NO:237: Nucleotide sequence of ORF in RNaseHII gene
from Pyrococcus horikoshii.
[1208] SEQ ID NO:238: Amino acid sequence of RNaseHII from
Pyrococcus horikoshii.
[1209] SEQ ID NO:239: Nucleotide sequence of AF0621 from
Archaeoglobus fulgidus.
[1210] SEQ ID NO:240: PCR primer AfuNde for cloning a gene encoding
a polypeptide having a RNaseHII activity from Archaeoglobus
fulgidus
[1211] SEQ ID NO:241: PCR primer AfuBam for cloning a gene encoding
a polypeptide having a RNaseHII activity from Archaeoglobus
fulgidus
[1212] SEQ ID NO:242: Nucleotide sequence of ORF in RNaseHII gene
from Archaeoglobus fulgidus.
[1213] SEQ ID NO:243: Amino acid sequence of RNaseHII from
Archaeoglobus fulgidus.
[1214] SEQ ID NO:244: Designed chimeric oligonucleotide primer
designated as MTIS2F to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 16 to 18 are ribonucleotides--other
nucleotides are deoxyribonucleotides.".
[1215] SEQ ID NO:245: Designed chimeric oligonucleotide primer
designated as MTIS2R to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 19 to 21 are ribonucleotides--other
nucleotides are deoxyribonucleotides.".
[1216] SEQ ID NO:246: Designed chimeric oligonucleotide primer
designated as CT2F to amplify a portion of Chlamydia trachomatis
cryptic plasmid DNA. "nucleotides 18 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides.".
[1217] SEQ ID NO:247: Designed chimeric oligonucleotide primer
designated as CT2R to amplify a portion of Chlamydia trachomatis
cryptic plasmid DNA. "nucleotides 16 to 18 are
ribonucleotides--other nucleotides are deoxyribonucleotides.".
[1218] SEQ ID NO:248: Designed chimeric oligonucleotide primer
designated as K-F-1033(60) to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 17 to 19 are ribonucleotides--other
nucleotides are deoxyribonucleotides.".
[1219] SEQ ID NO:249: Designed chimeric oligonucleotide primer
designated as K-R-1133(62) to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 18 to 20 are ribonucleotides--other
nucleotides are deoxyribonucleotides.".
[1220] SEQ ID NO:250: Designed chimeric oligonucleotide primer
designated as K-F-1033(68) to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 20 to 22 are ribonucleotides--other
nucleotides are deoxyribonucleotides.".
[1221] SEQ ID NO:251: Designed chimeric oligonucleotide primer
designated as K-R-1133(68) to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 20 to 22 are ribonucleotides--other
nucleotides are deoxyribonucleotides.".
[1222] SEQ ID NO:252: Designed oligonucleotide primer designated as
F26 to amplify a portion of Mycobacterium tuberculosis DNA.
[1223] SEQ ID NO:253: Designed oligonucleotide primer designated as
R1310 to amplify a portion of Mycobacterium tuberculosis DNA.
[1224] SEQ ID NO:254: Designed chimeric oligonucleotide primer
designated as pDON-AI-68-1 to amplify a portion of pDON-AI.
"nucleotides 20 to 22 are ribonucleotides--other nucleotides are
deoxyribonucleotides.".
[1225] SEQ ID NO:255: Designed chimeric oligonucleotide primer
designated as pDON-AI-68-2 to amplify a portion of pDON-AI.
"nucleotides 21 to 23 are ribonucleotides--other nucleotides are
deoxyribonucleotides."
[1226] SEQ ID NO:256: Nucleotide sequence of Homo sapiens
proto-oncogene Wn t-5a
[1227] SEQ ID NO:257: Nucleotide sequence of Homo sapiens ribosomal
protein S5
[1228] SEQ ID NO:258: Nucleotide sequence of Homo sapiens
diaphorase
[1229] SEQ ID NO:259: Nucleotide sequence of Human
protocadherin
[1230] SEQ ID NO:260: Designed oligonucleotide for making of
pIC62.
[1231] SEQ ID NO:261: Designed chimeric oligonucleotide primer
designated as ICAN2. "nucleotides 19 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides."
[1232] SEQ ID NO:262: Designed chimeric oligonucleotide primer
designated as ICAN6. "nucleotides 19 to 20 are
ribonucleotides--other nucleotides are deoxyribonucleotides.".
[1233] SEQ ID NO:263: Designed oligonucleotide primer designated as
ICAN2 DNA.
[1234] SEQ ID NO:264: Designed oligonucleotide primer designated as
ICAN6 DNA.
[1235] SEQ ID NO:265: Designed oligonucleotide primer to amplify a
portion of ribosomal protein S18-encoding sequence from mouse.
[1236] SEQ ID NO:266: Designed oligonucleotide primer to amplify a
portion of ribosomal protein S18-encoding sequence from mouse.
[1237] SEQ ID NO:267: Designed oligonucleotide primer to amplify a
portion of transferrin receptor (TFR)-encoding sequence from
mouse.
[1238] SEQ ID NO:268: Designed oligonucleotide primer to amplify a
portion of transferrin receptor (TFR)-encoding sequence from
mouse.
[1239] SEQ ID NO:269: Designed oligonucleotide primer to amplify a
portion of stromal cell derived factor 4 (Sdf4)-encoding sequence
from mouse.
[1240] SEQ ID NO:270: Designed oligonucleotide primer to amplify a
portion of stromal cell derived factor 4 (Sdf4)-encoding sequence
from mouse.
[1241] SEQ ID NO:271: Designed oligonucleotide primer to amplify a
portion of cytoplasmic beta-actin encoding sequence from mouse.
[1242] SEQ ID NO:272: Designed oligonucleotide primer to amplify a
portion of cytoplasmic beta-actin encoding sequence from mouse.
[1243] SEQ ID NO:273: Designed oligonucleotide primer to amplify a
portion of ornithine decarboxylase-encoding sequence from
mouse.
[1244] SEQ ID NO:274: Designed oligonucleotide primer to amplify a
portion of ornithine decarboxylase-encoding sequence from
mouse.
[1245] SEQ ID NO:275: Designed oligonucleotide primer to amplify a
portion of hypoxanthine guanine phosphoribosyl transferase
(HPRT)-encoding sequence from mouse.
[1246] SEQ ID NO:276: Designed oligonucleotide primer to amplify a
portion of hypoxanthine guanine phosphoribosyl transferase
(HPRT)-encoding sequence from mouse.
[1247] SEQ ID NO:277: Designed oligonucleotide primer to amplify a
portion of tyrosine 3-monooxygenase encoding sequence from
mouse.
[1248] SEQ ID NO:278: Designed oligonucleotide primer to amplify a
portion of tyrosine 3-monooxygenase encoding sequence from
mouse.
[1249] SEQ ID NO:279: Designed oligonucleotide primer designated as
MCS-F.
[1250] SEQ ID NO:280: Designed oligonucleotide primer designated as
MCS-R
[1251] SEQ ID NO:281: Designed chimeric oligonucleotide primer
designated as MF2N3(24). "nucleotides 22 to 24 are
ribonucleoitdes--other nucleotides are deoxyribonucleotides"
[1252] SEQ ID NO:282: Designed chimeric oligonucleotide primer
designated as MR1N3(24). "nucleotides 22 to 24 are
ribonucleoitdes--other nucleotides are deoxyribonucleotides"
[1253] SEQ ID NO:283: Designed chimeric oligonucleotide primer
designated as MTIS2F-16 to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 14 to 16 are ribonucleotides--other
nucleotides are deoxyribonucleotides.
[1254] SEQ ID NO:284: Designed chimeric oligonucleotide primer
designated as MTIS2R-ACC to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 18 to 20 are ribonucleotides--other
nucleotides are deoxyribonucleotides."
[1255] SEQ ID NO:285: Designed oligonucleotide primer designated as
MTIS-PCR-F-2 to amplify a portion of Mycobacterium tuberculosis
DNA
[1256] SEQ ID NO:286: Designed oligonucleotide primer designated as
MTIS-PCR-R-2 to amplify a portion of Mycobacterium tuberculosis
DNA
[1257] SEQ ID NO:287: Designed oligonucleotide primer designated as
SP6--HCV-F to amplify a portion of HCV
[1258] SEQ ID NO:288: Designed oligonucleotide primer designated as
SP6--HCV-R to amplify a portion of HCV
[1259] SEQ ID NO:289: Designed chimeric oligonucleotide primer
designated as HCV-A S to amplify a portion of HCV. "nucleotides 18
to 20 are ribonucleotides--other nucleotides are
deoxyribonucleotides."
[1260] SEQ ID NO:290: Designed chimeric oligonucleotide primer
designated as HCV-A A to amplify a portion of HCV. "nucleotides 18
to 20 are ribonucleotides--other nucleotides are
deoxyribonucleotides.
Sequence CWU 1
1
290 1 99 DNA Artificial Synthetic DNA corresponding to a portion of
human transferrin receptor-encoding sequence used as a template 1
ggacagcaac tgggccagca aagttgagaa actcacttta gagaattctg ctttcccttt
60 ccttgcatat tctgagcagt ttctttctgt ttttgcgag 99 2 22 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
human transferrin receptor-encoding sequence 2 cagcaactgg
gccagcaaag tt 22 3 22 DNA Artificial Designed oligonucleotide
primer to amplify a portion of human transferrin receptor-encoding
sequence 3 gcaaaaacag aaagaaactg ct 22 4 22 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of human
transferrin receptor-encoding sequence. "nucleotide 21 is
ribonucleotide-other nucleotides are deoxyribonucleotides" 4
cagcaactgg gccagcaaag ut 22 5 22 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of human transferrin
receptor-encoding sequence. "nucleotide 21 is ribonucleotide-other
nucleotides are deoxyribonucleotides" 5 gcaaaaacag aaagaaactg ct 22
6 22 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of human transferrin receptor-encoding sequence.
"nucleotide 22 is ribonucleotide-other nucleotides are
deoxyribonucleotides" 6 cagcaactgg gccagcaaag tu 22 7 22 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 7 gcaaaaacag aaagaaactg cu 22 8 22 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 8 cagcaactgg gccagcaaag uu 22 9 22 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 9 gcaaaaacag aaagaaactg cu 22 10 22 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence. "20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 10
cagcaactgg gccagcaaag tt 22 11 22 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of human transferrin
receptor-encoding sequence. "nucleotides 19 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 11
gcaaaaacag aaagaaacug ct 22 12 26 DNA Artificial Designed
oligonucleotide used as a probe for detecting an amplified portion
of human transferrin receptor- encoding sequence 12 tgctttccct
ttccttgcat attctg 26 13 25 DNA Artificial Designed chimeric
oligonucleotide primer designated as pUC19 upper(2)NN to amplify a
portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 13
attgcttaat cagtgaggca cctau 25 14 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 lower NN to
amplify a portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 14
gataacactg cggccaactt actuc 25 15 25 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of plasmid
pUC19. "nucleotides 24 to 25 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 15 actggcgaac tacttactct agcuu 25 16 26
DNA Artificial Designed chimeric oligonucleotide primer designated
as pUC19 lower 542 to amplify a portion of plasmid pUC19.
"nucleotides 24 to 25 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 16 agtcaccaga aaagcatctt acggau 26 17 25 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 17
gctcatgaga caataaccct gataa 25 18 25 DNA Artificial Designed
oligonucleotide primer designated as pUC19 upper 150 to amplify a
portion of plasmid pUC19. "nucleotides 23 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 18
ggtgtcacgc tcgtcgtttg gtaug 25 19 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 lower NN to
amplify a portion of plasmid pUC19. "nucleotides 23 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 19
gataacactg cggccaactt acuuc 25 20 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 upper 249 to
amplify a portion of plasmid pUC19. "nucleotides 23 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 20
cgcctccatc cagtctatta atugu 25 21 22 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of human
transferrin receptor-encoding sequence. "nucleotides 20 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 21
ctgattgaga ggattcctga gu 22 22 22 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of human transferrin
receptor-encoding sequence. "nucleotides 21 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 22
tagggagaga ggaagtgata cu 22 23 25 DNA Artificial Designed chimeric
oligonucleotide primer designated as pUC19 upper(2)NN to amplify a
portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 23
attgcttaat cagtgaggca cctau 25 24 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 upper(2)NN to
amplify a portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 24
attgcttaat cagtgaggca cctaa 25 25 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 upper(2)NN to
amplify a portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 25
attgcttaat cagtgaggca cctac 25 26 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 upper(2)NN to
amplify a portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 26
attgcttaat cagtgaggca cctag 25 27 22 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of human
transferrin receptor-encoding sequence. "nucleotides 21 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 27
ctgattgaga ggattcctga gu 22 28 22 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of human transferrin
receptor-encoding sequence. "nucleotides 21 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 28
tagggagaga ggaagtgata cu 22 29 24 DNA Artificial Designed chimeric
oligonucleotide primer designated as MF2N3(24) to amplify a portion
of plasmid pUC19-249 or plasmid pUC19-911. "nucleotides 22 to 24
are ribonucleotides- other nucleotides are deoxyribonucleotides" 29
gctgcaaggc gattaagttg ggua 24 30 24 DNA Artificial Designed
oligonucleotide primer designated as MR1N3(24) to amplify a portion
of plasmid pUC19-249 or plasmid pUC19-911. "nucleotides 22 to 24
are ribonucleotides-other nucleotides are deoxyribonucleotides" 30
ctttatgctt ccggctcgta tguu 24 31 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 upper 249 to
amplify a portion of plasmid pUC19. "nucleotides 24 to 25 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 31
cgcctccatc cagtctatta attgu 25 32 25 DNA Artificial Designed
oligonucleotide primer designated as pUC19 upper 150 to amplify a
portion of plasmid pUC19 32 ggtgtcacgc tcgtcgtttg gtatg 25 33 25
DNA Artificial Designed oligonucleotide primer designated as pUC19
upper 249 to amplify a portion of plasmid pUC19 33 cgcctccatc
cagtctatta attgt 25 34 25 DNA Artificial Designed oligonucleotide
primer designated as pUC19 lower NN to amplify a portion of plasmid
pUC19 34 gataacactg cggccaactt acttc 25 35 30 DNA Artificial
Designed chimeric oligonucleotide primer to amplify a portion of
plasmid pUC19. "nucleotides 28 to 30 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 35 ggatgtgctg caaggcgatt
aagttgggua 30 36 30 DNA Artificial Designed chimeric
oligonucleotide primer designated as MR1N3 to amplify a portion of
plasmid pUC19. "nucleotides 28 to 30 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 36 tttacacttt atgcttccgg
ctcgtatguu 30 37 30 DNA Artificial Designed oligonucleotide primer
to amplify a portion of plasmid pUC19 37 ggatgtgctg caaggcgatt
aagttgggta 30 38 30 DNA Artificial Designed oligonucleotide primer
designated as MR1N3 to amplify a portion of plasmid pUC19 38
tttacacttt atgcttccgg ctcgtatgtt 30 39 30 DNA Artificial Synthetic
RNA used as a probe for detecting an amplified portion of plasmid
pUC19 39 ugauccccca uguugugcaa aaaagcgguu 30 40 25 DNA Artificial
Designed chimeric oligonucleotide primer designated as pUC19 upper
150 to amplify a portion of plasmid pUC19. "nucleotides 24 to 25
are ribonucleotides-other nucleotides are deoxyribonucleotides" 40
ggtgtcacgc tcgtcgtttg gtaug 25 41 30 DNA Artificial Designed
chimeric oligonucleotide primer designated as MR1N3 to amplify a
portion of plasmid pUC19. "nucleotides 28 to 30 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 41
tttacacttt atgcttccgg ctcgtatguu 30 42 17 DNA Artificial Designed
oligonucleotide primer designated as M13M4 42 gttttcccag tcacgac 17
43 18 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 1-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 16 to 18 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 43
agttaatgtg gtggcgaa 18 44 17 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of vero toxin
1-encoding sequence from hemorrhagic Escherichia coli O-157.
"nucleotides 15 to 17 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 44 gactcttcca tctgcca 17 45 18 DNA Artificial
Designed chimeric oligonucleotide primer to amplify a portion of
vero toxin 2-encoding sequence from hemorrhagic Escherichia coli
O-157. "nucleotides 16 to 18 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 45 ttcggtatcc tattcccg 18 46 18 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 16 to 18 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 46
tctctggtca ttgtauua 18 47 22 DNA Artificial Designed
oligonucleotide primer designated as MCR-F to amplify a long DNA
fragment 47 ccattcaggc tgcgcaactg tt 22 48 22 DNA Artificial
Designed oligonucleotide primer designated as MCR-R to amplify a
long DNA fragment 48 tggcacgaca ggtttcccga ct 22 49 24 DNA
Artificial Designed chimeric oligonucleotide primer designated as
MF2N3(24) to amplify a long DNA fragment. "nucleotides 22 to 24 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 49
gctgcaaggc gattaagttg ggua 24 50 24 DNA Artificial Designed
chimeric oligonucleotide primer designated as MR1N3(24) to amplify
a long DNA fragment. "nucleotides 22 to 24 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 50
ctttatgctt ccggctcgta tguu 24 51 20 DNA Artificial Designed
oligonucleotide primer to amplify a portion of bacteriophage lambda
DNA 51 aacaacaaga aactggtttc 20 52 20 DNA Artificial Designed
oligonucleotide primer to amplify a portion of bacteriophage lambda
DNA 52 gcaatgcatg acgactgggg 20 53 17 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA. "nucleotides 16 to 17 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 53
gttttcccag tcacgac 17 54 17 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of bacteriophage lambda
DNA. "nucleotides 16 to 17 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 54 caggaaacag ctatgac 17 55 20 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA 55 gtacggtcat catctgacac 20 56 20 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA 56 gcaatcggca tgttaaacgc 20 57 20 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA 57 cgccatcctg ggaagactcc 20 58 44 DNA
Artificial Designed oligonucleotide primer designated as R1-S1 to
amplify a portion of bacteriophage lambda DNA 58 tttcacacag
gaaacagcta tgacaacaac aagaaactgg tttc 44 59 44 DNA Artificial
Designed oligonucleotide primer designated as R1-A3 to amplify a
portion of bacteriophage lambda DNA 59 tttcacacag gaaacagcta
tgacgcaatg catgacgact gggg 44 60 62 DNA Artificial Designed
oligonucleotide primer designated as R2-S1 to amplify a portion of
bacteriophage lambda DNA 60 attgtgagcg gataacaatt tcacacagga
aacagctatg acaacaacaa gaaactggtt 60 tc 62 61 62 DNA Artificial
Designed oligonucleotide primer designated as R2-A3 to amplify a
portion of bacteriophage lambda DNA 61 attgtgagcg gataacaatt
tcacacagga aacagctatg acgcaatgca tgacgactgg 60 gg 62 62 95 DNA
Artificial Designed oligonucleotide primer designated as R3-S1 to
amplify a portion of bacteriophage lambda DNA 62 cactttatgc
ttccggctcg tatgttgtgt ggaattgtga gcggataaca atttcacaca 60
ggaaacagct atgacaacaa caagaaactg gtttc 95 63 95 DNA Artificial
Designed oligonucleotide primer designated as R3-A3 to amplify a
portion of bacteriophage lambda DNA 63 cactttatgc ttccggctcg
tatgttgtgt ggaattgtga gcggataaca atttcacaca 60 ggaaacagct
atgacgcaat gcatgacgac tgggg 95 64 17 DNA Artificial Designed
chimeric oligonucleotide primer designated as M13RV-2N 17mer.
"nucleotides 16 to 17 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 64 caggaaacag ctatgac 17 65 20 DNA Artificial
Designed chimeric oligonucleotide primer designated as M13RV-2N
20mer. "nucleotides 19 to 20 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 65 acacaggaaa cagctatgac 20 66 70 DNA
Artificial Designed
oligonucleotide primer to amplify a portion of CDC2-related protein
kinase PISSLRE gene 66 gagttcgtgt ccgtacaact atttcacaca ggaaacagct
atgacccaac aagagcctat 60 agcttcgctc 70 67 67 DNA Artificial
Designed oligonucleotide primer to amplify a portion of
CDC2-related protein kinase PISSLRE gene 67 tcgaaatcag ccacagcgcc
atttcacaca ggaaacagct atgacccgct gtctttgagt 60 tgtggtg 67 68 70 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
type ii cytoskeltal 11 keratin gene 68 gagttcgtgt ccgtacaact
atttcacaca ggaaacagct atgacgctat tctgacatca 60 ctttccagac 70 69 66
DNA Artificial Designed oligonucleotide primer to amplify a portion
of type ii cytoskeltal 11 keratin gene 69 tcgaaatcag ccacagcgcc
atttcacaca ggaaacagct atgacgaatt ccactggtgg 60 cagtag 66 70 62 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA 70 attgtgagcg gataacaatt tcacacagga
aacagctatg acgtacggtc atcatctgac 60 ac 62 71 62 DNA Artificial
Designed oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA 71 attgtgagcg gataacaatt tcacacagga
aacagctatg acatgcgccg cctgaaccac 60 ca 62 72 62 DNA Artificial
Designed oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA 72 attgtgagcg gataacaatt tcacacagga
aacagctatg acctgctctg ccgcttcacg 60 ca 62 73 62 DNA Artificial
Designed oligonucleotide primer to amplify a portion of
bacteriophage lambda DNA 73 attgtgagcg gataacaatt tcacacagga
aacagctatg acgcaatcgg catgttaaac 60 gg 62 74 24 DNA Artificial
Designed oligonucleotide primer designated as MF2N3(24) to amplify
a portion of plasmid pUC19-249 or plasmid pUC19-911 74 gctgcaaggc
gattaagttg ggta 24 75 24 DNA Artificial Designed oligonucleotide
primer designated as MR1N3(24) to amplify a portion of plasmid
pUC19-249 or plasmid pUC19-911 75 ctttatgctt ccggctcgta tgtt 24 76
20 DNA Artificial Designed chimeric oligonucleotide primer
designated as M13M4-3N 20mer. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 76
agggttttcc cagtcacgac 20 77 20 DNA Artificial Designed chimeric
oligonucleotide primer designated as M13RV-3N 20mer. "nucleotides
18 to 20 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 77 acacaggaaa cagctatgac 20 78 24 DNA
Artificial Designed chimeric oligonucleotide primer designated as
M13M4-3N 24mer. "nucleotides 22 to 24 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 78 cgccagggtt ttcccagtca cgac
24 79 24 DNA Artificial Designed oligonucleotide primer designated
as M13RV-3N 24mer. "nucleotides 22 to 24 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 79 tttcacacag gaaacagcta tgac
24 80 69 DNA Artificial Designed oligonucleotide primer designated
as 5'ID to amplify a portion of cyclin A DNA 80 tcgaaatcag
ccacagcgcc atttcacaca ggaaacagct atgacatgtt ttgggagaat 60 taagtctga
69 81 69 DNA Artificial Designed oligonucleotide primer designated
as 3'ID to amplify a portion of cyclin A DNA 81 gagttcgtgc
cgtacaacta tttcacacag gaaacagcta tgacttacag atttagtgtc 60 tctggtggg
69 82 16 DNA Artificial Designed oligonucleotide primer designated
as M13RV-2N 16mer. "nucleotides 15 to 16 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 82 aggaaacagc tatgac 16 83 27
DNA Artificial Designed chimeric oligonucleotide primer to amplify
a portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 83 cagcaactgg gccagcaaag uugagaa 27 84 27 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 84 gcaaaaacag aaagaaactg cucagaa 27 85 26 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 85 cagcaactgg gccagcaaag uugaga 26 86 26 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 86 gcaaaaacag aaagaaactg cucaga 26 87 25 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 87 cagcaactgg gccagcaaag uugag 25 88 25 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 88 gcaaaaacag aaagaaactg cucag 25 89 24 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 89 cagcaactgg gccagcaaag uuga 24 90 24 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 90 gcaaaaacag aaagaaactg cuca 24 91 23 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 91 cagcaactgg gccagcaaag uug 23 92 23 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 92 gcaaaaacag aaagaaactg cuc 23 93 22 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 93 cagcaactgg gccagcaaag uu 22 94 22 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of human transferrin receptor-encoding sequence.
"nucleotides 21 to 22 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 94 gcaaaaacag aaagaaactg cu 22 95 22 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
human transferrin receptor-encoding sequence 95 caacttcaag
gtttctgcca gc 22 96 21 DNA Artificial Designed oligonucleotide
primer to amplify a portion of human transferrin receptor-encoding
sequence 96 aatagtccaa gtagctagag c 21 97 20 DNA Artificial PCR
primer BsuII-3 for cloning a gene encoding a polypeptide having a
RNaseHII activity from Bacillus caldotenax 97 gtcgccagcg cagtnathyt
20 98 20 DNA Artificial PCR primer BsuII-6 for cloning a gene
encoding a polypeptide having a RNaseHII activity from Bacillus
caldotenax 98 cggtccctcg tcacyttngc 20 99 20 DNA Artificial PCR
primer RNII-S1 for cloning a gene encoding a polypeptide having a
RNaseHII activity from Bacillus caldotenax 99 cgcgcttttc cggcgtcagc
20 100 20 DNA Artificial PCR primer RNII-S2 for cloning a gene
encoding a polypeptide having a RNaseHII activity from Bacillus
caldotenax 100 acggcgcacg cttcaatttg 20 101 20 DNA Artificial PCR
primer RNII-S5 for cloning a gene encoding a polypeptide having a
RNaseHII activity from Bacillus caldotenax 101 acgcctattt
gccggggctt 20 102 20 DNA Artificial PCR primer RNII-S6 for cloning
a gene encoding a polypeptide having a RNaseHII activity from
Bacillus caldotenax 102 atgaccgacg cagcggcgat 20 103 39 DNA
Artificial PCR primer RNII-Nde for cloning a gene encoding a
polypeptide having a RNaseHII activity from Bacillus caldotenax 103
tagaagaggg agaggcatat gaagcggtat acggtgaaa 39 104 780 DNA Bucillus
caldotenax 104 atgaagcggt atacggtgaa agacattgaa gcgctgcttc
cgaagcttgg cgcggacgac 60 ccgcgctggg agatgctgcg gcaggatgag
cgaaaaagcg tgcaggcgct tcttgcccgt 120 tttgaaaggc agaaagcgcg
ccggcacgcc atcgagcagc ggtgggaaga actaatgcgt 180 tatgagaggg
aactatacgc cgctggcgtt agacggatcg ccggcattga tgaggccggg 240
cgcggcccgc tggccggccc ggtcgtcgcc gccgcggtca tcttgccgaa agacgcctat
300 ttgccggggc ttgacgactc gaagcggctg acgccggaaa agcgcgaggc
attgtttgcg 360 caaattgaag cgtgcgccgt cgccatcggc atcggcatcg
tcagcgcggc ggagatcgat 420 gaaaggaata tttacgaagc gacaaggcaa
gcgatggcga aagcggtgaa cgccctttcc 480 ccgccgcctg aacatttgct
tgttgatgcg atggcggtgc cgtgcccact gccgcaacag 540 cgcctcataa
aaggagacgc caacagcgct tcaatcgccg ctgcgtcggt catcgccaaa 600
gtgacgcgcg accggtggat gaaagaactg gatcgccgct atccacaata cgggttcgcg
660 cgccatatgg gctacggaac gccggaacat ttcgaggcga tccgccgcta
cggcgttacg 720 cctgagcacc gtcgttcgtt cgcaccggtg agggaggtgc
tgaaggcgag cgagcagctc 780 105 260 PRT Bucillus caldotenax 105 Met
Lys Arg Tyr Thr Val Lys Asp Ile Glu Ala Leu Leu Pro Lys Leu 1 5 10
15 Gly Ala Asp Asp Pro Arg Trp Glu Met Leu Arg Gln Asp Glu Arg Lys
20 25 30 Ser Val Gln Ala Leu Leu Ala Arg Phe Glu Arg Gln Lys Ala
Arg Arg 35 40 45 His Ala Ile Glu Gln Arg Trp Glu Glu Leu Met Arg
Tyr Glu Arg Glu 50 55 60 Leu Tyr Ala Ala Gly Val Arg Arg Ile Ala
Gly Ile Asp Glu Ala Gly 65 70 75 80 Arg Gly Pro Leu Ala Gly Pro Val
Val Ala Ala Ala Val Ile Leu Pro 85 90 95 Lys Asp Ala Tyr Leu Pro
Gly Leu Asp Asp Ser Lys Arg Leu Thr Pro 100 105 110 Glu Lys Arg Glu
Ala Leu Phe Ala Gln Ile Glu Ala Cys Ala Val Ala 115 120 125 Ile Gly
Ile Gly Ile Val Ser Ala Ala Glu Ile Asp Glu Arg Asn Ile 130 135 140
Tyr Glu Ala Thr Arg Gln Ala Met Ala Lys Ala Val Asn Ala Leu Ser 145
150 155 160 Pro Pro Pro Glu His Leu Leu Val Asp Ala Met Ala Val Pro
Cys Pro 165 170 175 Leu Pro Gln Gln Arg Leu Ile Lys Gly Asp Ala Asn
Ser Ala Ser Ile 180 185 190 Ala Ala Ala Ser Val Ile Ala Lys Val Thr
Arg Asp Arg Trp Met Lys 195 200 205 Glu Leu Asp Arg Arg Tyr Pro Gln
Tyr Gly Phe Ala Arg His Met Gly 210 215 220 Tyr Gly Thr Pro Glu His
Phe Glu Ala Ile Arg Arg Tyr Gly Val Thr 225 230 235 240 Pro Glu His
Arg Arg Ser Phe Ala Pro Val Arg Glu Val Leu Lys Ala 245 250 255 Ser
Glu Gln Leu 260 106 20 DNA Artificial PCR primer BsuIII-1 for
cloning a gene encoding a polypeptide having a RNaseHIII activity
from Bacillus caldotenax 106 ggtaaggtct tgttycargg 20 107 20 DNA
Artificial PCR primer BsuIII-3 for cloning a gene encoding a
polypeptide having a RNaseHIII activity from Bacillus caldotenax
107 ggaaccggag attayttygg 20 108 20 DNA Artificial PCR primer
BsuIII-6 for cloning a gene encoding a polypeptide having a
RNaseHIII activity from Bacillus caldotenax 108 atgattgaag
cagcngcnac 20 109 20 DNA Artificial PCR primer BsuIII-8 for cloning
a gene encoding a polypeptide having a RNaseHIII activity from
Bacillus caldotenax 109 gtattggcga aatgnarytt 20 110 20 DNA
Artificial PCR primer RNIII-S3 for cloning a gene encoding a
polypeptide having a RNaseHIII activity from Bacillus caldotenax
110 cccgatcgtc gtcgccgccg 20 111 20 DNA Artificial PCR primer
BcaRNIII-3 for cloning a gene encoding a polypeptide having a
RNaseHIII activity from Bacillus caldotenax 111 gatacgtgga
cactttccgc 20 112 915 DNA Bucillus caldotenax 112 gtgattcaag
ccgaccaaca gctgcttgac gccttgcgcg cccactacca agacgcctta 60
tccgaccggc ttccggctgg agcgttgttt gccgtcaagc gcccggatgt cgtcatcacc
120 gcctaccgct caggcaaagt gctgtttcaa gggaaagcgg cggagcaaga
agcagcgaaa 180 tggatatcag gggcgagcgc ctcaaacgaa acagctgacc
accagccgtc cgctttggca 240 gctcatcaac tcgggtctct ttccgccatc
ggttccgatg aagtcggcac cggcgattat 300 ttcggcccga tcgtcgtcgc
cgccgcctac gtggatcggc cgcatatcgc caaaatcgcg 360 gcgcttggcg
tgaaagattc gaaacaattg aacgatgagg caatcaaacg gatcgccccc 420
gccatcatgg aaaccgtgcc gcatgcggtc accgtgttgg acaatgccga atacaaccgc
480 tggcagcgaa gcggcatgcc gcagacgaaa atgaaagcgc tccttcacaa
ccggacgctc 540 gtgaaactcg ttgacgccat cgcgcccgcc gaaccagaag
caatcatcat cgacgaattt 600 ttaaaacggg attcgtattt ccgttacctt
tccgatgaag atcgcattat ccgcgagcgg 660 gtgcactgcc ttcccaaggc
ggaaagtgtc cacgtatcag tcgccgccgc ctcgatcatc 720 gcccgctatg
tgtttttaga ggagatggag caattatccc gcgccgtcgg cctcctgctt 780
ccaaaaggcg ccggcgccat tgtcgatgaa gccgcggcca acatcatccg cgcgcggggg
840 gcggaagcgc ttgagacatg cgccaagctt catttcgcca atacaaaaaa
ggcgctggac 900 atcgccaaac gccgg 915 113 305 PRT Bucillus caldotenax
113 Met Ile Gln Ala Asp Gln Gln Leu Leu Asp Ala Leu Arg Ala His Tyr
1 5 10 15 Gln Asp Ala Leu Ser Asp Arg Leu Pro Ala Gly Ala Leu Phe
Ala Val 20 25 30 Lys Arg Pro Asp Val Val Ile Thr Ala Tyr Arg Ser
Gly Lys Val Leu 35 40 45 Phe Gln Gly Lys Ala Ala Glu Gln Glu Ala
Ala Lys Trp Ile Ser Gly 50 55 60 Ala Ser Ala Ser Asn Glu Thr Ala
Asp His Gln Pro Ser Ala Leu Ala 65 70 75 80 Ala His Gln Leu Gly Ser
Leu Ser Ala Ile Gly Ser Asp Glu Val Gly 85 90 95 Thr Gly Asp Tyr
Phe Gly Pro Ile Val Val Ala Ala Ala Tyr Val Asp 100 105 110 Arg Pro
His Ile Ala Lys Ile Ala Ala Leu Gly Val Lys Asp Ser Lys 115 120 125
Gln Leu Asn Asp Glu Ala Ile Lys Arg Ile Ala Pro Ala Ile Met Glu 130
135 140 Thr Val Pro His Ala Val Thr Val Leu Asp Asn Ala Glu Tyr Asn
Arg 145 150 155 160 Trp Gln Arg Ser Gly Met Pro Gln Thr Lys Met Lys
Ala Leu Leu His 165 170 175 Asn Arg Thr Leu Val Lys Leu Val Asp Ala
Ile Ala Pro Ala Glu Pro 180 185 190 Glu Ala Ile Ile Ile Asp Glu Phe
Leu Lys Arg Asp Ser Tyr Phe Arg 195 200 205 Tyr Leu Ser Asp Glu Asp
Arg Ile Ile Arg Glu Arg Val His Cys Leu 210 215 220 Pro Lys Ala Glu
Ser Val His Val Ser Val Ala Ala Ala Ser Ile Ile 225 230 235 240 Ala
Arg Tyr Val Phe Leu Glu Glu Met Glu Gln Leu Ser Arg Ala Val 245 250
255 Gly Leu Leu Leu Pro Lys Gly Ala Gly Ala Ile Val Asp Glu Ala Ala
260 265 270 Ala Asn Ile Ile Arg Ala Arg Gly Ala Glu Ala Leu Glu Thr
Cys Ala 275 280 285 Lys Leu His Phe Ala Asn Thr Lys Lys Ala Leu Asp
Ile Ala Lys Arg 290 295 300 Arg 305 114 39 DNA Artificial PCR
primer BcaRNIIINde for amplifying a gene
encoding a polypeptide having a RNaseHIII activity from Bacillus
caldotenax 114 cgaacgttgt caaaccatat gattcaagcc gaccaacag 39 115
663 DNA Pyrococcus horikoshii 115 atgaaggttg ctggagttga tgaagcgggg
agggggccgg taattggccc gttagtaatt 60 ggagtagccg ttatagatga
gaaaaatatt gagaggttac gtgacattgg ggttaaagac 120 tccaaacaat
taactcctgg gcaacgtgaa aaactattta gcaaattaat agatatccta 180
gacgattatt atgttcttct cgttaccccc aaggaaatag atgagaggca tcattctatg
240 aatgaactag aagctgagaa attcgttgta gccttgaatt ctttaaggat
caagccgcag 300 aagatatatg tggactctgc cgatgtagat cctaagaggt
ttgctagtct aataaaggct 360 gggttgaaat atgaagccac ggttatcgcc
gagcataaag ccgatgcaaa gtatgagata 420 gtatcggcag catcaataat
tgcaaaggtc actagggata gagagataga gaagctaaag 480 caaaagtatg
gggaatttgg ttctggctat ccgagtgatc cgagaactaa ggagtggctt 540
gaagaatatt acaaacaata tggtgacttt cctccaatag ttaggagaac ttgggaaacc
600 gctaggaaga tagaggaaag gtttagaaaa aatcagctaa cgcttgataa
attccttaag 660 tga 663 116 33 DNA Artificial PCR primer 1650Nde for
cloning a gene encoding a polypeptide having a RNaseHII activity
from Pyrococcus furiosus 116 caggaggaga gacatatgaa aataggggga att
33 117 33 DNA Artificial PCR primer 1650Bam for cloning a gene
encoding a polypeptide having a RNaseHII activity from Pyrococcus
furiosus 117 gaaggttgtg gatccacttt ctaaggtttc tta 33 118 672 DNA
Pyrococcus furiosus 118 atgaaaatag ggggaattga cgaagcagga agaggaccag
cgatagggcc attagtagta 60 gctactgtcg tcgttgatga gaaaaacatt
gagaagctca gaaacattgg agtaaaagac 120 tccaaacaac taacacccca
tgaaaggaag aatttatttt cccagataac ctcaatagcg 180 gatgattaca
aaatagtgat agtatcccca gaagaaatcg acaatagatc aggaacaatg 240
aacgagttag aggtagagaa gtttgctctc gccttaaatt cgcttcagat aaaaccagct
300 cttatatacg ctgatgcagc ggatgtagat gccaatagat ttgcaagctt
gatagagaga 360 agactcaatt ataaggcgaa gattattgcc gaacacaagg
ccgatgcaaa gtatccagta 420 gtttcagcag cttcaatact tgcaaaggtt
gttagggatg aggaaattga aaaattaaaa 480 aagcaatatg gagactttgg
ctctgggtat ccaagtgatc caaaaaccaa gaaatggctt 540 gaagagtact
acaaaaaaca caactctttc cctccaatag tcagacgaac ctgggaaact 600
gtaagaaaaa tagaggaaag cattaaagcc aaaaaatccc agctaacgct tgataaattc
660 tttaagaaac ct 672 119 224 PRT Pyrococcus furiosus 119 Met Lys
Ile Gly Gly Ile Asp Glu Ala Gly Arg Gly Pro Ala Ile Gly 1 5 10 15
Pro Leu Val Val Ala Thr Val Val Val Asp Glu Lys Asn Ile Glu Lys 20
25 30 Leu Arg Asn Ile Gly Val Lys Asp Ser Lys Gln Leu Thr Pro His
Glu 35 40 45 Arg Lys Asn Leu Phe Ser Gln Ile Thr Ser Ile Ala Asp
Asp Tyr Lys 50 55 60 Ile Val Ile Val Ser Pro Glu Glu Ile Asp Asn
Arg Ser Gly Thr Met 65 70 75 80 Asn Glu Leu Glu Val Glu Lys Phe Ala
Leu Ala Leu Asn Ser Leu Gln 85 90 95 Ile Lys Pro Ala Leu Ile Tyr
Ala Asp Ala Ala Asp Val Asp Ala Asn 100 105 110 Arg Phe Ala Ser Leu
Ile Glu Arg Arg Leu Asn Tyr Lys Ala Lys Ile 115 120 125 Ile Ala Glu
His Lys Ala Asp Ala Lys Tyr Pro Val Val Ser Ala Ala 130 135 140 Ser
Ile Leu Ala Lys Val Val Arg Asp Glu Glu Ile Glu Lys Leu Lys 145 150
155 160 Lys Gln Tyr Gly Asp Phe Gly Ser Gly Tyr Pro Ser Asp Pro Lys
Thr 165 170 175 Lys Lys Trp Leu Glu Glu Tyr Tyr Lys Lys His Asn Ser
Phe Pro Pro 180 185 190 Ile Val Arg Arg Thr Trp Glu Thr Val Arg Lys
Ile Glu Glu Ser Ile 195 200 205 Lys Ala Lys Lys Ser Gln Leu Thr Leu
Asp Lys Phe Phe Lys Lys Pro 210 215 220 120 28 DNA Artificial PCR
primer 915-F1 for cloning a gene encoding a polypeptide having a
RNaseHII activity from Thermotoga maritima 120 aaaaagcttg
ggaatagatg agctttac 28 121 26 DNA Artificial PCR primer 915-F2 for
cloning a gene encoding a polypeptide having a RNaseHII activity
from Thermotoga maritima 121 aaaccatggg aatagatgag ctttac 26 122 29
DNA Artificial PCR primer 915-R1 for cloning a gene encoding a
polypeptide having a RNaseHII activity from Thermotoga maritima 122
aaatctagat cctcaacttt gtcgatgtg 29 123 30 DNA Artificial PCR primer
915-R2 for cloning a gene encoding a polypeptide having a RNaseHII
activity from Thermotoga maritima 123 aatctagatt aaaaaagagg
gagattatgg 30 124 22 DNA Artificial Designed oligonucleotide primer
designated as MCS-F to amplify a long DNA fragment 124 ccattcaggc
tgcgcaactg tt 22 125 22 DNA Artificial Designed oligonucleotide
primer designated as MCS-R to amplify a long DNA fragment 125
tggcacgaca ggtttcccga ct 22 126 24 DNA Artificial Designed chimeric
oligonucleotide primer designated as MF2N3(24) to amplify a long
DNA fragment. "nucleotides 22 to 24 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 126 gctgcaaggc gattaagttg
ggua 24 127 24 DNA Artificial Designed chimeric oligonucleotide
primer designated as MR1N3(24) to amplify a long DNA fragment.
"nucleotides 22 to 24 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 127 ctttatgctt ccggctcgta tguu 24 128 20 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
lambda DNA. "nucleotides 18 to 20 are ribonucleotides- other
nucleotides are deoxyribonucleotides" 128 cctttctctg tttttgtccg 20
129 20 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of lambda DNA. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 129
aagcacctca ttaccctugc 20 130 24 DNA Artificial Designed
oligonucleotide primer to amplify a portion of lambda DNA 130
gggcggcgac ctcgcgggtt ttcg 24 131 24 DNA Artificial Designed
oligonucleotide primer to amplify a portion of lambda DNA 131
gctgcttatg ctctataaag tagg 24 132 20 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of
Flavobacterium species DNA. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 132
aggaatcttt atttaccaug 20 133 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of Flavobacterium
species DNA. "nucleotides 18 to 20 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 133 tggtgtttaa acttattgcg 20
134 24 DNA Artificial Designed oligonucleotide primer to amplify a
portion of Flavobacterium species DNA. 134 ccatcagcta taaacacaaa
cagc 24 135 24 DNA Artificial Designed oligonucleotide primer to
amplify a portion of Flavobacterium species DNA. 135 tgttttgacc
aaacatagta atgc 24 136 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic Escherichia coli O-157.
"nucleotides 19 to 21 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 136 tcgttaaata gtatacggac a 21 137 20 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 137
tgctcaataa tcagacgaag 20 138 24 DNA Artificial Designed
oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic Escherichia coli O-157. 138
aaatggggta ctgtgcctgt tact 24 139 24 DNA Artificial Designed
oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic Escherichia coli O-157. 139
ctctgtatct gcctgaagcg taag 24 140 21 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic Escherichia coli O-157.
"nucleotides 18 to 20 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 140 tacctgggtt tttcttcggu a 21 141 20 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 141
atagactttt cgacccaaca 20 142 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic Escherichia coli O-157.
"nucleotides 18 to 20 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 142 atagacatca agccctcgua 20 143 21 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
vero toxin 2-encoding sequence from hemorrhagic Escherichia coli
O-157. 143 tcgttaaata gtatacggac a 21 144 20 DNA Artificial
Designed oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic Escherichia coli O-157. 144
atagacatca agccctcgta 20 145 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of lambda DNA.
"nucleotides 18 to 20 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 145 gaacaatgga agtcaacaaa 20 146 20 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
viroid CSVd. 146 tacttgtggt tcctgtggtg 20 147 20 DNA Artificial
Designed oligonucleotide primer to amplify a portion of viroid
CSVd. 147 atactaaggt tccaagggct 20 148 18 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of viroid
CSVd. "nucleotides 16 to 18 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 148 ggaaacctgg aggaaguc 18 149 20 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of viroid CSVd. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 149
gtgaaaaccc tgtttaggau 20 150 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of Flavobacterium
species DNA. "nucleotides 18 to 20 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 150 acctagatat aagctctaca 20
151 20 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of Flavobacterium species DNA. "nucleotides 18 to
20 are ribonucleotides-other nucleotides are deoxyribonucleotides"
151 aaatagatgt tttagcagag 20 152 20 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of
Flavobacterium species DNA. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 152
atagataaaa aaaactccac 20 153 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic O-157. "nucleotides 19 to 21
are ribonucleotides- nucloetide 153 tcgttaaata gtatacgnac a 21 154
21 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. nucleotides 19 to 21 are
ribonucleotides-nucleotide 154 tcgttaaata gtatacngac a 21 155 21
DNA Artificial Designed chimeric oligonucleotide primer to amplify
a portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. nucleotides 19 to 21 are
ribonucleotides-nucleotide 155 tcgttaaata gtatanggac a 21 156 20
DNA Artificial Designed chimeric oligonucleotide primer to amplify
a portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. nucleotides 18 to 20 are
ribonucleotides-nucleotide 156 tgctcaataa tcagacnaag 20 157 20 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-nucleotide 157 tgctcaataa tcagangaag 20 158 20 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-nucleotide 158 tgctcaataa tcagncgaag 20 159 21 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of vero toxin 2-encoding sequence from hemorrhagic
Escherichia coli O-157. "nucleotides 9 to 11 and 19 to 21 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 159
tacctggguu uttcttcggu a 21 160 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic Escherichia coli O-157.
"nucleotides 8 to 10 and 18 to 20 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 160 atagacauca agccctcgua 20
161 20 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 161
gtcccctgag atatatguuc 20 162 30 DNA Artificial Designed
oligonucleotide probe to detect a DNA fragment amplifing a portion
of vero toxin 2-encoding sequence from hemorrhagic Escherichia coli
O-157. 162 ccaacaaagt tatgtctctt cgttaaatag 30 163 20 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of iNOS-encoding sequence from mouse. "nucleotides 18 to 20
are ribonucleotides-other nucleotides are deoxyribonucleotides" 163
atgccattga gttcatcaac 20 164 19 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of iNOS-encoding
sequence from mouse. "nucleotides 17 to 19 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 164
tcttggtggc aaagatgag 19 165 20 DNA Artificial Designed
oligonucleotide primer to amplify a portion of iNOS-encoding
sequence from mouse. 165 atgccattga gttcatcaac 20 166 19 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
iNOS-encoding sequence from mouse 166 tcttggtggc aaagatgag 19 167
20 DNA Artificial Designed oligonucleotide primer designated as
GMO-PCR-F 20mer 167 atcgttgaag atgcctctgc 20 168 20 DNA Artificial
designed oligonucleotide primer designated as GMO-PCR-R 20mer 168
tccgtatgat cgcgcgtcat 20 169 20 DNA Artificial Designed chimeric
oligonucleotide primer designated as GMO-S1 20mer. "nucleotides 19
to 20 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 169 tttggagagg acacgctgac 20 170 20 DNA
Artificial Designed oligonucleotide primer designated as GMO-S2
20mer. "nucleotides 19 to 20 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 170 ggacacgctg acaagctgac 20 171 20 DNA
Artificial Designed oligonucleotide primer designated as GMO-A1
20mer. "nucleotides 19 to 20 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 171 ggctgtagcc actgatgcug 20
172 20 DNA Artificial Designed oligonucleotide primer designated as
GMO-A2 20 mer. "nucleotides 19 to 20 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 172 ttccggaaag gccagaggau 20
173 20 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of vero toxin 2-encoding sequence from
hemorrhagic Escherichia coli O-157. "nucleotides 18 to 20 are
(alpha-thio)ribonucleotides-other nucleotides are 173 tactgggttt
ttcttcggua 20 174 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of vero toxin
2-encoding sequence from hemorrhagic O-157. "nucleotides 18 to 20
are (alpha-thio)ribonucleotides-other nucleotides are 174
atagacatca agccctcgua 20 175 22 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of INOS-encoding
sequence from mouse. "nucleotides 20 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 175
tcatgccatt gagttcatca ac 22 176 22 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of INOS-encoding
sequence from mouse. "nucleotides 20 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 176
tggtaggttc ctgttgtttc ua 22 177 22 DNA Artificial Designed
oligonucleotide primer to amplify a portion of INOS-encoding
sequence from mouse. 177 tcatgccatt gagttcatca ac 22 178 22 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
INOS-encoding sequence from mouse. 178 tggtaggttc ctgttgtttc ta 22
179 20 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of lambda DNA."nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 179
ctgcgaggcg gtggcaaggg 20 180 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of lambda
DNA."nucleotides 19 to 21 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 180 ctgcctcgct ggccgtgccg c 21 181 23 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of INOS-encoding sequence from mouse. "nucleotides 21 to 23
are ribonucleotides-other nucleotides are deoxyribonucleotides" 181
ctcatgccat tgagttcatc aac 23 182 22 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of
INOS-encoding sequence from mouse. "nucleotides 20 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 182
gctggtaggt tcctgttgtu uc 22 183 19 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of pDON-AI
DNA."nucleotides 17 to 19 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 183 agctctgtat ctggcggac 19 184 21 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of pDON-AI DNA."nucleotides 19 to 21 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 184
gatcgggatt tttggactca g 21 185 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of HPV type16
DNA."nucleotides 19 to 21 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 185 caaaagagaa ctgcaatguu u 21 186 25 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of HPV type16 DNA."nucleotides 19 to 21 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 186
cgcctccatc cagtctatta atugu 25 187 27 DNA Artificial Designed
oligonucleotide probe to detect a DNA fragment amplifing a portion
of HPV DNA. 187 gaggacccac aggagcgacc cagaaag 27 188 20 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
HCV. 188 cactccacca tgaatcactc 20 189 20 DNA Artificial Designed
oligonucleotide primer to amplify a portion of HCV. 189 ggtgcacggt
ctacgagacc 20 190 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of HCV."nucleotides 19
to 21 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 190 ctgtgaggaa ctactgtcuu c 21 191 18 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of HCV."nucleotides 16 to 18 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 191 gcagaccact atggcucu 18
192 30 DNA Artificial Designed oligonucleotide probe to detect a
DNA fragment amplifing portion of HCV. 192 gtatgagtgt cgtgcagcct
ccaggacccc 30 193 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of
adenovirus."nucleotides 19 to 21 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 193 tgagacatat tatctgccac g
21 194 21 DNA Artificial Designed chimeric oligonucleotide primer
to amplify a portion of adenovirus."nucleotides 19 to 21 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 194
aaatggctag gaggtggaag a 21 195 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of
adenovirus."nucleotides 19 to 21 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 195 ttatcagcca gtacctctuc g
21 196 21 DNA Artificial Designed oligonucleotide primer to amplify
a portion of adenovirus 196 tgagacatat tatctgccac g 21 197 21 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
adenovirus. 197 aaatggctag gaggtggaag a 21 198 20 DNA Artificial
Designed oligonucleotide primer to amplify a portion of viroid
CSVd. 198 ggggaaacct ggaggaagtc 20 199 20 DNA Artificial Designed
oligonucleotide primer to amplify a portion of viroid CSVd. 199
cgggtagtag ccaaaggaag 20 200 19 DNA Artificial Designed
oligonucleotide primer to amplify a portion of pDON-AI DNA. 200
agctctgtat ctggcggac 19 201 21 DNA Artificial Designed
oligonucleotide primer to amplify a portion of pDON-AI DNA. 201
gatcgggatt tttggactca g 21 202 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of verotoxin-1 encoding
sequence from hemorrhagic Escherichia coli 0-157."nucleotides 18 to
20 are ribonucleotides-other nucleotides are deoxyribonucleotides"
202 ggggataatt tgtttgcagu 20 203 20 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of verotoxin-1
encoding sequence from hemorrhagic Escherichia coli
0-157."nucleotides 18 to 20 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 203 tcgttcaaca ataagccgua 20 204 30 DNA
Artificial Designed oligonucleotide probe to detect a DNA fragment
amplifying a portion of verotoxin-1 encoding sequence from
hemorrhagic Escherichia coli 0-157. 204 cgcccttcct ctggatctac
ccctctgaca 30 205 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of botulinum toxin A
encoding sequence from Clostridium botulinum."nucleotides 19 to 21
are ribonucleotides- other nucleotides are deoxyribonucleotides"
205 caccagaagc aaaacaaguu c 21 206 23 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of botulinum
toxin A encoding sequence from Clostridium botulinum."nucleotides
21 to 23 are ribonucleotides- other nucleotides are
deoxyribonucleotides" 206 ctattgatgt taacaacatt cuu 23 207 30 DNA
Artificial Designed oligonucleotide probe to detect a DNA fragment
amplifying a portion of botulinum toxin A encoding sequence
Clostridium botulinum. 207 gggagttaca aaattatttg agagaattta 30 208
21 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of viroid CSVd."nucleotides 19 to 21 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 208
cacccttcct ttagtttccu u 21 209 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of viroid
CSVd."nucleotides 18 to 20 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 209 cgttgaagct tcagttguuu 20 210 30 DNA
Artificial Designed oligonucleotide probe to detect a DNA fragment
amplifying a portion of viroid CSVd. 210 ccttcctctc ctggagaggt
cttctgccct 30 211 21 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of viroid
CSVd."nucleotides 19 to 21 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 211 cacccttcct ttagtttccu u 21 212 21 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of viroid CSVd."nucleotides 19 to 21 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 212
cgttgaagct tcagttgtuu c 21 213 21 DNA Artificial Designed
oligonucleotide primer to amplify a portion of viroid CSVd. 213
cacccttcct ttagtttcct t 21 214 21 DNA Artificial Designed
oligonucleotide primer to amplify a portion of viroid CSVd. 214
cgttgaagct tcagttgttt c 21 215 20 DNA Artificial Designed chimeric
oligonucleotide primer to amplify a portion of c-ki-ras
oncogene."nucleotides 18 to 20 are ribonucleotides-other
nucleotides are deoxyribonucleotides" 215 gactgaatat aaacttgugg 20
216 20 DNA Artificial Designed chimeric oligonucleotide primer to
amplify a portion of c-ki-ras oncogene."nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 216
ctattgttgg atcatatucg 20 217 20 DNA Artificial Designed
oligonucleotide primer to amplify a portion of c-ki-ras oncogene.
217 gactgaatat aaacttgtgg 20 218 20 DNA Artificial Designed
oligonucleotide primer to amplify a portion of c-ki-ras oncogene.
218 ctattgttgg atcatattcg 20 219 20 DNA Artificial Designed
chimeric oligonucleotide primer to amplify a portion of verotoxin-2
encoding sequence from hemorrhagic Escherichia coli
O-157."nucleotides 18 to 20 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 219 gacttttcga cccaacaaag 20 220 20 DNA
Artificial Designed chimeric oligonucleotide primer to amplify a
portion of verotoxin-2 encoding sequence from hemorrhagic
Escherichia coli O-157."nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 220
atatccacag caaaataacu 20 221 21 DNA Artificial Designed
oligonucleotide primer to amplify a portion of INOS-encoding
sequence from mouse. 221 cacaaggcca catcggattt c 21 222 21 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
INOS-encoding sequence from mouse. 222 tgcataccac ttcaacccga g 21
223 25 DNA Artificial Designed oligonucleotide primer designated as
pUC19 upper 150 to amplify a portion of plasmid pUC19. 223
ggtgtcacgc tcgtcgtttg gtatg 25 224 25 DNA Artificial Designed
chimeric oligonucleotide primer designated as pUC19 lower NN to
amplify a portion of plasmid pUC19. 224 gataacactg cggccaactt acttc
25 225 21 DNA Artificial Designed chimeric oligonucleotide primer
designated as SEA-1 to amplify a portion of Staphylococcus aureus.
"nucleotides 19 to 21 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 225 tgtatgtatg gtggtgtaac g 21 226 21 DNA
Artificial Designed chimeric oligonucleotide primer designated as
SEA-2 to amplify a portion of Staphylococcus aureus. "nucleotides
19 to 21 are ribonucleotides-other nucleotides are
deoxyribonucleotides" 226 taaccgtttc caaaggtacu g 21 227 19 DNA
Artificial Designed chimeric oligonucleotide primer designated as
HCV-F3 to amplify a portion of HCV. "nucleotides 17 to 19 are
ribonucleotides-other nucleotides are deoxyribonucleotides" 227
gcgtctagcc atggcguua 19 228 18 DNA Artificial Designed chimeric
oligonucleotide primer designated as HCV-R1 to amplify a portion of
HCV. "nucleotides 16 to 18 are ribonucleotides-other nucleotides
are deoxyribonucleotides" 228 gcagaccact atggcucu 18 229 30 DNA
Artificial Designed oligonucleotide primer designated as MF2 to
amplify a portion of pUC19 plasmid DNA. 229 ggatgtgctg caaggcgatt
aagttgggta 30 230 30 DNA Artificial Designed oligonucleotide primer
designated as MR1 to amplify a portion of pUC19 plasmid DNA. 230
tttacacttt atgcttccgg ctcgtatgtt 30 231 21 DNA Artificial Designed
oligonucleotide primer to amplify a portion of adenovirus. 231
ttatcagcca gtacctcttc g 21 232 714 DNA Thermotoga maritima 232
atgggaatag atgagcttta caaaaaagag tttggaatcg tagcaggtgt ggatgaagcg
60 ggaagagggt gcctcgcagg tcccgttgtg gcggccgctg tcgttctgga
aaaagaaata 120 gaaggaataa acgattcaaa acagctttcc cctgcgaaga
gggaaagact tttagatgaa 180 ataatggaga aggcagcagt tgggttagga
attgcgtctc cagaggaaat agatctctac 240 aacatattca atgccacaaa
acttgctatg aatcgagcac tggagaacct gtctgtgaaa 300 ccatcatttg
tactcgttga cgggaaagga atcgagttga gcgttcccgg tacatgctta 360
gtgaagggag accagaaaag caaattgata ggagcagctt ccattgttgc gaaggtcttc
420 agagatagat tgatgagcga gtttcacagg atgtatccac agttttcctt
ccacaaacac 480 aaaggttacg ccacaaaaga acatctgaac gaaatcagaa
agaacggagt tttaccaatc 540 caccggctga gttttgaacc tgttttagaa
cttctgaccg atgatttgtt gagggagttc 600 ttcgaaaaag gcctcatctc
cgaaaatcga ttcgaacgaa tattgaatct tctgggggcg 660 agaaaaagtg
tggttttccg gaaagaaaga acaaaccata atctccctct tttt 714 233 238 PRT
Thermotoga maritime 233 Met Gly Ile Asp Glu Leu Tyr Lys Lys Glu Phe
Gly Ile Val Ala Gly 1 5 10 15 Val Asp Glu Ala Gly Arg Gly Cys Leu
Ala Gly Pro Val Val Ala Ala 20 25 30 Ala Val Val Leu Glu Lys Glu
Ile Glu Gly Ile Asn Asp Ser Lys Gln 35 40 45 Leu Ser Pro Ala Lys
Arg Glu Arg Leu Leu Asp Glu Ile Met Glu Lys 50 55 60 Ala Ala Val
Gly Leu Gly Ile Ala Ser Pro Glu Glu Ile Asp Leu Tyr 65 70 75 80 Asn
Ile Phe Asn Ala Thr Lys Leu Ala Met Asn Arg Ala Leu Glu Asn 85 90
95 Leu Ser Val Lys Pro Ser Phe Val Leu Val Asp Gly Lys Gly Ile Glu
100 105 110 Leu Ser Val Pro Gly Thr Cys Leu Val Lys Gly Asp Gln Lys
Ser Lys 115 120 125 Leu Ile Gly Ala Ala Ser Ile Val Ala Lys Val Phe
Arg Asp Arg Leu 130 135 140 Met Ser Glu Phe His Arg Met Tyr Pro Gln
Phe Ser Phe His Lys His 145 150 155 160 Lys Gly Tyr Ala Thr Lys Glu
His Leu Asn Glu Ile Arg Lys Asn Gly 165 170 175 Val Leu Pro Ile His
Arg Leu Ser Phe Glu Pro Val Leu Glu Leu Leu 180 185 190 Thr Asp Asp
Leu Leu Arg Glu Phe Phe Glu Lys Gly Leu Ile Ser Glu 195 200 205 Asn
Arg Phe Glu Arg Ile Leu Asn Leu Leu Gly Ala Arg Lys Ser Val
210 215 220 Val Phe Arg Lys Glu Arg Thr Asn His Asn Leu Pro Leu Phe
225 230 235 234 663 DNA Pyrococcus horikoshii 234 atgaaggttg
ctggagttga tgaagcgggg agggggccgg taattggccc gttagtaatt 60
ggagtagccg ttatagatga gaaaaatatt gagaggttac gtgacattgg ggttaaagac
120 tccaaacaat taactcctgg gcaacgtgaa aaactattta gcaaattaat
agatatccta 180 gacgattatt atgttcttct cgttaccccc aaggaaatag
atgagaggca tcattctatg 240 aatgaactag aagctgagaa attcgttgta
gccttgaatt ctttaaggat caagccgcag 300 aagatatatg tggactctgc
cgatgtagat cctaagaggt ttgctagtct aataaaggct 360 gggttgaaat
atgaagccac ggttatcgcc gagcataaag ccgatgcaaa gtatgagata 420
gtatcggcag catcaataat tgcaaaggtc actagggata gagagataga gaagctaaag
480 caaaagtatg gggaatttgg ttctggctat ccgagtgatc cgagaactaa
ggagtggctt 540 gaagaatatt acaaacaata tggtgacttt cctccaatag
ttaggagaac ttgggaaacc 600 gctaggaaga tagaggaaag gtttagaaaa
aatcagctaa cgcttgataa attccttaag 660 tga 663 235 30 DNA Artificial
PCR primer PhoNde for cloning a gene encoding a polypeptide having
a RNaseHII activity from Pyrococcus horikoshii 235 aggaggaaaa
tcatatgaag gttgctggag 30 236 30 DNA Artificial PCR primer PhoBam
for cloning a gene encoding a polypeptide having a RNaseHII
activity from Pyrococcus horikoshii 236 ttacatgaag gatccaagat
cacttaagga 30 237 673 DNA Pyrococcus horikoshii 237 atgaaggttg
ctggagttga tgaagcgggg agggggccgg taattggccc gttagtaatt 60
ggagtagccg ttatagatga gaaaaatatt gagaggttac gtgacattgg ggttaaagac
120 tccaaacaat taactcctgg gcaacgtgaa aaactattta gcaaattaat
agatatccta 180 gacgattatt atgttcttct cgttaccccc aaggaaatag
atgagaggca tcattctatg 240 aatgaactag aagctgagaa attcgttgta
gccttgaatt ctttaaggat caagccgcag 300 aagatatatg tggactctgc
cgatgtagat cctaagaggt ttgctagtct aataaaggct 360 gggttgaaat
atgaagccac ggttatcgcc gagcataaag ccgatgcaaa gtatgagata 420
gtatcggcag catcaataat tgcaaaggtc actagggata gagagataga gaagctaaag
480 caaaagtatg gggaatttgg ttctggctat ccgagtgatc cgagaactaa
ggagtggctt 540 gaagaatatt acaaacaata tggtgacttt cctccaatag
ttaggagaac ttgggaaacc 600 gctaggaaga tagaggaaag gtttagaaaa
aatcagctaa cgcttgataa attccttaag 660 tgatcttgga tcc 673 238 220 PRT
Pyrococcus horikoshii 238 Met Lys Val Ala Gly Val Asp Glu Ala Gly
Arg Gly Pro Val Ile Gly 1 5 10 15 Pro Leu Val Ile Gly Val Ala Val
Ile Asp Glu Lys Asn Ile Glu Arg 20 25 30 Leu Arg Asp Ile Gly Val
Lys Asp Ser Lys Gln Leu Thr Pro Gly Gln 35 40 45 Arg Glu Lys Leu
Phe Ser Lys Leu Ile Asp Ile Leu Asp Asp Tyr Tyr 50 55 60 Val Leu
Leu Val Thr Pro Lys Glu Ile Asp Glu Arg His His Ser Met 65 70 75 80
Asn Glu Leu Glu Ala Glu Lys Phe Val Val Ala Leu Asn Ser Leu Arg 85
90 95 Ile Lys Pro Gln Lys Ile Tyr Val Asp Ser Ala Asp Val Asp Pro
Lys 100 105 110 Arg Phe Ala Ser Leu Ile Lys Ala Gly Leu Lys Tyr Glu
Ala Thr Val 115 120 125 Ile Ala Glu His Lys Ala Asp Ala Lys Tyr Glu
Ile Val Ser Ala Ala 130 135 140 Ser Ile Ile Ala Lys Val Thr Arg Asp
Arg Glu Ile Glu Lys Leu Lys 145 150 155 160 Gln Lys Tyr Gly Glu Phe
Gly Ser Gly Tyr Pro Ser Asp Pro Arg Thr 165 170 175 Lys Glu Trp Leu
Glu Glu Tyr Tyr Lys Gln Tyr Gly Asp Phe Pro Pro 180 185 190 Ile Val
Arg Arg Thr Trp Glu Thr Ala Arg Lys Ile Glu Glu Arg Phe 195 200 205
Arg Lys Asn Gln Leu Thr Leu Asp Lys Phe Leu Lys 210 215 220 239 626
DNA Archaeogobus fulgidus 239 atgaaggcag gcatcgatga ggctggaaag
ggctgcgtca tcggcccact ggttgttgca 60 ggagtggctt gcagcgatga
ggataggctg agaaagcttg gtgtgaaaga ctccaaaaag 120 ctaagtcagg
ggaggagaga ggaactagcc gaggaaataa ggaaaatctg cagaacggag 180
gttttgaaag tttctcccga aaatctcgac gaaaggatgg ctgctaaaac cataaacgag
240 attttgaagg agtgctacgc tgaaataatt ctcaggctga agccggaaat
tgcttatgtt 300 gacagtcctg atgtgattcc cgagagactt tcgagggagc
ttgaggagat tacggggttg 360 agagttgtgg ccgagcacaa ggcggacgag
aagtatcccc tggtagctgc ggcttcaatc 420 atcgcaaagg tggaaaggga
gcgggagatt gagaggctga aagaaaaatt cggggatttc 480 ggcagcggct
atgcgagcga tccgaggaca agagaagtgc tgaaggagtg gatagcttca 540
ggcagaattc cgagctgcgt gagaatgcgc tggaagacgg tgtcaaatct gaggcagaag
600 acgcttgacg atttctaaac gaaacc 626 240 30 DNA Artificial PCR
primer AfuNde for cloning a gene encoding a polypeptide having a
RNaseHII activity from Archaeoglobus fulgidus 240 aagctgggtt
tcatatgaag gcaggcatcg 30 241 30 DNA Artificial PCR primer AfuBam
for cloning a gene encoding a polypeptide having a RNaseHII
activity from Archaeoglobus fulgidus 241 tggtaataac ggatccgttt
agaaatcgtc 30 242 638 DNA Archaeoglobus fulgidus 242 catatgaagg
caggcatcga tgaggctgga aagggctgcg tcatcggccc actggttgtt 60
gcaggagtgg cttgcagcga tgaggatagg ctgagaaagc ttggtgtgaa agactccaaa
120 aagctaagtc aggggaggag agaggaacta gccgaggaaa taaggaaaat
ctgcagaacg 180 gaggttttga aagtttctcc cgaaaatctc gacgaaagga
tggctgctaa aaccataaac 240 gagattttga aggagtgcta cgctgaaata
attctcaggc tgaagccgga aattgcttat 300 gttgacagtc ctgatgtgat
tcccgagaga ctttcgaggg agcttgagga gattacgggg 360 ttgagagttg
tggccgagca caaggcggac gagaagtatc ccctggtagc tgcggcttca 420
atcatcgcaa aggtggaaag ggagcgggag attgagaggc tgaaagaaaa attcggggat
480 ttcggcagcg gctatgcgag cgatccgagg acaagagaag tgctgaagga
gtggatagct 540 tcaggcagaa ttccgagctg cgtgagaatg cgctggaaga
cggtgtcaaa tctgaggcag 600 aagacgcttg acgatttcta aacggatccc cgggtacc
638 243 205 PRT Archaeoglobus fulgidus 243 Met Lys Ala Gly Ile Asp
Glu Ala Gly Lys Gly Cys Val Ile Gly Pro 1 5 10 15 Leu Val Val Ala
Gly Val Ala Cys Ser Asp Glu Asp Arg Leu Arg Lys 20 25 30 Leu Gly
Val Lys Asp Ser Lys Lys Leu Ser Gln Gly Arg Arg Glu Glu 35 40 45
Leu Ala Glu Glu Ile Arg Lys Ile Cys Arg Thr Glu Val Leu Lys Val 50
55 60 Ser Pro Glu Asn Leu Asp Glu Arg Met Ala Ala Lys Thr Ile Asn
Glu 65 70 75 80 Ile Leu Lys Glu Cys Tyr Ala Glu Ile Ile Leu Arg Leu
Lys Pro Glu 85 90 95 Ile Ala Tyr Val Asp Ser Pro Asp Val Ile Pro
Glu Arg Leu Ser Arg 100 105 110 Glu Leu Glu Glu Ile Thr Gly Leu Arg
Val Val Ala Glu His Lys Ala 115 120 125 Asp Glu Lys Tyr Pro Leu Val
Ala Ala Ala Ser Ile Ile Ala Lys Val 130 135 140 Glu Arg Glu Arg Glu
Ile Glu Arg Leu Lys Glu Lys Phe Gly Asp Phe 145 150 155 160 Gly Ser
Gly Tyr Ala Ser Asp Pro Arg Thr Arg Glu Val Leu Lys Glu 165 170 175
Trp Ile Ala Ser Gly Arg Ile Pro Ser Cys Val Arg Met Arg Trp Lys 180
185 190 Thr Val Ser Asn Leu Arg Gln Lys Thr Leu Asp Asp Phe 195 200
205 244 18 DNA Artificial Designed chimeric oligonucleotide primer
designated as MTIS2F to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 16 to 18 are ribonucleotides-other
nucleotides are deoxyribonucleotides." 244 tctcgtccag cgccgcuu 18
245 21 DNA Artificial Designed chimeric oligonucleotide primer
designated as MTIS2R to amplify a portion of Mycobacterium
tuberculosis DNA. "nucleotides 19 to 21 are ribonucleotides-other
nucleotides are deoxyribonucleotides." 245 gacaaaggcc acgtaggcga a
21 246 20 DNA Artificial Designed chimeric oligonucleotide primer
designated as CT2F to amplify a portion of Chlamydia trachomatis
cryptic plasmid DNA."nucleotides 18 to 20 are ribonucleotides-
other nucleotides are deoxyribonucleotides." 246 ctggatttat
cggaaaccuu 20 247 18 DNA Artificial Designed chimeric
oligonucleotide primer designated as CT2R to amplify a portion of
Chlamydia trachomatis cryptic plasmid DNA."nucleotides 16 to 18 are
ribonucleotides- other nucleotides are deoxyribonucleotides." 247
aggcctctga aacgacuu 18 248 19 DNA Artificial Designed chimeric
oligonucleotide primer designated as K-F-1033(60) to amplify a
portion of Mycobacterium tuberculosis DNA."nucleotides 17 to 19 are
ribonucleotides-other nucleotides are deoxyribonucleotides." 248
cacatcgatc cggttcagc 19 249 20 DNA Artificial Designed chimeric
oligonucleotide primer designated as K-R-1133(62) to amplify a
portion of Mycobacterium tuberculosis DNA."nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides." 249
tgatcgtctc ggctagtgca 20 250 22 DNA Artificial Designed chimeric
oligonucleotide primer designated as K-F-1033(68) to amplify a
portion of Mycobacterium tuberculosis DNA."nucleotides 20 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides." 250
gtacacatcg atccggttca gc 22 251 22 DNA Artificial Designed chimeric
oligonucleotide primer designated as K-R-1133(68) to amplify a
portion of Mycobacterium tuberculosis DNA."nucleotides 20 to 22 are
ribonucleotides-other nucleotides are deoxyribonucleotides." 251
gttgatcgtc tcggctagtg ca 22 252 20 DNA Artificial Designed
oligonucleotide primer designated as F26 to amplify a portion of
Mycobacterium tuberculosis DNA. 252 ccggagactc cagttcttgg 20 253 20
DNA Artificial Designed oligonucleotide primer designated as R1310
to amplify a portion of Mycobacterium tuberculosis DNA. 253
gtctctggcg ttgagcgtag 20 254 22 DNA Artificial Designed chimeric
oligonucleotide primer designated as pDON-AI-68-1 to amplify a
portion of pDON-AI. "nucleotides 20 to 22 are ribonucleotides-other
nucleotides are deoxyribonucleotides." 254 actagctctg tatctggcgg ac
22 255 23 DNA Artificial Designed chimeric oligonucleotide primer
designated as pDON-AI-68-2 to amplify a portion of pDON-AI.
"nucleotides 21 to 23 are ribonucleotides-other nucleotides are
deoxyribonucleotides." 255 acgatcggga tttttggact cag 23 256 300 DNA
Homo sapiens proto-oncogene Wnt-5a 256 cactagattt tttgtttggg
gaggttggct tgaacataaa tgaaatatcc tgtattttct 60 tagggatact
tggttagtaa attataatag tagaaataat acatgaatcc cattcacagg 120
tttctcagcc caagcaacaa ggtaattgcg tgccattcag cactgcacca gagcagacaa
180 cctatttgag gaaaaacagt gaaatccacc ttcctcttca cactgagccc
tctctgattc 240 ctccgtgttg tgatgtgatg ctggccacgt ttccaaacgg
cagctccact gggtcccctt 300 257 300 DNA Homo sapiens ribosomal
protein S5 257 cgccgagtga cagagacgct caggctgtgt tctcaggatg
accgagtggg agacagcagc 60 accagcggtg gcagagaccc cagacatcaa
gctctttggg aagtggagca ccgatgatgt 120 gcagatcaat gacatttccc
tgcaggatta cattgcagtg aaggagaagt atgccaagta 180 cctccctcac
agtgcagggc ggtatgccgc aaacgctttc cgcaaagctc agtgtcccat 240
tgtggagcgc ctcactaact ccatgatgat gcacggccgc aacaacggca agaagctcat
300 258 300 DNA Homo sapiens diaphorase 258 tctatacaaa ttttcagaag
gttattttct ttatcattgc taaactgatg acttaccatg 60 ggatggggtc
cagtcccatg accttggggt acaattgtaa acctagagtt ttatcaactt 120
tggtgaacag ttttggcata atagtcaatt tctacttctg gaagtcatct cattccactg
180 ttggtattat ataattcaag gagaatatga taaaacactg ccctcttgtg
gtgcattgaa 240 agaagagatg agaaatgatg aaaaggttgc ctgaaaaatg
ggagacagcc tcttacttgc 300 259 300 DNA Human protocadherin 259
agtctcttgg gatcccctaa ccagagcctt tttgccatag ggctgcacac tggtcaaatc
60 agtactgccc gtccagtcca agacacagat tcacccaggc agactctcac
ggtcttgatc 120 aaagacaatg gggagccttc gctctccacc actgctaccc
tcactgtgtc agtaaccgag 180 gactctcctg aagcccgagc cgagttcccc
tctggctctg ccccccggga gcagaaaaaa 240 aatctcacct tttatctact
tctttcccta atcctggttt ctgtggggtt tgtggtcaca 300 260 80 DNA
Artificial Designed oligonucleotide for making of pIC62. 260
catgtacatc acagtagtcg ttcacagggt tttccggcca taatggcctt tcctgtgtgt
60 gtgctacagc tagtcagtca 80 261 20 DNA Artificial Designed chimeric
oligonucleotide primer designated as ICAN2."nucleotides 19 to 20
are ribonucleotides- other nucleotides are deoxyribonucleotides."
261 actgactagc tgtagcacac 20 262 20 DNA Artificial Designed
chimeric oligonucleotide primer designated as ICAN6."nucleotides 19
to 20 are ribonucleotides- other nucleotides are
deoxyribonucleotides." 262 acatcacagt agtcgttcac 20 263 20 DNA
Artificial Designed oligonucleotide primer designated as ICAN2
DNA." 263 actgactagc tgtagcacac 20 264 20 DNA Artificial Designed
oligonucleotide primer designated as ICAN6 DNA. 264 acatcacagt
agtcgttcac 20 265 23 DNA Artificial Designed oligonucleotide primer
to amplify a portion of ribosomal protein S18-encoding sequence
from mouse. 265 gtctctagtg atccctgaga agt 23 266 23 DNA Artificial
Designed oligonucleotide primer to amplify a portion of ribosomal
protein S18-encoding sequence from mouse. 266 tggatacacc cacagttcgg
ccc 23 267 23 DNA Artificial Designed oligonucleotide primer to
amplify a portion of transferrin receptor (TFR)-encoding sequence
from mouse. 267 ccgcgctccg acaagtagat gga 23 268 23 DNA Artificial
Designed oligonucleotide primer to amplify a portion of transferrin
receptor (TFR)-encoding sequence from mouse. 268 ccaaagagtg
caaggtctgc ctc 23 269 23 DNA Artificial Designed oligonucleotide
primer to amplify a portion of stromal cell derived factor 4
(Sdf4)-encoding sequence from mouse. 269 tctgatggat gcaaccgcta gac
23 270 23 DNA Artificial Designed oligonucleotide primer to amplify
a portion of stromal cell derived factor 4 (Sdf4)-encoding sequence
from mouse. 270 gaactcttca tgcacgttgc ggg 23 271 23 DNA Artificial
Designed oligonucleotide primer to amplify a portion of cytoplasmic
beta-actin encoding sequence from mouse. 271 tgatggtggg aatgggtcag
aag 23 272 23 DNA Artificial Designed oligonucleotide primer to
amplify a portion of cytoplasmic beta-actin encoding sequence from
mouse. 272 agaagcactt gcggtgcacg atg 23 273 23 DNA Artificial
Designed oligonucleotide primer to amplify a portion of ornithine
decarboxylase-encoding sequence from mouse. 273 gatgaaagtc
gccagagcac atc 23 274 23 DNA Artificial Designed oligonucleotide
primer to amplify a portion of ornithine decarboxylase-encoding
sequence from mouse. 274 ttgatcctag cagaagcaca ggc 23 275 23 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
hypoxanthine guanine phosphoribosyl transferase (HPRT)- encoding
sequence from mouse. 275 ggacaggact gaaagacttg ctc 23 276 23 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
hypoxanthine guanine phosphoribosyl transferase (HPRT)- encoding
sequence from mouse. 276 gtctggcctg tatccaacac ttc 23 277 23 DNA
Artificial Designed oligonucleotide primer to amplify a portion of
tyrosine 3-monooxygenase encoding sequence from mouse. 277
atgagctggt gcagaaggcc aag 23 278 23 DNA Artificial Designed
oligonucleotide primer to amplify a portion of tyrosine
3-monooxygenase encoding sequence from mouse. 278 ttcccctcct
tctcctgctt ctg 23 279 21 DNA Artificial Designed oligonucleotide
primer designated as MCS-F. 279 ccattcaggc tgcgcaatgt t 21 280 22
DNA Artificial Designed oligonucleotide primer designated as MCS-R
280 tggcacgaca ggtttcccga ct 22 281 24 DNA Artificial Designed
chimeric oligonucleotide primer designated as MF2N3(24).
"nucleotides 22 to 24 are ribonucleoitdes-other nucleotides are
deoxyribonucleotides." 281 gctgcaaggc gattaagttg ggua 24 282 24 DNA
Artificial Designed chimeric oligonucleotide primer designated as
MR1N3(24). "nucleotides 22 to 24 are ribonucleoitdes-other
nucleotides are
deoxyribonucleotides." 282 ctttatgctt ccggctcgta tguu 24 283 16 DNA
Artificial Designed chimeric oligonucleotide primer designated as
MTIS2F-16 to amplify a portion of Mycobacterium tuberculosis
DNA."nucleotides 14 to 16 are ribonucleotides-other nucleotides are
deoxyribonucleotides." 283 tcgtccagcg ccgcuu 16 284 20 DNA
Artificial Designed chimeric oligonucleotide primer designated as
MTIS2R-ACC to amplify a portion of Mycobacterium tuberculosis
DNA."nucleotides 18 to 20 are ribonucleotides-other nucleotides are
deoxyribonucleotides." 284 caaaggccac gtaggcgaac 20 285 20 DNA
Artificial Designed oligonucleotide primer designated as
MTIS-PCR-F-2 to amplify a portion of Mycobacterium tuberculosis
DNA. 285 cgaccgcatc aaccgggagc 20 286 20 DNA Artificial Designed
oligonucleotide primer designated as MTIS-PCR-R-2 to amplify a
portion of Mycobacterium tuberculosis DNA. 286 cccaggatcc
tgcgagcgta 20 287 45 DNA Artificial Designed oligonucleotide primer
designated as SP6-HCV-F to amplify a portion of HCV. 287 ccatttaggt
gacactatag aatactgatg ggggcgacac tccac 45 288 45 DNA Artificial
Designed oligonucleotide primer designated as SP6-HCV-R to amplify
a portion of HCV 288 agctctaata cgactcacta tagggtcgca agcaccctat
caggc 45 289 20 DNA Artificial Designed chimeric oligonucleotide
primer designated as HCV-A S to amplify a portion of
HCV."nucleotides 18 to 20 are ribonucleotides-other nucleotides are
deoxyribonucleotides." 289 gggtcctttc ttggatcaac 20 290 20 DNA
Artificial Designed chimeric oligonucleotide primer designated as
HCV-A A to amplify a portion of HCV. "nucleotides 18 to 20 are
ribonucleotides-other nucleotides are deoxyribonucleotides." 290
gacccaacac tactcggcua 20
* * * * *
References