U.S. patent application number 10/269031 was filed with the patent office on 2003-09-18 for annealing control primer and its uses.
Invention is credited to Chun, Jong-Yoon.
Application Number | 20030175749 10/269031 |
Document ID | / |
Family ID | 28038596 |
Filed Date | 2003-09-18 |
United States Patent
Application |
20030175749 |
Kind Code |
A1 |
Chun, Jong-Yoon |
September 18, 2003 |
Annealing control primer and its uses
Abstract
The present invention relates to an annealing control primer for
improving annealing specificity in nucleic acid amplification and
its applications to all fields of nucleic acid
amplification-involved technology. The present primer comprises (a)
a 3'-end portion having a hybridizing nucleotide sequence
substantially complementary to a site on a template nucleic acid to
hybridize therewith; (b) a 5'-end portion having a pre-selected
arbitrary nucleotide sequence; and (c) a regulator portion
positioned between said 3'-end portion and said 5'-end portion
comprising at least one universal base or non-discriminatory base
analog, whereby said regulator portion is capable of regulating an
annealing portion of said primer in association with annealing
temperature.
Inventors: |
Chun, Jong-Yoon; (Seoul,
KR) |
Correspondence
Address: |
McDERMOTT, WILL & EMERY
600 13th Street, N.W.
Washington
DC
20005-3096
US
|
Family ID: |
28038596 |
Appl. No.: |
10/269031 |
Filed: |
October 11, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
10269031 |
Oct 11, 2002 |
|
|
|
10014496 |
Dec 14, 2001 |
|
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Current U.S.
Class: |
435/6.14 ;
536/24.3 |
Current CPC
Class: |
C12Q 2525/101 20130101;
C12Q 1/6853 20130101; C12Q 1/6853 20130101; C12Q 1/6876
20130101 |
Class at
Publication: |
435/6 ;
536/24.3 |
International
Class: |
C12Q 001/68; C07H
021/04 |
Foreign Application Data
Date |
Code |
Application Number |
Dec 8, 2001 |
WO |
PCT/KR01/02133 |
Claims
What is claimed is:
1. An annealing control primer for improving annealing specificity
in nucleic acid amplification, which comprises: (a) a 3'-end
portion having a hybridizing nucleotide sequence substantially
complementary to a site on a template nucleic acid to hybridize
therewith; (b) a 5'-end portion having a pre-selected arbitrary
nucleotide sequence; and (c) a regulator portion positioned between
said 3'-end portion and said 5'-end portion comprising at least one
universal base or non-discriminatory base analog, whereby said
regulator portion is capable of regulating an annealing portion of
said primer in association with annealing temperature.
2. The annealing control primer according to claim 1, wherein said
pre-selected arbitrary nucleotide sequence of said 5'-end portion
is substantially not complementary to any site on said template
nucleic acid.
3. The annealing control primer according to claim 1, wherein said
template nucleic acid is gDNA, cDNA or mRNA.
4. The annealing control primer of claim 3, wherein said gDNA or
cDNA is single or double-stranded DNA.
5. The annealing control primer according to claim 1, wherein said
nucleic acid amplification is performed under a first and a second
annealing temperatures.
6. The annealing control primer according to claim 5, wherein said
first annealing temperature in said nucleic acid amplification is
identical to or lower than said second annealing temperature.
7. The annealing control primer according to claim 5, wherein said
3'-end portion is involved in annealing at said first annealing
temperature and said 5'-end portion serves as a priming site at
said second annealing temperature.
8. The annealing control primer according to claim 5, wherein said
regulator portion is capable of restricting said annealing portion
of said primer to said 3'-end portion at said first annealing
temperature.
9. The annealing control primer according to claim 5, wherein said
first annealing temperature is between about 30.degree. C. and
68.degree. C.
10. The annealing control primer according to claim 5, wherein said
second annealing temperature is between about 50.degree. C. and
72.degree. C.
11. The annealing control primer according to claim 1, wherein said
annealing control primer has a general formula of
5'-X.sub.p-Y.sub.q-Z.su- b.r-3', wherein X.sub.p represents said
5'-end portion having said pre-selected arbitrary nucleotide
sequence substantially not complementary to any site on the
template nucleic acid; Y.sub.q represents said regulator portion
comprising at least one universal base or non-discriminatory base
analog; Z.sub.r represents said 3'-end portion having a hybridizing
nucleotide sequence substantially complementary to a site on the
template nucleic acid to hybridize therewith; wherein p, q and r
represent the number of nucleotides; and wherein X, Y and Z is
deoxyribonucleotide or ribonucleotide.
12. The annealing control primer according to claim 11, wherein
said universal base or non-discriminatory base analog is capable of
forming base-pairs with each of the natural DNA/RNA bases with
little discrimination between said natural DNA/RNA bases.
13. The annealing control primer according to claim 11, wherein
said universal base or non-discriminatory base analog is selected
from the group consisting of deoxyinosine, inosine,
7-deaza-2'-deoxyinosine, 2-aza-2'-deoxyinosine, 2'-OMe inosine,
2'-F inosine, deoxy 3-nitropyrrole, 3-nitropyrrole, 2'-OMe
3-nitropyrrole, 2'-F 3-nitropyrrole,
1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, deoxy
5-nitroindole, 5-nitroindole, 2'-OMe 5-nitroindole, 2'-F
5-nitroindole, deoxy 4-nitrobenzimidazole, 4-nitrobenzimidazole,
deoxy 4-aminobenzimidazole, 4-aminobenzimidazole, deoxy nebularine,
2'-F nebularine, 2'-F 4-nitrobenzimidazole, PNA-5-introindole,
PNA-nebularine, PNA-inosine, PNA-4-nitrobenzimidazole,
PNA-3-nitropyrrole, morpholino-5-nitroindole,
morpholino-nebularine, morpholino-inosine,
morpholino-4-nitrobenzimidazole, morpholino-3-nitropyrrole,
phosphoramidate-5-nitroindole, phosphoramidate-nebularine,
phosphoramidate-inosine, phosphoramidate-4-nitrobenzimidazole,
phosphoramidate-3-nitropyrrole, 2'-0-methoxyethyl inosine,
2'0-methoxyethyl nebularine, 2'-0-methoxyethyl 5-nitroindole,
2'-O-methoxyethyl 4-nitro-benzimidazole, 2'-0-methoxyethyl
3-nitropyrrole, and combinations thereof.
14. The annealing control primer according to claim 11, wherein
said universal base or non-discriminatory base analog is
deoxyinosine, 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole or
5-nitroindole.
15. The annealing control primer according to claim 11, wherein
said regulator portion comprises contiguous nucleotides having
universal base or non-discriminatory base analog.
16. The annealing control primer according to claim 11, wherein
said deoxyribonucleotide is naturally occurring dNMP, modified
nucleotide and non-natural nucleotide.
17. The annealing control primer according to claim 11, wherein p
represents an integer of 15 to 60.
18. The annealing control primer according to claim 11, wherein q
is at least 2.
19. The annealing control primer according to claim 11, wherein q
is at least 3.
20. The annealing control primer according to claim 11, wherein q
represents an integer of 2 to 15.
21. The annealing control primer according to claim 11, wherein r
represents an integer of 6 to 50.
22. The annealing control primer according to claim 11, wherein p
is an integer of 15 to 60, q is an integer of 2 to 15 and r is an
integer of 6 to 30.
23. The annealing control primer according to claim 11, wherein
X.sub.p comprises a universal primer sequence.
24. The annealing control primer according to claim 11, wherein
X.sub.p includes a sequence or sequences recognized by a
restriction endonuclease or restriction endonucleases.
25. The annealing control primer according to claim 11, wherein
X.sub.p comprises at least one nucleotide with a label for
detection or isolation.
26. The annealing control primer according to claim 11, wherein
Z.sub.r is a nucleotide sequence which hybridizes to the
polyadenosine (polyA) tail of an mRNA.
27. The annealing control primer according to claim 26, wherein
Z.sub.r comprises at least 10 contiguous deoxythymidine
nucleotides.
28. The annealing control primer according to claim 26, wherein
Z.sub.r comprises at least 10 contiguous deoxythymidine nucleotides
having 3'-V at its 3'-end; in which V is one selected from the
group consisting of deoxyadenosine, deoxycytidine and
deoxyguanosine.
29. The annealing control primer according to claim 26, wherein
Z.sub.r comprises at least 10 contiguous deoxythymidine nucleotides
having 3'-NV at its 3'-end; in which V is one selected from the
group consisting of deoxyadenosine, deoxycytidine and
deoxyguanosine, and N is one selected from the group consisting of
deoxyadenosine, deoxythymidine, deoxycytidine and
deoxyguanosine.
30. The annealing control primer according to claim 11, wherein
Z.sub.r is a nucleotide sequence substantially complementary to a
target sequence in the template nucleic acid.
31. The annealing control primer according to claim 11, wherein
Z.sub.r is a random nucleotide sequence.
32. The annealing control primer according to claim 11, wherein
Z.sub.r is a nucleotide sequence substantially complementary to a
consensus sequence found in a gene family.
33. The annealing control primer according to claim 11, wherein
Z.sub.r is a degenerate nucleotide sequence selected from a
plurality of combinations of nucleotides encoding a predetermined
amino acid sequence.
34. The annealing control primer according to claim 11, wherein
Z.sub.r comprises at least one ribonucleotide.
35. The annealing control primer according to claim 11, wherein
Z.sub.r comprises at least one nucleotide complementary to allelic
site.
36. The annealing control primer according to claim 11, wherein
Z.sub.r comprises at least one mismatch nucleotide to a target
nucleic acid for mutagenesis.
37. A kit comprising the primer or the primer set according to any
one of claims 1-36.
38. The kit according to claim 37, wherein the kit further
comprises a primer or a primer pair having a nucleotide sequence
corresponding to the 5'-end portion of said primer.
39. A method for amplifying a nucleic acid sequence from a DNA or a
mixture of nucleic acids, wherein said method comprises performing
an amplification reaction using primers, characterized in that at
least one primer has the same structure as the primer of claim
1.
40. The method according to claim 39, wherein said method is
performed using two stage amplifications, which comprises: (a)
performing a first-stage amplification of said nucleic acid
sequence at a first annealing temperature comprising at least two
cycles of primer annealing, primer extending and denaturing, using
the primer pair of claim leach having at its 3'-end portion a
hybridizing sequence substantially complementary to a region of
said nucleic acid sequence to hybridize therewith, under conditions
in which each primer anneals to said region of said nucleic acid
sequence, whereby the amplification product of said nucleic acid
sequence is generated; and (b) performing a second-stage
amplification of said amplification product generated from step (a)
at a second annealing temperature, which is high stringent
conditions, comprising at least one cycle of primer annealing,
primer extending and denaturing, using the same primers as used in
step (a) or a primer pair each comprising a pre-selected arbitrary
nucleotide sequence corresponding to each 5'-end portion of said
primers used in step (a), under conditions in which each primer
anneals to the 3'- and 5'-ends of said amplification product,
respectively, whereby said amplification product is
re-amplified.
41. A method for selectively amplifying a target nucleic acid
sequence from a DNA or a mixture of nucleic acids, wherein said
method comprises performing an amplification reaction using
primers, characterized in that at least one primer has the same
structure as the primer of claim 1.
42. The method according to claim 41, wherein said method is
performed using two stage amplifications, which comprises: (a)
performing a first-stage amplification of said target nucleic acid
sequence at a first annealing temperature comprising at least two
cycles of primer annealing, primer extending and denaturing, using
the primer pair of claim 1 each having at its 3'end portion a
hybridizing sequence substantially complementary to a region of
said target nucleic acid sequence to hybridize therewith, under
conditions in which each primer anneals to its target nucleotide
sequence, whereby the amplification product of said target
nucleotide sequence is generated; and (b) performing a second-stage
amplification of said amplification product generated from step (a)
at a second annealing temperature, which is high stringent
conditions, comprising at least one cycle of primer annealing,
primer extending and denaturing, using the same primers as used in
step (a) or a primer pair each comprising a pre-selected arbitrary
nucleotide sequence corresponding to each 5'-end portion of said
primers used in step (a), under conditions in which each primer
anneals to the 3'- and 5'-ends of said amplification product,
respectively, whereby said amplification product is
re-amplified.
43. A method for selectively amplifying a target nucleic acid
sequence from an mRNA, wherein said method comprises reverse
transcribing said mRNA and performing an amplification reaction
using primers, characterized in that at least one primer has the
same structure as the primer of claim 1.
44. The method according to claim 43, wherein said method is
performed using two stage amplifications, which comprises: (a)
contacting said mRNA with an oligonucleotide dT primer which is
hybridized to polyA tail of said mRNA under conditions sufficient
for template driven enzymatic deoxyribonucleic acid synthesis to
occur; (b) reverse transcribing said mRNA to which said
oligonucloetide dT pirmer hybridizes to produce a first DNA strand
that is complementary to said mRNA to which said oligonucloetide dT
pirmer hybridizes; (c) performing a first-stage amplification of
said target nucleic acid sequence from said first DNA strand
obtained from step (b) at a first annealing temperature comprising
at least two cycles of primer annealing, primer extending and
denaturing, using the primer pair of clai 1 each having at its
3'end portion a hybridizing sequence substantially complementary to
a region of said target nucleic acid sequence to hybridize
therewith, under conditions in which each primer anneals to its
target nucleotide sequence, whereby the amplification product of
said target nucleotide sequence is generated; and (d) performing a
second-stage amplification of said amplification product generated
from step (c) at a second annealing temperature, which is high
stringent conditions, comprising at least one cycle of primer
annealing, primer extending and denaturing, using the same primers
as used in step (c) or a primer pair each comprising a pre-selected
arbitrary nucleotide sequence corresponding to each 5'-end portion
of said primers used in step (c), under conditions in which each
primer anneals to the 3'- and 5'-ends of said amplification
product, respectively, whereby said amplification product is
re-amplified.
45. A method for detecting DNA complementary to differentially
expressed mRNA in two or more nucleic acid samples, wherein said
method comprises reverse transcribing said mRNA and performing an
amplification reaction using primers, characterized in that at
least one primer has the same structure as the primer of claim
1.
46. The method according to claim 45, wherein said method is
performed using two stage amplifications, which comprises: (a)
providing a first sample of nucleic acids representing a first
population of mRNA transcripts and a second sample of nucleic acids
representing a second population of mRNA transcripts; (b)
separately contacting each of said first nucleic acid sample and
said second nucleic acid sample with a first primer of claim 1, in
which the 3'-end portion of said first primer comprises a
hybridizing nucleotide sequence substantially complementary to a
first site in said differentially expressed mRNA to hybridize
therewith, under conditions sufficient for template driven
enzymatic deoxyribonucleic acid synthesis to occur; (c) reverse
transcribing said differentially expressed mRNA to which said first
primer hybridizes to produce a first population of first cDNA
strands that are complementary to said differentially expressed
mRNA in said first nucleic acid sample to which said first primer
hybridizes, and a second population of first cDNA strands that are
complementary to said differentially expressed mRNA in said second
nucleic acid sample to which said first primer hybridizes; (d)
purifying and quantifying each of said first and second populations
of first cDNA strands; (e) performing a first-stage amplification
of each of said first and second population of first DNA strands
obtained from step (d) at a first annealing temperature comprising
at least one cycle of primer annealing, primer extending and
denaturing, using a second primer of claim 1 having at its 3 end
portion a hybridizing sequence substantially complementary to a
second site in said first and second populations of first cDNA
strands, under conditions in which said second primer anneals to
said second site in each population of said first cDNA strands,
whereby first and second populations of second cDNA strands are
generated; (f) performing a second-stage amplification of each
second cDNA strand generated from step (e) at a second annealing
temperature, which is high stringent conditions, comprising at
least two cycles of primer annealing, primer extending and
denaturing, using the same first and second primers as used in
steps (b) and (e), respectively, or a primer pair each comprising a
pre-selected arbitrary nucleotide sequence corresponding to each
5'-end portion of said first and second primers used in steps (b)
and (e), respectively, under conditions in which each primer
anneals to the 3'- and 5'-end sequences of each second cDNA strand,
respectively, whereby amplification products of said second cDNA
strands are generated, and (g) comparing the presence or level of
individual amplification products in said first and second
populations of amplification products obtained from step (f).
47. A method for rapidly amplifying a target cDNA fragment
comprising a cDNA region corresponding to the 3'-end region of an
mRNA, wherein said method comprises reverse transcribing said mRNA
and performing an amplification reaction using primers,
characterized in that at least one primer has the same structure as
the primer of claim 1.
48. The method according to claim 47, wherein said method is
performed using two stage amplifications, which comprises: (a)
contacting mRNAs with a first primer of claim 1, in which the
3'-end portion of said primer comprises a hybridizing nucleotide
sequence substantially complementary to poly A tails of said mRNAs
to hybridize therewith, under conditions sufficient for template
driven enzymatic deoxyribonucleic acid synthesis to occur; (b)
reverse transcribing said mRNAs to which said first primer
hybridizes to produce a population of first cDNA strands that are
complementary to said mRNAs to which said first primer hybridizes;
(c) performing a first-stage amplification of said first cDNA
strands at a first annealing temperature comprising at least one
cycle of primer annealing, primer extending and denaturing, using a
second primer of claim 1 having at its 3'-end portion a
gene-specific hybridizing nucleotide sequence substantially
complementary to a site in one of said first cDNA strands to
hybridize therewith, under conditions in which said second primer
anneals to a gene-specific site on one of said first cDNA strands,
whereby a gene-specific second cDNA strand is generated; and (d)
performing a second-stage amplification of said gene-specific
second cDNA strand generated from step (c) at a second annealing
temperature, which is high stringent conditions, comprising at
least two cycles of primer annealing, primer extending and
denaturing, using the same first and second primers as used in
steps (a) and (c), respectively, or a primer pair each comprising a
pre-selected arbitrary nucleotide sequence corresponding to each
5'-end portion of said first and second primers used in steps (a)
and (c), respectively, under conditions in which each primer
anneals to the 3'- and 5'-end sequences of a gene-specific second
cDNA strand, respectively, whereby an amplification product of a
gene-specific cDNA strand is generated.
49. A method for rapidly amplifying a target DNA fragment
comprising a cDNA region corresponding to the 5'-end region of an
mRNA, wherein said method comprises reverse transcribing said mRNA
and performing an amplification reaction using primers,
characterized in that at least one primer has the same structure as
the primer of claim 1.
50. The method according to claim 49, wherein said method is
performed using two stage amplifications, which comprises: (a)
contacting mRNAs with an oligonucleotide dT primer or random primer
as a cDNA synthesis primer under conditions sufficient for template
driven enzymatic deoxyribonucleic acid synthesis to occur, in which
said cDNA synthesis primer comprises a hybridizing nucleotide
sequence substantially complementary to a region of an mRNA to
hybridize therewith; (b) reverse transcribing said mRNAs, using a
reverse transcriptase, to which said cDNA synthesis primer
hybridizes to produce a population of first cDNA strands that are
complementary to said mRNAs to which said cDNA synthesis primer
hybridizes, whereby mRNA-cDNA intermediates are generated; (c)
permitting cytosine residues to be tailed at the 3'-ends of said
first cDNA strands in the form of said mRNA-cDNA intermediates by
the terminal transferase reaction of reverse transcriptase; (d)
contacting the cytosine tails at the 3'-ends of said first cDNA
strands generated from step (c) with an oligonucleotide which
comprises a 3'-end portion and a 5'-end portion separated by a
group of universal base or non-discriminatory base analog, wherein
the 3'-end portion comprises at least three guanine residues at its
3'-end to hybridize with said cytosine tails at the 3'-ends of said
first cDNA strands and the 5'-end portion comprises a pre-selected
arbitrary nucleotide sequence, under conditions in which said 3-end
portion of said oligonucleotide is hybridized to said cytosine
tails; (e) extending the tailed 3'-ends of said first cDNA strands
to generate an additional sequence complementary to said
oligonucleotide using reverse transcriptase, in which said
oligonucleotide serves as a template in the extension reaction,
whereby full-length first cDNA strands are extended; (f) performing
a first-stage amplification of said full-length first cDNA strands
obtained from step (e) at a first annealing temperature, which
comprises the steps of: (i) at least one cycle of primer annealing,
primer extending and denaturing using a first primer comprising a
nucleotide sequence substantially complementary to the 3'-end
sequences of said full-length first cDNA strands under conditions
in which said first primer anneals to said full-length first cDNA
strands, under conditions in which said first primer anneals to the
3'- ends of said full-length first cDNA strands, whereby
full-length second cDNA strands are generated; (ii) at least one
cycle of primer annealing, primer extending and denaturing using a
second primer of claim 1 having at its 3'-end portion a
gene-specific hybridizing sequence substantially complementary to a
region on one of said full-length second cDNA strands to hybridize
therewith, under conditions in which said second primer anneals to
a gene-specific site on one of said full-length second cDNA
strands, whereby a gene-specific cDNA strand is generated; and (g)
performing a second-stage amplification of said gene-specific cDNA
strand at a second annealing temperature, which is high stringent
conditions, comprising at least two cycles of primer annealing,
primer extending and denaturing, using the same first and second
primers as used in steps (f)-(i) and (f)-(ii), respectively, or a
primer pair each comprising a nucleotide sequence corresponding to
each 5'-end portion of said first and second primers as used in
steps (f)-(i) and (f)-(ii), respectively, under conditions in which
each primer anneals to the 3'- and 5'-end sequences of a
gene-specific cDNA strand, respectively, whereby an amplification
product of a gene-specific cDNA strand is generated.
51. A method for amplifying a population of full-length
double-stranded cDNAs complementary to mRNAs, wherein said method
comprises reverse transcribing said mRNA and performing an
amplification reaction using primers, characterized in that at
least one primer has the same structure as the primer of claim
1.
52. The method according to claim 51, wherein said method
comprises: (a) contacting said mRNAs with a first primer of claim
1, in which the 3'-end portion of said first primer has a
hybridizing nucleotide sequence substantially complementary to poly
A tails of said mRNAs to hybridize therewith, under conditions
sufficient for template driven enzymatic deoxyribonucleic acid
synthesis to occur; (b) reverse transcribing said mRNAs, using a
reverse transcriptase, to which said first primer hybridizes to
produce said population of first cDNA strands that are
complementary to said mRNAs to which said primer hybridizes,
whereby mRNA-cDNA intermediates are generated; (c) permitting
cytosine residues to be tailed at the 3'-ends of said first cDNA
strands in the form of said mRNA-cDNA intermediates by the terminal
transferase reaction of reverse transcriptase; (d) contacting the
cytosine tails at the 3'-ends of said first cDNA strands generated
from step (c) with an oligonucleotide which comprises a 3'-end
portion and a 5'-end portion separated by a group of universal base
or non-discriminatory base analog, wherein the 3'-end portion
comprises at least three guanine residues at its 3'-end to
hybridize with said cytosine tails at the 3'-ends of said first
cDNA strands and the 5'-end portion comprises a pre-selected
arbitrary nucleotide sequence, under conditions in which said 3-end
portion of said oligonucleotide is hybridized to said cytosine
tails; (e) extending the tailed 3'-ends of said first cDNA strands
to generate an additional sequence complementary to said
oligonucleotide using reverse transcriptase, in which said
oligonucleotide serves as a template in the extension reaction,
whereby full-length first cDNA strands are extended; and (f)
performing an amplification of said full-length first cDNA strands
generated from step (e) comprising at least two cycles of primer
annealing, primer extending and denaturing, 4 0 using a primer pair
each comprising a nucleotide sequence corresponding to the same
first primer and oligonucleotide as used in steps (a) and (d),
respectively, or a primer pair each comprising a nucleotide
sequence corresponding to each 5'-end portion of said first primer
and oligonucleotide used in steps (a) and (d), respectively, under
conditions in which each primer anneals to the 3'- and 5'-end
sequences of said full-length first cDNA strands, respectively,
whereby amplification products of full-length cDNA strands
complementary to said mRNAs are generated.
53. A method for amplifying 5'-enriched double-stranded cDNAs
complementary to mRNAs, wherein said method comprises comprising
reverse transcribing said mRNAs and performing an amplification
reaction using primers, characterized in that at least one primer
has the same structure as the primer of claim 1.
54. The method according to claim 53, wherein said method
comprises: (a) contacting said mRNAs with a first primer of claim 1
under conditions sufficient for template driven enzymatic
deoxyribonucleic acid synthesis to occur, wherein the 3'-end
portion of said first primer has at least six random nucleotide
sequences; (b) performing the steps (b)-(e) of claim 52, whereby
5'-enriched first cDNA strands are extended; (c) performing an
amplification of said 5'-enriched first cDNA strands generated from
step (b) comprising at least two cycles of primer annealing, primer
extending and denaturing, using a primer pair each comprising a
nucleotide sequence corresponding to each 5'-end portion of said
primer and oligonucleotide used in steps (a) and (b), respectively,
under conditions in which each primer anneals to the 3'- and 5'-end
sequences of said 5'-enriched first cDNA strands, respectively,
whereby amplification products of 5'-enriched cDNA strands are
generated.
55. A method for amplifying more than one target nucleotide
sequence simultaneously using more than one pair of primers in the
same reaction, wherein said method comprises performing an
amplification reaction using primers, characterized in that at
least one primer has the same structure as the primer of claim
1.
56. The method according to claim 55, wherein said method is
performed using two stage amplifications, which comprises: (a)
performing a first-stage amplification of more than one target
nucleotide sequence at a first annealing temperature comprising at
least two cycles of primer annealing, primer extending and
denaturing, using the primer pairs of claim 1 in which its 3'end
portion each of each primer pair has a hybridizing nucleotide
sequence substantially complementary to a region of said target
nucleic acid sequence to hybridize therewith, under conditions in
which each of said primer pairs anneals to its target nucleotide
sequence, whereby the amplification products of target nucleotide
sequences are generated; and (b) performing a second-stage
amplification of said amplification products generated from step
(a) at a second annealing temperature, which is high stringent
conditions, comprising at least one cycle of primer annealing,
primer extending and denaturing, using the same primer pairs as
used in step (a) or primer pairs each comprising a pre-selected
arbitrary nucleotide sequence corresponding to each 5'-end portion
of said primer pairs used in step (a), under conditions in which
each of each primer pair anneals to the 3'- and 5'-end sequences of
said amplification products generated from step (a), respectively,
whereby said amplification products are re-amplified in the same
reaction.
57. A method for producing a DNA fingerprint of gDNA, wherein said
method comprises performing an amplification reaction using
primers, characterized in that at least one primer has the same
structure as the primer of claim 1.
58. The method according to claim 57, wherein said method is
performed using two stage amplifications, which comprises: (a)
performing a first-stage amplification of said DNA fingerprint,
which is a set of discrete DNA segments characteristic of genome,
from said gDNA at a first annealing temperature comprising at least
two cycles of primer annealing, primer extending and denaturing,
using the primer or the primer pair of claim 1, wherein each primer
has at its 3'-end portion an arbitrary nucleotide sequence
substantially complementary to sites on said gDNA to hybridize
therewith, under conditions in which said primer or said primer
pair anneals to said gDNA, whereby said set of discrete DNA
segments characterized as a DNA fingerprint is produced; and (b)
performing a second-stage amplification of said set of discrete DNA
segments generated from step (a) at a second annealing temperature,
which is high stringent conditions, comprising at least one cycle
of primer annealing, primer extending and denaturing, using the
same primer or primer pair as used in step (a) or a primer or a
primer pair each comprising a nucleotide sequence corresponding to
each 5'-end portion of said primer or primer pair used in step (a),
under conditions in which said primer or each of said primer pair
anneals to the 3'- and 5'-end sequences of said set of discrete DNA
segments generated from step (a), respectively, whereby said set of
discrete DNA segments is re-amplified.
59. A method for producing a RNA fingerprint of an mRNA sample,
wherein said method comprises reverse transcribing and performing
an amplification reaction using primers, characterized in that at
least one primer has the same structure as the primer of claim
1.
60. The method according to claim 59, wherein said method is
performed using two stage amplifications, which comprises: (a)
contacting said mRNA sample with a first primer of claim 1, in
which said first primer has a hybridizing nucleotide sequence
substantially complementary to poly A tails of said mRNA sample to
hybridize therewith, under conditions sufficient for template
driven enzymatic deoxyribonucleic acid synthesis to occur; (b)
reverse transcribing said mRNA sample to which said first primer
hybridizes to produce a population of first cDNA strands that are
complementary to said mRNA sample to which said first primer
hybridizes; (c) performing a first-stage amplification of said
population of first cDNA strands generated from step (b) at a first
annealing temperature comprising at least one cycle of primer
annealing, primer extending and denaturing, using a second primer
or primer pair of claim 1, wherein each primer has at its 3'-end
portion an arbitrary nucleotide sequence substantially
complementary to sites on said first cDNA strands to hybridize
therewith, under conditions in which said primer or primer pair
anneals to said mRNA sample, whereby a set of discrete cDNA
segments characterized as a RNA fingerprint is produced; and (d)
performing a second stage amplification of said set of discrete
cDNA segments generated from step (c) at a second annealing
temperature which is high stringent conditions, comprising at least
one cycle of primer annealing, primer extending and denaturing,
using the same primer or primer pair as used in step (c) or a
primer or primer pair each comprising a nucleotide sequence
corresponding to each 5'-end portion of said primer or primer pair
used in step (c), under conditions in which said primer or each of
said primer pair anneals to the 3'- and 5'-end sequences of said
set of discrete cDNA segments generated from step (c),
respectively, whereby said set of discrete cDNA segments is
re-amplified.
61. A method for identifying conserved homology segments in a
multigene family from an mRNA sample, wherein said method comprises
reverse transcribing and performing an amplification reaction using
primers, characterized in that at least one primer has the same
structure as the primer of claim 1.
62. The method according to claim 61, wherein said method is
performed using two stage amplifications, which comprises: (a)
contacting said mRNA sample with a first primer of claim 1, in
which said first primer has a hybridizing nucleotide sequence
substantially complementary to poly A tails of said mRNA sample to
hybridize therewith, under conditions sufficient for template
driven enzymatic deoxyribonucleic acid synthesis to occur; (b)
reverse transcribing said mRNA sample to which said first primer
hybridizes to produce a population of first cDNA strands that are
complementary to said mRNA sample to which said first primer
hybridizes; (c) performing a first-stage amplification of said
population of first cDNA strands generated from step (b) at a first
annealing temperature comprising at least one cycle of claim 1
having at its 3'end portion a hybridizing sequence substantially
complementary to a consensus sequence or a degenerate sequence
encoding amino acid sequence of a conserved homology segment on
said first cDNA strands to hybridize therewith, under conditions in
which said second primer anneals to said consensus sequence or
degenerate sequence of first cDNA strands, whereby 3'-end cDNA
segments having said consensus sequence or degenerate sequence are
generated; and (d) performing a second stage amplification of said
3'-end cDNA segments generated from step (c) at a second annealing
temperature which is high stringent conditions, comprising at least
two cycles of primer annealing, primer extending and denaturing,
using the same first and second primers as used in steps (a) and
(c) or a primer pair each comprising a nucleotide sequence
corresponding to each 5'-end portion of said first and second
primers used in steps (a) and (c), respectively, under conditions
in which each primer anneals to the 3'- and 5'-end sequences of
said 3'-end cDNA segments, respectively, whereby said 3'-end
conserved homology cDNA segments are amplified.
63. The method according to claim 61, wherein said method is
performed using two stage 10 amplifications, which comprises: (a)
performing steps of (a)-(e) of claim 52, whereby full-length cDNA
strands are generated; (b) performing a first-stage amplification
of said full-length first cDNA strands obtained from step (a) at a
first annealing temperature, which comprises the steps of: (i) at
least one cycle of primer annealing, primer extending and
denaturing using a first primer comprising a nucleotide sequence
substantially complementary to the 3'-end sequences of said
full-length first cDNA strands under conditions in which said first
primer anneals to said full-length first cDNA strands, under
conditions in which said first primer anneals to the 3'- ends of
said full-length first cDNA strands, whereby full-length second
cDNA strands are generated; and (ii) at least one cycle of primer
annealing, primer extending and denaturing using a second primer of
claim 1 having at its 3'end portion a hybridizing sequence
substantially complementary to a consensus sequence or a degenerate
sequence encoding amino acid sequence of a conserved homology
segment on said full-length second cDNA strands to hybridize
therewith, under conditions in which said second primer anneals to
said consensus sequence or degenerate sequence of full-length
second cDNA strands, whereby 5'-end cDNA segments having said
consensus sequence or degenerate sequence are generated; and (c)
performing a second stage amplification of said 5'-end cDNA
segments generated from step (b) at a second annealing temperature
which is high stringent conditions, comprising at least two cycles
of primer annealing, primer extending and denaturing, using the
same first and second primers as used in steps (b)-(i) and
(b)-(ii), respectively, or a primer pair each comprising a
nucleotide sequence corresponding to each 5'-end portion of said
first and second primers used in steps (b)-(i) and (b)-(ii),
respectively, under conditions in which each primer anneals to the
3'- and 5'-end sequences of said 5'-end cDNA segments,
respectively, whereby said 5'-end conserved homology cDNA segments
are amplified.
64. A method for identifying conserved homology segments in a
multigene family from gDNA, wherein said method comprises
performing an amplification reaction using primers, characterized
in that at least one primer has the same structure as the primer of
claim 1.
65. The method according to claim 64, wherein said method is
performed using two stage amplifications, which comprises: (a)
performing a first-stage amplification of said conserved homology
segments from said gDNA at a first annealing temperature comprising
at least two cycles of primer annealing, primer extending and
denaturing, using the primer or the primer pair of claim 1, wherein
each primer has at its 3' end portion a hybridizing sequence
substantially complementary to a consensus sequence or a degenerate
sequence encoding amino acid sequence of a conserved homology
segment on said gDNA to hybridize therewith, under conditions in
which said primer or said primer pair anneals to said consensus
sequence or degenerate sequence of gDNA, whereby genomic DNA
segments having said consensus sequence or degenerate sequence are
generated; and (b) performing a second-stage amplification of said
genomic DNA segments generated from step (a) at a second annealing
temperature, which is high stringent conditions, comprising at
least one cycle of primer annealing, primer extending and
denaturing, using the same primer or primer pair as used in step
(a) or a primer or a primer pair each comprising a nucleotide
sequence corresponding to each 5'-end portion of said primer or
primer pair used in step (a), under conditions in which said primer
or each of said primer pair anneals to the 3'- and 5'-end sequences
of said genomic DNA segments generated from step (a), respectively,
whereby said conserved homology genomic segments are amplified.
66. A method for identifying a nucleotide variation in a target
nucleic acid, wherein said method comprises performing an
amplification reaction using primers, characterized in that at
least one primer has the same structure as the primer of claim
1.
67. The method according to claim 66, wherein said method is
performed using two stage amplifications, which comprises: (a)
performing a first-stage amplification to produce a first DNA
strand complementary to said target nucleic acid including said
nucleotide variation at a first annealing temperature comprising at
least one cycle of primer annealing, primer extending and
denaturing, using a first primer of claim 1 having at its 3'-end
portion a hybridizing sequence substantially complementary to a
pre-selected sequence at a first site of said target nucleic acid
to hybridize therewith, wherein each of said first primer and said
first site comprises an interrogation position corresponding to
said nucleotide variation, whereby said first DNA strand
complementary to said target nucleic acid including said nucleotide
variation is generated when said interrogation position is occupied
by the complementary nucleotide of said first primer to its
corresponding nucleotide of said first site; and (b) performing a
second-stage amplification of said first DNA strand generated from
step (a) at a second annealing temperature, which is high stringent
conditions, comprising the steps: (i) at least one cycle of primer
annealing, primer extending and denaturing using a second primer of
claim 1 having at its 3'-end portion a hybridizing sequence
substantially complementary to a pre-selected sequence at a second
site of said target nucleic acid to hybridize therewith under
conditions in which said second primer anneals to said second site
of the target nucleic acid, whereby a second DNA strand
complementary to said first DNA strand including said nucleotide
variation is generated; and (ii) at least one cycle of primer
annealing, primer extending and denaturing using the same first and
second primers as used in steps (a) and (b)-(i) or a primer pair
each having a hybridizing sequence complementary or corresponding
to the 3'- and 5'-ends of said second DNA strand generated from
step (b)-(i) to hybridize therewith, under conditions in which each
primer anneals to the 3'- and 5'-end sequences of said second DNA
strand, respectively, whereby said second DNA strand which
comprises said first and second sites of said target nucleic acid
at its 3'-and 5'-ends is amplified so that a short target
nucleotide segment corresponding to said second DNA strand
containing said nucleotide variation is generated.
68. The method according to claim 66, wherein said method is
performed using two individual amplifications of a first and a
second amplifications in which said second amplification is
performed using two stage amplifications, which comprises: (a)
performing said first amplification to produce a short DNA strand
fragment containing said nucleotide variation between its ends
comprising at least two cycles of primer annealing, primer
extending and denaturing, using a primer pair each primer
comprising a hybridizing sequence substantially complementary to a
pre-selected sequence at a site of said target nucleic acid under
conditions that said nucleotide variation is positioned between
said pre-selected sequences, in which at least one primer of said
primer set is the primer of claim 1 having at its 3'-end portion
said hybridizing sequence, whereby said short DNA strand fragment
containing said nucleotide variation between its ends is amplified;
(b) performing a first-stage amplification of said second
amplification to produce a first DNA strand complementary to said
short DNA strand fragment including said nucleotide variation at a
first annealing temperature comprising at least one cycle of primer
annealing, primer extending and denaturing, using a first primer of
claim lhaving at its 3'-end portion a hybridizing sequence
substantially complementary to a pre-selected sequence at a first
site of said target nucleic acid to hybridize therewith, wherein
each of said first primer and said first site comprises an
interrogation position corresponding to said nucleotide variation,
whereby said first DNA strand complementary to said target nucleic
acid including said nucleotide variation is generated when said
interrogation position is occupied by the complementary nucleotide
of said first primer to its corresponding nucleotide of said first
site; and (c) performing a second-stage amplification of said
second amplification of said first DNA strand generated from step
(a) at a second annealing temperature, which is high stringent
conditions, comprising at least one cycle of primer annealing,
primer extending and denaturing using a primer pair in which
amongst said primer pair one is the same as said primer of claim 1
used in step (a) the other is the same as said first primer used in
step (b), or a primer pair each having a hybridizing sequence
complementary or corresponding to the 3'- and 5'-ends of said first
DNA strand generated from step (b) to hybridize therewith, under
conditions in which each primer anneals to the 3'- and 5'-end
sequences of said first DNA strand, respectively, whereby said
first DNA strand is amplified so that a short target nucleotide
segment corresponding to said first DNA strand containing said
nucleotide variation is generated.
69. A method for mutagenesis in a target nucleic acid, comprising
performing an amplification reaction using primers, characterized
in that at least one primer has the same structure as the primer of
claim 1.
70. The method according to claim 69, wherein said mutagenesis is
site-directed and uses two stages amplifications, comprising the
steps of: (a) performing a first-stage amplification of said target
nucleic acid sequence at a first annealing temperature comprising
at least two cycles of primer annealing, primer extending and
denaturing, using a primer pair of claim 1 each having at its 3'end
portion a hybridizing sequence substantially complementary to a
region of said target nucleic acid sequence to hybridize therewith,
wherein said hybridizing sequence has at least one mismatch
nucleotide to generate site-directed mutation, under conditions in
which said primer or primer pair anneals to its target nucleotide
sequence, whereby an amplification product containing site-directed
mutation site is generated; and (b) performing a second-stage
amplification of said amplification product generated from step (a)
at a second annealing temperature, which is high stringent
conditions, comprising at least one cycle of primer annealing,
primer extending and denaturing, using the same primers as used in
step (a) or a primer pair each comprising a pre-selected arbitrary
nucleotide sequence corresponding to each 5'-end portion of said
primers used in step (a), under conditions in which each primer
anneals to the 3'- and 5'-ends of said amplification product,
respectively, whereby said amplification product containing
site-directed mutation site is re-amplified.
71. A kit for nucleic acid amplification, which comprises the
annealing control primer or annealing control primer set described
in claim 40.
72. A kit for selective amplification of a target nucleic acid
sequence from DNA, which comprises the annealing control primer or
annealing control primer set described in claim 42.
73. A kit for selective amplification of a target nucleic acid
sequence from mRNA, which comprises the annealing control primer or
annealing control primer set described in claim 44.
74. A kit for detecting DNA complementary to differentially
expressed mRNA, which comprises the annealing control primer or
annealing control primer set described in claim 46.
75. A kit for rapidly amplifying a target cDNA fragment comprising
a cDNA region corresponding to the 3'-end region of an mRNA, which
comprises the annealing control primer or annealing control primer
set described in claim 48.
76. A kit for rapidly amplifying a target cDNA fragment comprising
a cDNA region corresponding to the 5'-end region of an mRNA, which
comprises the annealing control primer or annealing control primer
set described in claim 50.
77. A kit for amplifying a population of full-length
double-stranded cDNAs complementary to mRNAs, which comprises the
annealing control primer or annealing control primer set described
in claim 52.
78. A kit for amplifying 5'-enriched double-stranded cDNAs
complementary to the 5'-end regions of mRNAs, which comprises the
annealing control primer or annealing control primer set described
in claim 54.
79. A kit for amplifying more than one target nucleotide sequence
simultaneously, which comprises the annealing control primer or
annealing control primer set described in claim 56.
80. A kit for producing a DNA fingerprint by use of gDNA, which
comprises the annealing control primer or annealing control primer
set described in claim 58.
81. A kit for producing a RNA fingerprint by use of mRNA, which
comprises the annealing control primer or annealing control primer
set described in claim 60.
82. A kit for identifying a conserved homology segment in a
multigene family by use of mRNA, which comprises the annealing
control primer or annealing control primer set described in claim
62 or 63.
83. A kit for identifying a conserved homology segment in a
multigene family by use of gDNA, which comprises the annealing
control primer or annealing control primer set described in claim
65.
84. A kit for identifying a nucleotide variation in a target
nucleic acid, which comprises the annealing control primer or
annealing control primer set described in claim 67 or 68.
85. A kit for mutagenesis in a target nucleic acid, which comprises
the annealing control primer or annealing control primer set
described in claim 70.
Description
BACKGROUND OF THE INVENTION
[0001] 1. Field of the Invention
[0002] The present invention relates to an annealing control primer
and its applications. More particularly, the present invention
relates to an annealing control primer for improving annealing
specificity in nucleic acid amplification and its applications to
all fields of nucleic acid amplification-involved technology.
[0003] 2. Description of the Related Art
[0004] Nucleic acid amplification is a pivotal process for a wide
variety of methods in molecular biology, so that various
amplification methods have been proposed. For example, Miller, H.
I. et al. (WO 89/06700) disclose a nucleic acid sequence
amplification based on the hybridization of a promoter/primer
sequence to a target single-stranded DNA ("ssDNA") followed by
transcription of many RNA copies of the sequence. Other known
nucleic acid amplification procedures include transcription-based
amplification systems (Kwoh, D. et al., Proc. Natl. Acad. Sci.
U.S.A., 86:1173(1989); and Gingeras T. R. et al., WO 88/10315).
[0005] Schemes based on ligation of two or more oligonucleotides in
the presence of nucleic acid having the sequence of the resulting
"di-oligonucleotide", thereby amplifying the di-oligonucleotide,
are also known (Wu, D. Y. et al., Genomics 4:560 (1989)), which are
called "Ligation Chain Reaction" (LCR).
[0006] Davey, C. et al. (European Pat. Appln. Publication No.
329,822) disclose a nucleic acid amplification process involving
cyclically synthesizing single-stranded RNA ("ssRNA"), ssDNA, and
double-stranded DNA (dsDNA). The ssRNA is a first template for a
first primer oligonucleotide, which is elongated by reverse
transcriptase (RNA-dependent DNA polymerase). The RNA is then
removed from resulting DNA:RNA duplex by the action of ribonuclease
H. The resultant ssDNA is a second template for a second primer,
which also includes the sequences of an RNA polymerase promoter.
This primer is then extended by DNA polymerase, resulting as a
double-stranded DNA ("dsDNA") molecule, having a sequence identical
to that of the original RNA between the primers and having
additionally, at one end, a promoter sequence. This promoter
sequence can be used by the appropriate RNA polymerase to produce
many RNA copies of the DNA. These copies can then re-enter the
cycle leading to very rapid amplification.
[0007] The most predominant process for nucleic acid amplification
known as polymerase chain reaction (hereinafter referred to as
"PCR"), is based on repeated cycles of denaturation of
double-stranded DNA, followed by oligonucleotide primer annealing
to the DNA template, and primer extension by a DNA polymerase
(Mullis et al. U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,800,159;
Saiki et al. 1985). The oligonucleotide primers used in PCR are
designed to anneal to opposite strands of the DNA, and are
positioned so that the DNA polymerase catalyzed extension product
of one primer can serve as the template strand for the other
primer. The PCR amplification process results in the exponential
increase of discrete DNA fragments whose length is defined by the
5' ends of the oligonucleotide primers.
[0008] The success in the nucleic acid amplifications, in
particular PCR amplification, relies on the specificity with which
a primer anneals only to its target (and not non-target) sequences
and therefore it is important to optimize this molecular
interaction. Whether a primer can anneal only to its perfect
complement or also to sequences that have one or more mismatches,
depends critically upon the annealing temperature. In general, the
higher the annealing temperature, the more specific annealing of
the primer to its perfect matched template and so the greater the
likelihood of only target sequence amplification can be
accomplished. The lower the temperature, the more mismatches
between template and primer can be tolerated, leading to increased
amplification of non-target sequences. Adjusting the annealing
temperature can alter the specificity of pairing between template
and primer. For examples, if there is no product, the temperature
may be too high and can be reduced. If there are products in
control where only one primer is present, this indicates that the
single primer is annealing to more than one region of the template.
In this case, the annealing temperature should be increased.
Considering such effect of annealing temperature on primer
annealing specificity, there remains a strong need for an annealing
control primer system which is capable of controlling primer
annealing in accordance with annealing temperature to enhance
primer annealing specificity regardless of primer design.
[0009] In addition to annealing temperature, several "primer search
parameters" such as primer length, GC content and PCR product
length (Dieffenbach et al., 1995) should be considered for primer
annealing specificity. If a primer, which satisfies all such
parameters, were employed, primer annealing would be specified,
resulting in the significant enhancement of primer annealing
specificity during target DNA amplification and the freedom from
the problems such as backgrounds and non-specific products arising
from primers used in the experiments. It is usual that
well-designed primers can help avoid non-specific annealing and
backgrounds as well as distinguish between cDNAs or genomic
templates in RNA-PCR.
[0010] Many approaches have been developed to improve primer
annealing specificity and therefore accomplish the amplification of
the desired product. Examples are touchdown PCR (Don et al., 1991),
hot start PCR (D'Aquila et al., 1991), nested PCR (Mullis and
Faloona, 1987) and booster PCR (Ruano et al., 1989). Another
alternative approaches have been also reported that various
`enhancer` compounds can improve the specificity of PCR. The
enhancer compounds include chemicals that increase the effective
annealing temperature of the reaction, DNA binding proteins and
commercially available reagents. However, there is no `magic`
additive that will ensure the success in every PCR and it is very
tedious to test different additives under different conditions such
as annealing temperature. Although these approaches have
contributed to the improvement of primer annealing specificity in
some cases, they have not accessed fundamentally to a solution for
the problems arising from primers used in the PCR amplification,
such as non-specific products and high backgrounds.
[0011] In many cases, the primer sequence does not need to be a
perfect complement to the template sequence. The region of the
primer that should be perfectly matched to the template is the
3'-end because this end is the region of the primer extended by the
DNA polymerase and is therefore the most important for ensuring the
specificity of annealing to the correct target sequence. The 5'-end
of the primer is less important in determining specificity of
annealing to the target sequence and can be modified to carry
additional sequence such as restriction sites and promoter
sequences that are not complementary to the template (McPherson and
Moller 2000). This notion is adapted to the design of the annealing
control primers of this invention as described below.
[0012] PCR-based techniques have been widely used not only for
amplification of a target DNA sequence but also for scientific
applications or methods in the fields of biological and medical
research such as Reverse transcriptase PCR (RT-PCR), Differential
Display PCR (DD-PCR), Cloning of known or unknown genes by PCR,
Rapid amplification of EDNA ends (RACE) and PCR-based genomic
analysis (McPherson and Moller, 2000). The followings are only
representatives of PCR applications.
[0013] Techniques designed to identify genes that are
differentially regulated by cells under various physiological or
experimental conditions (for example, differentiation,
carcinogenesis, pharmacological treatment) have become pivotal in
modern biology. One such method for screening differences in gene
expression between various cell types or between different stages
of cell development with the availability of PCR is known as
Differential Display PCR (DD-PCR), described by Liang and Pardee in
1992. This method uses combinations of 10-mer arbitrary primers
with anchored cDNA primers and generates fragments that originate
mostly from the poly(A) tail and extend about 50-600 nucleotide
upstream. By combining 3' anchored Oligo(dT) primers and short 5'
arbitrary primers, the subsets of the transcriptome are amplified,
the resulting cDNA fragments are generally separated on denaturing
polyacrylamide gel and visualized autoradiographically.
[0014] Although this method is simple and rapid and only requires
small amounts of total RNA, there are a number of disadvantages in
the conventional DD-PCR methods. The differential banding patterns
are often only poorly reproducible due to the use of short
arbitrary primer so that many laboratories have had difficulty in
obtaining reproducible results with these methods. It has been
shown that at least 40% of the differentially displayed bands are
not reproducible between experiments even in well-trained hands
(Bauer el al., 1994). Furthermore, the pattern of differential
expression often cannot be reproducible on Northern blots and the
percentage of these false positives can arise up to 90% (Sompayrac
et al., 1995). As a modification used for an alternative, the use
of longer random primers of, e.g. 20 bases in length does not
satisfactorily solve the problem of reproducibility (Ito et al.,
1994). There are another factors responsible for the relatively low
reproducibility of DD-PCR such as an insufficient amount of
starting material and very low concentration of dNTP (2-5 .mu.M)
employed to prepare the different banding patterns (Matz and
Lukyanov, 1998). It is also difficult to detect rare transcripts
with these methods (Matz and Lukyanov, 1998). In addition, because
the cDNA fragments obtained from DD-PCR are short (typically
100-500 bp) and correspond to the 3'-end of the gene that represent
mainly the 3' untranslated region, they usually do not contain a
large portion of the coding region. Therefore, the labor-intensive
full-length cDNA screening is needed unless significant sequence
homology, information for gene classification and prediction of
function is obtained (Matz and Lukyanov, 1998).
[0015] Differential Display methods generally use radioactive
detection techniques using denaturing polyacrylamide gels. The
radioactive detection of the reaction products restricts the use of
this technique to laboratories with the appropriate equipment.
Relatively long exposure times and problems with the isolation of
interesting bands from the polyacrylamide gels are additional
drawbacks of Differential Display technique. Although modified
non-radioactive Differential Display methods have recently been
described, which include silver staining (Gottschlich et al. 1997;
Kociok et al., 1998), fluorescent-labeled oligonucleotides (Bauer
et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith et al.,
1997), the use of biotinylated primers (Korn et al., 1992; Tagle et
al., 1993; Rosok et al., 1996) and ethidium bromide-stained agarose
gels (Rompf and Kahl, 1997; Jefferies et al., 1998; Gromova et al.,
1999), these methods have met with only limited success. If the
reaction products could be simply detected on ethidium
bromide-stained agarose gel and the results were reproducible and
reliable, it would greatly ncrease the speed of DD-PCR analysis and
avoid the use of radioactivity.
[0016] Another PCR-based approach called targeted differential
display uses an oligonucleotide primer that directs the
amplification of multigene family members with conserved protein
domains. Gene families are groups of genes which are often
functionally characterized by a particular type of function
undertaken by the gene products in a cell and which structurally
have one or more conserved regions (domains) in common. Examples of
gene families include the MADS-box and the homeogene family as well
as further transcription factor families. The cyclin, cytokine and
globin gene families are examples of medical interest. The Prosite
Database provides a list of proteins that have common domains and
sequence motifs. The oligonucleotide used in the PCR can either be
a specific primer that is used at a low annealing temperature or,
as is more often the case, a degenerate primer mixture for use at
higher stringencies (Stone and Wharton, 1994). However,
amplifications using degenerate primers can sometimes be
problematic and may require optimization. It is important to keep
the annealing temperature as high as possible to avoid extensive
nonspecific amplification and a good rule of thumb is to use
55.degree. C. as a starting temperature. In general, it is
difficult to keep this rule because degenerate primers should be
designed on the basis of amino acid sequences or conserved domain
sequences as a precondition. In order to generate a satisfied
relationship between degenerate primer and annealing temperature in
this approach, it is required to use an annealing control primer
which can tolerate the alternation of annealing temperature,
particularly high temperature such as 68.degree. C. regardless of
primer design.
[0017] Still another PCR-based technique is arbitrary primed PCR
(AP-PCR) for RNA fingerprinting. One great strength of AP-PCR
methods is their simplicity (Welsh and McClelland, 1991; Williams
et al., 1990). AP-PCR uses a single primer or a pair of primers,
wherein the primers are 10-mers or 18-mers as longer primer. This
method has previously been used to provide DNA fingerprints of
hybrid cell lines (Ledbetter et al., 1990) and particular genomic
regions (Welsh and McClelland, 1990; Williams et al., 1990). It
provides a very useful tool for genome analysis in bacteria, fungi
and plant identification and population studies, where individual
isolates can be compared rapidly. For example, they can be used as
a tool to identify pathogens or the occurrence of particular
strains or pathotypes. Commonly, AP-PCR uses a single primer to
initiate DNA synthesis from regions of a template where the primer
matches imperfectly. In order for this to work, the initial cycles
have to be performed at low stringency (37-50.degree. C.), normally
for the first five cycles, which allows primer annealing to
imperfect sites throughout the genome. The stringency is then
increased (55.degree. C.) as for standard PCR amplification and the
reaction is allowed for an additional 30-35 cycles. AP-PCR is not
recommended for use in such applications as paternity testing where
unequivocal results are demanded, because nonparental products are
occasionally produced. Although alternative AP-PCR approaches
including nested AP-PCR have been developed (McClelland et al.,
1993; Ralph et al., 1993), the issue of reproducibility is still of
main concern. One concern is that the patterns may vary from day to
day or from lab to lab (see, e.g., Meunier and Grimont, 1993).
[0018] Still yet another PCR-based application is RACE (rapid
amplification of cDNA end) technology. RACE is a procedure for
amplification of cDNA regions corresponding to the 5'- or 3'-end of
mRNA (Frohman et al., 1988) and it has been used to isolate rare
transcripts successfully. The gene-specific primer may be derived
from sequence data from a partial cDNA, genomic exon or peptide. In
3' RACE, the polyA tail of mRNA molecules is exploited as a priming
site for PCR amplification. mRNAs are converted into cDNAs using
reverse transcriptase and an Oligo-dT primer as known in the art.
The generated cDNAs can then be directly PCR amplified using a
gene-specific primer and a primer that anneals to the polyA
region.
[0019] The same principle as 3' RACE applies to 5' RACE but there
is no polyA tail. Thus, 5' RACE is made by tagging the 5'-end of a
cDNA by means of different methods (Fromont-Racine et al., 1993;
Schaefer, 1995; Franz et al., 1999). Most approaches for the 5'
RACE such as homopolymeric tailing and ligation anchored tailing
require a set of enzymatic reactions after completion of first
strand cDNA synthesis (Schaefer, 1995). Each enzymatic step has the
potential to introduce failures and to destroy the integrity of the
cDNA. Recently, an alternative has been introduced, the so-called
CapFinder approach (Chenchik et al., 1998; Chenchik et al. U.S.
Pat. Nos. 5,962,271 and 5,962,272). The technique relies on dual
functions of the reverse transcriptases: one is the terminal
transferase activity to add non-templated nucleotides to the 3'-end
of a cDNA and the other is the template switching activity to
switch a template to a second template. This property is utilized
during the retroviral life cycle (Clark, 1988; Kulpa et al., 1997).
Moloney murine leukemia virus (M-MLV) reverse transcriptase (RT)
often adds three to four non-template-derived cytosine residues to
the 3'-end of newly synthesized cDNAs in the presence of manganese
or high magnesium (Schmidt and Mueller, 1999). This approach allows
the amplification of full-length cDNAs because the M-MLV RT adds C
residues preferentially to the cDNA if complete (capped) mRNA
serves as template.
[0020] However, the CapFinder approach for 5'-RACE experiments
could not be free from background problems such as DNA smear
arising from the contamination of the CapFinder and Oligo-dT
primers, which are used in cDNA synthesis (Chenchik et al., 1998).
Even residual amounts of these primers result in a high background
because both ideally fit to all cDNAs present in the reaction
mixture. In addition, 3'-RACE and full-length cDNA amplification
have the same background problems due to the contamination of
primers used for cDNA synthesis in which they generate non-specific
products in PCR reaction (Chenchik et al., 1998). New approaches to
overcome the problems above have been recently introduced. One
approach is step-out PCR to suppress unwanted PCR products (Matz et
al., 1999) but it has been pointed out that this approach still
remains a smear of DNA rather than a single DNA (Schramm et al.,
2000). Another approach which is introduced more recently is to use
solid-phase cDNA synthesis and procedures to remove all
contaminants used in cDNA synthesis (Schramm et al., 2000), but the
major drawback of this technique is costly and time-consuming by
requiring solid-phase cDNA synthesis and following procedures.
Therefore, more effective, simple, rapid and inexpensive strategies
are required to completely eliminate problems arising from
contamination of the primers such as Oligo-dT or CapFinder primer
used for cDNA synthesis.
[0021] In addition to RACE technologies, in current technologies
for cDNA library construction, the 5'-ends of genes tend to be
under-represented in cDNA populations, especially where a poly(dT)
primer is used during first cDNA strand synthesis and the starting
material is limited. Although a number of different approaches have
been developed to overcome this problem, most suffer from common
limitations producing full-length cDNAs or 5'-enriched cDNAs with a
number of inherent problems. These approaches are complex or costly
and time-consuming by requiring multiple enzymatic steps and/or are
not pronounced sensitive (Caminci et al., 1997; Suzuki et al.,
1997; Guegler et al. U.S. Pat. Nos. 6,083,727 and 6,326,175;
Hayashizaki. U.S. Pat. No. 6,143,528). Therefore, there is
continued interest in the development of improved methods for
generating full-length or 5'-enriched cDNAs, particularly with the
limited starting material.
[0022] Multiplex PCR is another variant of PCR in which more than
one target sequence can be simultaneously amplified with more than
one pair of primers in the same reaction. Since its first
description in 1988 (Chamberlain et al., 1988), this method has
been successfully applied in many areas of DNA testing, including
analyses of gene deletion (Anonymous, 1992; Henegariu, et al.,
1994), mutation and polymorphism analysis (Shuber et al., 1993;
Mutirangura et al., 1993), quantitative analysis (Zimmermann et
al., 1996), and RNA detection (Zou et al., 1998). In the field of
infection diseases, the technique has been shown to be a valuable
method for identification of viruses, bacteria, fungi, and/or
parasites.
[0023] However, the results obtained with multiplex PCR are
frequently complicated by the artifacts of the amplification
procedure. These include "false-negative" results due to reaction
failure and "false-positive" results such as the amplification of
spurious products, which may be caused by annealing of the primers
to sequences which are related to but distinct from the true
recognition sequences. For use in multiplex PCR, a primer should be
designed so that its predicted hybridization kinetics are similar
to those of the other primers used in the sample multiplex
reaction. While the annealing temperature and primer concentrations
may be calculated to some degree, the conditions generally have to
be empirically determined for each multiplex reaction. Since the
possibility of non-specific priming increases with each additional
primer pair, the conditions must be modified as necessary as
individual primer sets are added. Moreover, the artifacts that
result from competition for resources (e.g., depletion of primers)
are augmented in multiplex PCR, since the differences in the yields
of unequally amplified fragments are enhanced with each cycle.
Thus, the optimization of the reaction conditions for multiplex PCR
can become labor-intensive and time-consuming. Since the different
multiplex PCRs may have unique reaction conditions, the development
of new diagnostic tests can become very costly.
[0024] Therefore, there is a need in the art for primers that allow
multiplex PCR reactions to be designed and carried out without
elaborate optimization steps, irrespective of the potentially
divergent properties of the different primers used. Furthermore,
there is a need in the art for primers that allow multiplex PCR
reactions that, under the same reaction conditions, simultaneously
produce equivalent amounts of each of many amplification
products.
[0025] Single nucleotide polymorphisms (SNPs), the most common
genetic variations found in the human genome, are important markers
for identifying disease-associated loci and for pharmaco-genetic
studies (Landegren et al., 1998; Roses, 2000). SNPs appear in the
human genome with an average of once every 1000 bp and totaling
>3 million. A variety of approaches have been used to detect
SNPs. However, one of the key bottlenecks is the amplification of
DNA. Most current assays include a step that produces many copies
of a short segment of the sample DNA spanning each target SNP. This
amplification is usually necessary because only small amounts of
DNA can be harvested from typical clinical samples. Also, the
amplification improves the signal-to-noise ratio of the assays,
increasing the reliability of detection. Most genotyping techniques
accomplish this amplification using PCR. Most importantly, the
specificity of PCR amplification is critical in the application of
PCR in the SNP genotyping. Therefore, it would be beneficial if the
methods for improving PCR specificity are available and applied to
the development of SNP genotyping assay. It would also be
beneficial if such methods are capable of providing multiple
analyses in a single assay (multiplex assays).
[0026] As described above, all these methods and techniques
involving nucleic acid amplification, in particular PCR
amplification, could not be completely free from the limitations
and problems resulting from the non-specificity of primers used in
each method, such as false positives, poor reproducibility, high
backgrounds and so on, although improved approaches to each method
has been continuously introduced. Therefore, there remains a need
of novel primer for improving annealing specificity and methods,
which can give rise to true results.
[0027] Throughout this application, various patents and
publications are referenced and citations are provided in
parentheses. The disclosure of these patents and publications in
their entities are hereby incorporated by references into this
application in order to more fully describe this invention and the
state of the art to which this invention pertains.
SUMMARY OF THE INVENTION
[0028] Endeavoring to resolve the problems of such conventional
primer and various methods involving nucleic acid amplification,
the present inventor has developed a novel annealing control primer
that can permit nucleic acid amplification with much higher
specificity and its unlimited applications in all fields of nucleic
acid amplification-based technology.
[0029] Accordingly, it is an object of this invention to provide an
annealing control primer for improving annealing specificity in
nucleic acid amplification.
[0030] It is another object of this invention to provide a method
for amplifying a nucleic acid sequence from a DNA or a mixture of
nucleic acids as template.
[0031] It is still another object of this invention to provide a
method for selectively amplifying a target nucleic acid sequence
from a DNA or a mixture of nucleic acids as template
[0032] It is further object of this invention to provide a method
for selectively amplifying a target nucleic acid sequence from an
mRNA.
[0033] It is still further object of this invention to provide a
method for detecting DNA complementary to differentially expressed
mRNA in two or more nucleic acid samples.
[0034] It is another object of this invention to provide a method
for rapidly amplifying a target cDNA fragment comprising a cDNA
region corresponding to the 3'-end region of an mRNA.
[0035] It is still another object of this invention to provide a
method for amplifying a target cDNA fragment comprising a cDNA
region corresponding to the 5'-end region of an mRNA.
[0036] It is further object of this invention to provide a method
for amplifying a population of full-length double-stranded cDNAs
complementary to mRNAs.
[0037] It is still further object of this invention to provide a
method for amplifying 5'-enriched double-stranded cDNAs
complementary to mRNAs.
[0038] It is another object of this invention to provide a method
for amplifying more than one target nucleotide sequence
simultaneously,
[0039] It is still another object of this invention to provide a
method for producing a DNA fingerprint of gDNA. It is still another
object of this invention to provide a method for producing a RNA
fingerprint of an mRNA sample.
[0040] It is further object of this invention to provide a method
for identifying a conserved homology segment in a multigene
family.
[0041] It is still further object of this invention to provide a
method for identifying a nucleotide variation in a target nucleic
acid.
[0042] It is another object of this invention to provide a method
for mutagenesis in a target nucleic acid.
[0043] It is still another object of this invention to provide a
kit comprising an annealing control primer.
[0044] It is further object of this invention to provide kits for a
variety of methods involving nucleic acid amplification.
[0045] It is still further object of this invention to provide a
use of an annealing control primer for a process involving nucleic
acid amplification.
[0046] Other objects and advantages of the present invention will
become apparent from the detailed description to follow taken in
conjugation with the appended claims and drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0047] FIGS. 1A and 1B show schematic representations for
selectively amplifying a target nucleic acid of double-stranded DNA
(1A) or mRNA (1B) using the ACP of the present invention.
[0048] FIGS. 2A and 2B show schematic representations for
identifying differentially expressed genes using the ACP of the
present invention.
[0049] FIG. 3 shows a schematic representation for amplifying a
target cDNA fragment comprising 3'-end region corresponding to the
3'-end of mRNA using the ACP of the present invention.
[0050] FIGS. 4A and 4B show schematic representations for
amplifying a target cDNA fragment comprising 5'-end region
corresponding to the 5'-end of mRNA using the ACP of the present
invention. The Oligo dT (4A) or random primer (4B) is used as a
first-strand cDNA synthesis primer.
[0051] FIG. 5 shows a schematic representation for amplifying
full-length cDNA molecules complementary to the mRNA molecules
using the ACP of the present invention.
[0052] FIG. 6 shows a schematic representation for amplifying 5'
enriched cDNA molecules complementary to the mRNA molecules
comprising the 5'-end information using the ACP of the present
invention.
[0053] FIG. 7A shows a schematic representation for detecting
single nucleotide polymorphism (SNP) using the ACP of the present
invention.
[0054] FIG. 7B shows another schematic representation for detecting
single nucleotide polymorphism (SNP) using the ACP of the present
invention.
[0055] FIG. 8 is an agarose gel photograph to show the effect of a
deoxyinosine group positioned between the 3'- and 5'-end portions
of ACP. The cDNA was amplified using total RNA isolated from
conceptus tissues at E4.5 (lanes 1 and 4), E11.5 (lanes 2 and 5),
and E18.5 (lanes 3 and 6), with a set of the dT.sub.10-JYC2 (SEG ID
NO. 29) and ACP10 (lanes 1-3) (SEG ID NO. 13), and a set of the
dT.sub.10-ACP1 (SEG ID NO. 30) and ACP10 (lanes 4-6),
respectively.
[0056] FIG. 9 is an agarose gel photograph to show the effect of
deoxyinosine residues positioned between the 3'- and 5'-end
portions of ACP in association with the alteration of number of
deoxyinosine during PCR. The lanes 0, 2, 4, 6, and 8 represent the
number of deoxyinosine residues, respectively.
[0057] FIG. 10A is an agarose gel photograph to show the results of
two stage PCR amplifications for Esx1 using a set of EsxN7 and
EsxC6 primers (lane 1) and a set of EsxN7-ACP and EsxC6-ACP primers
(lane 2).
[0058] FIG. 10B is an agarose gel photograph to show the results of
two stage PCR amplifications for Esx1 using EsxN1 (lane 1), EsxC2
(lane 2), a set of EsxN1-ACP and EsxC2 (lane 3), and a set of
EsxN1-ACP and EsxC2-ACP (lane 4).
[0059] FIG. 10C is an agarose gel photograph to show the results of
two stage PCR amplifications for Esx1 using a set of EsxN3 and
EsxC5 (lanes I and 2) and a set of EsxN3-ACP and EsxC5-ACP (lane
3).
[0060] FIG. 10D is an agrasoe gel photograph to show the results of
non-stop two stage PCR amplifications for Esx1 using the primer
EsxN1 (lane 1), EsxC2 (lane 2), a pair of EsxN1 and EsxC2 (lane 3)
and a pair of EsxN1-ACP and EsxC2-ACP (lane 4).
[0061] FIG. 11A is a photograph of agarose gels to show examples of
the ACP used for detecting differentially expressed mRNAs during
embryonic development using different stages of mouse conceptus
tissues. The cDNAs were amplified using total RNA isolated from
conceptus tissues at E4.5 (lane 1), E11.5 (lane 2), and E18.5 (lane
3), with a set of ACP3 (SEG ID NO. 3) and dT.sub.10-ACP1. The bands
indicated by arrows represent the cDNA fragments amplified from
differentially expressed mRNAs. The numbers of the arrows indicate
the cDNA fragments used as probes in the Northern blot analysis of
FIG. 13.
[0062] FIG. 11B is a photograph of agarose gels to show examples of
the ACP used for detecting differentially expressed mRNAs during
embryonic development using different stages of mouse conceptus
tissues. The cDNAs were amplified using total RNA isolated from
conceptus tissues at E4.5 (lanes 1-2 and 7-8), E11.5 (lanes 3-4 and
9-10), and E18.5 (lanes 5-6 and 11-12), with a set of ACP5 (SEG ID
NO. 5) and dT.sub.10-ACP1 (the lanes 1-6), and a set of ACP8 (SEG
ID NO. 8) and dT.sub.10-ACP1 (lanes 7-12), respectively. The bands
indicated by arrows represent the cDNA fragments amplified from
differentially expressed mRNAs. The numbers of the arrows indicate
the cDNA fragments used as probes in the Northern blot analysis of
FIG. 13.
[0063] FIG. 11C is an agarose gel photograph to show the amplified
cDNA products obtained from different stages of mouse conceptus
samples (E4.5: lanes 1 and 2; E11.5: lanes 3 and 4; E18.5: lanes 5
and 6) using a set of ACP10 and dT.sub.10-ACP primers.
[0064] FIG. 11D is an agarose gel photograph to show the amplified
cDNA products obtained from different stages of mouse conceptus
samples (E4.5: lanes 1 and 2; E11.5: lanes 3 and 4; E18.5: lanes 5
and 6) using a set of ACP14 and T.sub.10-ACP1 primers.
[0065] FIG. 12A is an agarose gel photograph to show the amplified
cDNA products obtained from different stages of mouse conceptus
samples (E4.5: lane 1; E11.5: lane 2; E18.5: lane 3) by one-stop
two-stage PCR amplification using a set of ACP10 and
JYC5-T.sub.15-ACP primers.
[0066] FIG. 12B is an agarose gel photograph to show the amplified
cDNA products obtained from different stages of mouse conceptus
samples (E4.5: lane 1; El 1.5: lane 2; E18.5: lane 3) by non-stop
two-stage PCR amplification using a set of ACP10 and
JYC5-T.sub.15-ACP primers.
[0067] FIG. 13 shows Northern blot analysis of six cDNA fragments
amplified from differentially expressed mRNAs during embryonic
development. The six .sup.32P-labeled fragments indicated by arrows
in FIG. 11 were used as probes for Northern blot analysis. The
arrows 1, 2, 3, 4, 5, and 6 are DEG1 (FIG. 13A), DEG3 (FIG. 13B),
DEG2 (FIG. 13C), DEG8 (FIG. 13D), DEG5 (FIG. 13E), and DEG7 (FIG.
13F), respectively, wherein the results of the DEG sequence
analysis are shown in Table 1. DEG2 (SEG ID NO. 31) and DEG5 (SEG
ID NO. 32) are turned out as novel genes (Table 2). The control
panels (the lower part of each panel) show each gel before
blotting, stained with ethidium bromide and photographed under UV
light, demonstrating similar levels of 18S and 28S rRNA as a
loading control.
[0068] FIG. 14 shows the expression patterns of a novel gene, DEG5,
in a full stage of mouse conceptus. Northern blot analysis was
performed using the radio-labeled DEG5 cDNA fragment as a probe.
Total RNA (20 .mu.g/lane) was prepared from mouse conceptuses at
the gestation times as indicated. The control panel at the lower
part shows a gel before blotting, stained with ethidium bromide and
photographed under UV light, demonstrating similar levels of 18S
and 28S rRNA as a loading control.
[0069] FIG. 15 is an agarose gel photograph to show the difference
between the conventional 3'-RACE (lane 1) and the ACP-based 3
'-RACE (lane 2) with regard to beta-actin 3 '-RACE.
[0070] FIG. 16 is an agarose gel photograph to show the difference
between CapFinder methods and ACP-based methods for mouse JunB
(lanes 1 and 2) and beta-actin 5'-RACE (lanes 3 and 4) using the
conventional primer (lanes 1 and 3) and ACP (lanes 2 and 4),
respectively
[0071] FIG. 17 is an agarose gel photograph to show the difference
between CapFinder methods and ACP-based methods for mouse PLP-C
alpha 5'-RACE using the conventional primer (lane 1) and ACP (lanes
2, 3, and 4), respectively.
[0072] FIG. 18 shows the results of virtual Northern analysis by
the CapFinder methods or ACP-based methods for the amplification of
mouse full-length GAPDH cDNA.
[0073] FIG. 19 shows agarose gel photographs to show the results of
genomic fingerprintings of 7 mouse stains using two different sets
of arbitrary ACPs.
[0074] FIG. 20 shows agarose gel photographs to show the amplified
products of multiplex PCR by the conventional methods (A) or
ACP-based methods (B) for the amplification of three target nucleic
acids.
[0075] FIG. 21 shows agarose gel photographs to show the amplified
products of multiplex PCR by the conventional methods (A) or
ACP-based methods (B and C) for the amplification of four target
nucleic acids. The ACP-based multiplex was conducted by one-stop
(B) or non-stop (C) two-stage PCR amplification.
[0076] FIG. 22 shows an agarose gel photograph to show the results
of allele-specific amplification for a SNP in exon 4 of the human
TP53 gene using ACP.
[0077] FIG. 23 shows six agarose gel photographs which show the
results of allele-specific amplifications using ACPs for six
additional SNPs each present in different gene such as Beta-2
adrenergic receptor (ADRB2) (A), Chemokine (c-c motif) receptor 5
(CCR5) (B), Interleukin 13 receptor (C), Leukocyte adhesion
molecule-1 (LAM-1) (D), Tachykinin receptor 3 (TACR3) (E), and
Interleukin 1, beta (IL1B) (F).
DETAILED DESCRIPTION OF THIS INVETNION
[0078] The present invention is generally directed to (a) an
annealing control primer for the specificity of nucleic acid
amplification and (b) its applications. The annealing control
primer of this invention (hereinafter referred to as "ACP") allows
primer annealing to be controlled in association with annealing
temperature, such that the specificity of nucleic acid
amplification (in particular, PCR) can be significantly improved.
The principle of the ACP is based on the composition of an
oligonucleotide primer having 3'- and 5'-ends distinct portions
separated by at least one universal base or non-discriminatory
base. The present inventor has discovered that the universal base
or non-discriminatory base group positioned between the 3'- and 5'-
end portions plays as a regulator in controlling primer annealing
to a template nucleic acid in associated with annealing temperature
during nucleic acid amplification. The presence of universal base
or non-discriminatory base residue group positioned between the 3'-
and 5'- end portions interrupts the annealing of the 5'-end portion
as well as limits primer annealing to the 3'-end portion at certain
annealing temperature, which results in dramatic improvement of
annealing specificity. A universal base group positioned between
the 3'- and 5'-end portions of ACP is designed to define each
portion. For these reasons, the ACP is fundamentally different from
the conventional primers in terms of the function for improving
primer annealing specificity under a particular stringency
conditions during nucleic acid amplification.
[0079] The ACP of this invention is significantly effective and
widely accessible to nucleic acid amplification-based applications.
Also, various problems related to primer annealing specificity in
the conventional PCR techniques can be fundamentally solved by the
ACP. The main benefits to be obtained from the use of the ACP
during nucleic acid amplification (particularly PCR) are as
follows:
[0080] (a) since the presence of an universal base residue group
positioned between the 3'- and 5'-end portions restricts primer
annealing portion to the 3'-end portion under such conditions that
the 3'-end portion anneals to the template, the annealing sequence
of a primer can be precisely controlled, which make it possible to
design a primer with a desired number of annealing sequence. It is
particularly useful when an annealing portion of a primer has to be
limited (e.g., single nucleotide polymorphism (SNP) genotyping, DNA
microarrary screening, and detection of differentially expressed
genes);
[0081] (b) since the presence of an universal base residue group
positioned between the 3'- and 5'-end portions interrupts the
annealing of the 5'-end portion to the template under such
conditions that the 3'-end portion anneals to the template,
eventually the 5'-end portion not involved in the annealing
provides the 3'-end portion with primer annealing specificity;
[0082] (c) the specificity of primer annealing is highly sensitive
enough to detect even a single-base mismatching. Thus, it is
particularly useful for the identification of a nucleotide
variation in a target nucleic acid, including, for example, single
nucleotide polymorphisms and point mutations;
[0083] (d) ACP is capable of providing a primer with a high
tolerance in "primer search parameters" for primer design such as
primer length, annealing temperature, GC content, and PCR product
length;
[0084] (e) ACP system provides two-stage PCR amplifications which
allow the products to be excluded from non-specific
amplification;
[0085] (f) the efficiency of PCR amplification is increased, which
makes it easier to detect rare mRNAs; and
[0086] (g) the reproducibility of PCR products is increased, which
saves a great amount of time and cost.
[0087] Principle of ACP
[0088] In one aspect of this invention, there is provided an
annealing control primer for improving annealing specificity in
nucleic acid amplification, which comprises: (a) a 3'-end portion
having a hybridizing nucleotide sequence substantially
complementary to a site on a template nucleic acid to hybridize
therewith; (b) a 5'-end portion having a pre-selected arbitrary
nucleotide sequence; and (c) a regulator portion positioned between
said 3'-end portion and said 5'-end portion comprising at least one
universal base or non-discriminatory base analog, whereby said
regulator portion is capable of regulating an annealing portion of
said primer in association with annealing temperature.
[0089] The principle of ACP is based on the composition of an
oligonucleotide primer having 3'- and 5'-end distinct portions
separated by a regulator portion comprising at least one universal
base or non-discriminatory base and the effect of the regulator
portion on the 3'- and 5'-end portions in the oligonucleotide
primer. The presence of the regulator portion comprising at least
one universal base or non-discriminatory base between the 3'- and
5'-end portions of ACP acts as a main factor which is responsible
for the improvement of primer annealing specificity.
[0090] The term "template" refers to nucleic acid. The term
"nucleic acid" is a deoxyribonucleotide or ribonucleotide polymer
in either single or double-stranded form, including known analogs
of natural nucleotides unless otherwise indicated. Therefore, the
ACP of this invention can be employed in nucleic acid amplification
using single or double-stranded gDNA, cDNA or mRNA as template. The
term "portion" used herein in conjunction with the primer of this
invention refers to a nucleotide sequence separated by the
regulator portion. The term "3'-end portion" or "5'-end portion"
refers to a nucleotide sequence at the 3'-end or 5'-end of the
primer of this invention, respectively, which is separated by the
regulator portion.
[0091] The term "primer"0 as used herein refers to an
oligonucleotide, whether occurring naturally or produced
synthetically, which is capable of acting as a point of initiation
of synthesis when placed under conditions in which synthesis of
primer extension product which is complementary to a nucleic acid
strand (template) is induced, i.e., in the presence of nucleotides
and an agent for polymerization such as DNA polymerase and at a
suitable temperature and pH. The primer is preferably single
stranded for maximum efficiency in amplification. Preferably, the
primer is an oligodeoxyribonucleotide. The primer of this invention
can be comprised of naturally occurring dNMP (i.e., dAMP, dGM, dCMP
and dTMP), modified nucleotide or non-natural nucleotide. The
primer can also include ribonucleotides. The primer must be
sufficiently long to prime the synthesis of extension products in
the presence of the agent for polymerization. The exact length of
the primers will depend on many factors, including temperature,
application and source of primer. The term "annealing" or "priming"
as used herein refers to the apposition of an oligodeoxynucleotide
or nucleic acid to a template nucleic acid, whereby said apposition
enables the polymerase to polymerize nucleotides into a nucleic
acid molecule which is complementary to the template nucleic acid
or a portion thereof.
[0092] The 3'-end portion of ACP has a nucleotide sequence
substantially complementary to a site on a template nucleic acid
molecule. The term "substantially complementary" in reference to
primer is used herein to mean that the primer is sufficiently
complementary to hybridize selectively to a template nucleic acid
sequence under the designated annealing conditions, such that the
annealed primer can be extended by polymerase to form a
complementary copy of the template. Therefore, this term has a
different meaning from "perfectly complementary" or related terms
thereof. It will be appreciated that the 3'-end portion of ACP can
have one or more mismatches to template to an extent that the ACP
can serve as primer. Most preferably, the 3'-end portion of ACP has
a nucleotide sequence perfectly complementary to a site on a
template, i.e., no mismatches.
[0093] The 3'-end portion of ACP may have a wide variety of
nucleotide sequences depending on its applications as well as
template sequence. For example, where the ACP is applied to the
process involving reverse transcription such as differential
display PCR, RACE, amplification of full-length cDNA,
fingerprinting, identification of conserved homology segment and
the like, its 3'-end portion may have the nucleotide sequence which
hybridizes to the polyadenosine (poly A) tail of an mRNA,
preferably at least 8 deoxythymidine nucleotides, more preferably
at least 10 deoxythymidine nucleotides and the most preferably, at
least 10 contiguous deoxythymidine nucleotides. For the process
involving reverse transcription as above, in one embodiment, the
3'-end portion of ACP has at least 10 contiguous deoxythymidine
nucleotides having 3'-V at its 3'-end; in which V is one selected
from the group consisting of deoxyadenosine, deoxycytidine and
deoxyguanosine, in another embodiment, at least 10 contiguous
deoxythymidine nucleotides having 3'-NV at its 3'-end; in which V
is one selected from the group consisting of deoxyadenosine,
deoxycytidine and deoxyguanosine, and N is one selected from the
group consisting of deoxyadenosine, deoxythymidine, deoxycytidine
and deoxyguanosine.
[0094] Furthermore, where the ACP is employed in amplification of a
target nucleic acid sequence, its 3'-end portion comprises a
nucleotide sequence substantially complementary to a target
sequence; in differential display PCR, an arbitrary sequence
substantially complementary to a site in a cDNA from an mRNA; in
RACE, a gene-specific sequence substantially complementary to a
site in a cDNA from an mRNA; in amplification of 5'-enriched cDNAs,
a random sequence of at least six nucleotides substantially
complementary to sites in mRNAs; in identification of conserved
homology segment, a nucleotide sequence substantially complementary
to a consensus sequence found in a gene family or degenerate
sequence selected from a plurality of combinations of nucleotides
encoding a predetermined amino acid sequence; in identification of
a nucleotide variation (e.g., allelic site) in a target nucleic
acid, a nucleotide sequence comprising a nucleotide complementary
to the corresponding nucleotide of a nucleotide variation; and in
mutagenesis, a nucleotide sequence comprising at least one mismatch
nucleotide to a target nucleic acid.
[0095] The term "arbitrary" nucleotide sequence is used herein to
mean the nucleotide sequence that is chosen without knowledge of
the sequence of the target nucleic acids to be amplified. The term
arbitrary should not to be confused with "random" in reference to
primer which connotes a primer composed of a random population of
primers each of different and random sequence. The term
"degenerate" sequence in conjunction with ACP for identification of
conserved homology segment refers to the nucleotide sequence that
is deducted from amino acid sequence, so that the degenerate
sequence can form a pool of the nucleotide sequences from one amino
acid sequence due to degeneracy of genetic codon.
[0096] According to a preferred embodiment of the ACP, the
pre-selected arbitrary nucleotide sequence of the 5'-end portion is
substantially not complementary to any site on the template nucleic
acid.
[0097] According to a preferred embodiment, the annealing control
primer of this invention can be represented by a general formula
(1) of 5'-X.sub.p-Y.sub.q-Z.sub.r-3', wherein X.sub.p represents
the 5'-end portion having the pre-selected arbitrary nucleotide
sequence substantially not complementary to any site on the
template nucleic acid; Yq represents the regulator portion
comprising at least one universal base or non-discriminatory base
analog; Zr represents the 3'-end portion having a nucleotide
sequence substantially complementary to a site on the template
nucleic acid; wherein p, q and r represent the number of
nucleotides; and wherein X, Y and Z is deoxyribonucleotide or
ribonucleotide.
[0098] The regulator portion comprising at least one universal base
or non-discriminatory base analog is responsible for the main
function of ACP in associated with alteration of annealing
temperature during nucleic acid amplification. The term "universal
base or non-discriminatory base analog" used herein refers to one
capable of forming base pairs with each of the natural DNA/RNA
bases with little discrimination between them.
[0099] It has been widely known that nucleotides at some ambiguous
positions of degenerate primers have been replaced by universal
base or a non-discriminatory analogue such as deoxyinosine (Ohtsuka
et al, 1985; Sakanari et al., 1989),
1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole (Nichols et al.,
1994) and 5-nitroindole (Loakes and Brown, 1994) for solving the
design problems associated with the degenerate primers because such
universal bases are capable of non-specifically base pairing with
all four conventional bases. However, there has not been any report
that this universal base or a non-discriminatory analogue such as
deoxyinosine, 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and
5-nitroindole is used to increase the specificity of primer
annealing during PCR.
[0100] The presence of universal base such as deoxyinosine,
1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and 5-nitroindole
in a primer generates low annealing temperatures due to its weaker
hydrogen bonding interactions in base pairing. As an extension of
this theory, the present inventor has induced that the presence of
the contiguous universal bases between the 3'-end and 5'-end of a
primer could generate a region which has lower melting temperature,
forms a boundary to each of 3'-and 5'-end portions of the primer,
and affect the annealing of each portion, respectively. This theory
provides the basis of the annealing control primers of this
invention.
[0101] In a preferred embodiment, the ACP contains at least 2
universal base or non-discriminatory base analog residues between
the 3'- and 5'-end portion sequences, more preferably, at least 3
universal bases or non-discriminatory base analogs. Advantageously,
the universal base residues between the 3'- and 5'-end portion
sequences can be up to 15 residues in length. According to one
embodiment, the ACP contains 2-15 universal base or
non-discriminatory base analog residues. Most preferably, the
universal bases between the 3'- and 5'-end portion sequences are
about 5 residues in length.
[0102] With reference to the optimum number of universal base,
i.e., 5 residues, the minimum number of universal base residues
between the 3'- and 5'-end portions of ACP is preferred in order to
interrupt the annealing of the 5'-end portion to the template
during nucleic acid amplification at certain annealing temperature.
It is very likely that the length of universal base in the sequence
(8-10 bases) does not make a significant difference on its own
function in ACP.
[0103] The use of universal base residues between the 3'- and
5'-end portion sequences is considered as a key feature in the
present invention because it provides each portion (3'- and 5'-end)
with a distinct annealing specificity in association with an
annealing temperature during nucleic acid amplification, e.g.
PCR.
[0104] According to a preferred embodiment, the universal base or
non-discriminatory base analog in the regulator portion includes
deoxyinosine, inosine, 7-deaza-2'-deoxyinosine,
2-aza-2'-deoxyinosine, 2'-OMe inosine, 2'-F inosine, deoxy
3-nitropyrrole, 3-nitropyrrole, 2'-OMe 3-nitropyrrole, 2'-F
3-nitropyrrole, 1-(2'-deoxy-beta-D-ribofurano- syl)-3-nitropyrrole,
deoxy 5-nitroindole, 5-nitroindole, 2'-OMe 5-nitroindole, 2'-F
5-nitroindole, deoxy 4-nitrobenzimidazole, 4-nitrobenzimidazole,
deoxy 4-aminobenzimidazole, 4-aminobenzimidazole, deoxy nebularine,
2'-F nebularine, 2'-F 4-nitrobenzimidazole, PNA-5-introindole,
PNA-nebularine, PNA-inosine, PNA-4-nitrobenzimidazole,
PNA-3-nitropyrrole, morpholino-5-nitroindole,
morpholino-nebularine, morpholino-inosine,
morpholino-4-nitrobenzimidazole, morpholino-3-nitropyrrole,
phosphoramidate-5-nitroindole, phosphoramidate-nebularine,
phosphoramidate-inosine, phosphoramidate-4-nitrobenzimidazole,
phosphoramidate-3-nitropyrrole, 2'-0-methoxyethyl inosine,
2'0-methoxyethyl nebularine, 2'-0-methoxyethyl 5-nitroindole,
2'-0-methoxyethyl 4-nitrobenzimidazole, 2'-0-methoxyethyl
3-nitropyrrole and combinations thereof, but not limited to. More
preferably, the universal base or non-discriminatory base analog is
deoxyinosine, 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole or
5-nitroindole, most preferably, deoxyinosine.
[0105] The preferred length of an oligonucleotide primer, as used
herein, is determined from desired specificity of annealing and the
number of oligonucleotides having the desired specificity that are
required to hybridize to the template. For example, an
oligonucleotide primer of 20 nucleotides is more specific than an
oligonucleotide primer of 10 nucleotides because the addition of
each nucleotide to an oligonucleotide increases the annealing
temperature of the primer to the template.
[0106] The lengths of the 3'- and 5'-end portion sequences of the
ACP may vary and depend in part on the objective of each
application using ACP. In a preferred embodiment, the 3'-end
portion of ACP is at least 6 nucleotides in length, which is
considered a minimal requirement of length for primer annealing.
More preferably, the 3'-end portion sequence is from 10 to 25
nucleotides and can be up to 60 nucleotides in length. In another
embodiment, the 3'-end portion of ACP can include ribonucleotides
as well as deoxyribonucleotides.
[0107] In another preferred embodiment, the 5'-end portion of ACP
contains at least 15 nucleotides in length, which is considered a
minimal requirement of length for annealing under high stringent
conditions. Preferably, the 5'-end portion sequence can be up to 60
nucleotides in length. More preferably, the 5'-end portion sequence
is from 6 to 50 nucleotides, most preferably, from 20 to 25
nucleotides in length. The entire ACP is preferably from 35 to 50
nucleotides in length, and can be up to 100 nucleotides in
length.
[0108] The 5'-end portion of ACP has a pre-selected arbitrary
nucleotide sequence substantially not complementary to any site on
the template nucleic acid and this nucleotide sequence can serves
as a priming site for subsequent amplification. The term
"pre-selected arbitrary" nucleotide sequence used herein refers as
any defined or pre-selected deoxyribonucleotide, ribonucleotide, or
mixed deoxyribonucleotide sequence which contains a particular
sequence of natural or modified nucleotides. In some embodiment,
the pre-selected arbitrary nucleotide sequence of the 5'-end
portion can be composed of a universal primer sequence such as T3
promoter sequence, T7 promoter sequence, SP6 promoter sequence, and
M13 forward or reverse universal sequence. Using a longer arbitrary
sequence (about 25 to 60 bases) at the 5'-end portion of ACP
reduces the efficiency of ACP, but shorter sequences (about 15 to
17 bases) reduce the efficiency of annealing at high stringent
conditions of ACP. It is also a key feature of the present
invention to use a pre-selected arbitrary nucleotide sequence at
the 5'-end portion of ACP as a priming site for subsequent
amplification.
[0109] According to one embodiment of the present invention, some
modifications in the 5'-end portion of ACP can be made unless the
modifications abolish the advantages of the ACP, i.e., improvement
in annealing specificity. For example, the 5'-end portion can
comprises a sequence or sequences recognized by a restriction
endonuclease(s), which makes it feasible to clone the amplified
product into suitable vector. In addition, the 5'-end portion can
comprises at least one nucleotide with a label for detection or
isolation of amplified product. Suitable labels include, but not
limited to, fluorophores, chromophores, chemiluminescers, magnetic
particles, radioisotopes, mass labels, electron dense particles,
enzymes, cofactors, substrates for enzymes and haptens having
specific binding partners, e.g., an antibody, streptavidin, biotin,
digoxigenin and chelating group. The 5'-end portion also comprises
bacteriophage RNA polymerase promoter region.
[0110] According to the preferred embodiment of this invention, the
ACP is applied to PCR. More preferably, the PCR is performed under
a first and a second annealing temperature, i.e., under different
stringent conditions. The first annealing temperature may be equal
to or lower than the second annealing temperature and preferably,
the second annealing temperature is higher than the first annealing
temperature. In the PCR process performed under two different
annealing temperatures, i.e., two-stage PCR, the 3'-end of ACP is
involved in annealing at the first annealing temperature and the
5'-end of ACP incorporated into amplified product of first
amplification stage serves as a priming site at the second
annealing temperature. In this case, the advantages of ACP will be
demonstrated in accordance with the following assumptions:
[0111] (1) since a regulator portion of ACP is composed of at least
one universal base or non-discriminatory analogue which has lower
Tm than other portion in ACP due to its weaker hydrogen bonding
interactions in base pairing, the regulator portion of ACP is not
favorable in annealing to the template nucleic acid under the
conditions that the 3'-end portion of ACP anneals to a site of the
template at a first annealing temperature. Consequently, the
presence of a regulator portion comprising at least one universal
base or non-discriminatory analogue between the 3'- and 5'-end
portions of ACP restricts primer annealing portion to the 3'-end
portion at first annealing temperature;
[0112] (2) the 5'-end portion which is not involved in the
annealing under the first annealing temperature keeps bothering the
annealing of the 3'-end portion to the template;
[0113] (3) thus, the strength in which the specific annealing of
the 3'-end portion sequence occurs is relatively stronger than the
strength in which non-specific annealing occurs, under the first
annealing temperature, which results in the improvement of primer
annealing specificity at the 3'-end portion;
[0114] (4) where the 5'-end portion comprises a pre-selected
arbitrary, nucleotide sequence, the portion serves as a priming
site at a second annealing temperature, which is high stringency
conditions and also should be higher than the first annealing
temperature, for subsequent amplification of reaction product
generated from annealing and extension of the 3'-end portion
sequence; and
[0115] (5) consequently, only the reaction product generated from
annealing and extension of the 3'-end portion sequence can be
amplified close to the theoretical optimum of a two-fold increase
of product for each PCR cycle under the second annealing
temperature.
[0116] Therefore, the 3'-end portion of ACP acts only as annealing
site to the template at the first annealing temperature and the
5'-end portion of ACP is used as a priming site at the second
annealing temperature for the subsequent amplification of the
product generated by contacting and extending the 3'-end portion of
ACP to the template.
[0117] It may be appreciated that the ACP of the present invention
is very useful in a variety of primer-based nucleic acid
amplification methods including the methods of Miller, H. I. (WO
89/06700) and Davey, C. et al. (EP 329,822), Ligase Chain Reaction
(LCR, Wu, D. Y. et al., Genomics 4:560 (1989)), Polymerease Ligase
Chain Reaction (Barany, PCR Methods and Applic., 1:5-16(1991)),
Gap-LCR (WO 90/01069), Repair Chain Reaction (EP 439,182), 3SR
(Kwoh et al., PNAS, USA, 86:1173(1989)) and NASBA (U.S. Pat. No.
5,130,238), but not limited to.
[0118] In another aspect of this invention, there is provided a kit
comprising the annealing control primer or the annealing control
primer set according to the present invention. According to one
embodiment of this invention, this kit further comprises a primer
or a primer pair having a nucleotide sequence corresponding to the
5'-end portion of the ACP; in case that the 5'-end portion
comprises universal primer sequence, it is more preferred that the
kit comprises the universal primers. The present kits may
optionally include the reagents required for performing PCR
reactions such as buffers, DNA polymerase, DNA polymerase
cofactors, and deoxyribonucleotide-5'-triphosphates. Optionally,
the kits may also include various polynucleotide molecules, reverse
transcriptase, various buffers and reagents, and antibodies that
inhibit DNA polymerase activity. The kits may also include reagents
necessary for performing positive and negative control reactions.
Optimal amounts of reagents to be used in a given reaction can be
readily determined by the skilled artisan having the benefit of the
current disclosure. The kits, typically, are adapted to contain in
separate packaging or compartments the constituents
afore-described.
[0119] The ACP of the subject invention can be applied to a variety
of nucleic acid amplification-based technologies. Representative
examples to prove the effect of ACP are:
[0120] I. Application to amplifying a nucleic acid sequence;
[0121] II. Application to amplifying a target nucleic acid
sequence;
[0122] III. Application to multiplex DNA amplification;
[0123] IV. Application to the identification of differentially
expressed genes;
[0124] V. Application to rapid amplification of cDNA ends
(RACE);
[0125] VI. Application to amplifying full-length cDNA;
[0126] VII. Application to amplifying 5'-enriched cDNA;
[0127] VIII. Application to DNA or RNA fingerprinting;
[0128] IX. Application to the identification of conserved homology
segments in multigene families;
[0129] X. Application to identification of a nucleotide sequence
variation;
[0130] XI. Application to mutagenesis; and
[0131] XII. Other applications.
[0132] I. Application to Amplifying a (target) Nucleic Acid
Sequence
[0133] In still another of this invention, there is provided a
method for amplifying a nucleic acid sequence from a DNA or a
mixture of nucleic acids, comprising performing an amplification
reaction using primers, characterized in that at least one primer
is derived from any one of ACP described above. Preferably, the
primer according to the structure of ACP is one having at its 3'end
portion a hybridizing sequence substantially complementary to a
region of the nucleic acid sequence to hybridize therewith.
[0134] In a specific embodiment of this method, there is provided a
method using two stage amplifications for amplifying a nucleic acid
sequence from a DNA or a mixture of nucleic acids, which
comprises:
[0135] (a) performing a first-stage amplification of the nucleic
acid sequence at a first annealing temperature comprising at least
two cycles of primer annealing, primer extending and denaturing,
using the primer pair of any one of the ACP described above each
having at its 3' end portion a hybridizing sequence substantially
complementary to a region of the nucleic acid sequence to hybridize
therewith, under conditions in which each primer anneals to the
region of the nucleic acid sequence, whereby the amplification
product of the nucleic acid sequence is generated; and
[0136] (b) performing a second-stage amplification of the
amplification product generated from step (a) at a second annealing
temperature, which is high stringent conditions, comprising at
least one cycle of primer annealing, primer extending and
denaturing, using the same primers as used in step (a) or a primer
pair each comprising a pre-selected arbitrary nucleotide sequence
corresponding to each 5'-end portion of the primers used in step
(a), under conditions in which each primer anneals to the 3'- and
5'-ends of the amplification product, respectively, whereby the
amplification product is re-amplified.
[0137] Where the method is applied to the amplification of a target
nucleic acid sequence, the primer pair used has at its 3'-end
portion a hybridizing sequence substantially complementary to a
region of the target nucleic acid sequence to hybridize therewith.
Therefore, in a further aspect of this invention, there is provided
a method for selectively amplifying a target nucleic acid sequence
from a DNA or a mixture of nucleic acids, wherein the method
comprises performing an amplification reaction using primers,
characterized in that at least one primer is derived from the ACP
described above. Preferably, the primer according to the structure
of ACP is one having at its 3'end portion a hybridizing sequence
substantially complementary to a region of the target nucleic acid
sequence to hybridize therewith.
[0138] In a specific embodiment of this method, there is provided a
method using two stage amplifications for selectively amplifying a
target nucleic acid sequence from a DNA or a mixture of nucleic
acids, which comprises:
[0139] (a) performing a first-stage amplification of the target
nucleic acid sequence at a first annealing temperature comprising
at least two cycles of primer annealing, primer extending and
denaturing, using the primer pair of any one of the ACP described
above each having at its 3'end portion a hybridizing sequence
substantially complementary to a region of the target nucleic acid
sequence to hybridize therewith, under conditions in which each
primer anneals to its target nucleotide sequence, whereby the
amplification product of the target nucleotide sequence is
generated; and
[0140] (b) performing a second-stage amplification of the
amplification product generated from step (a) at a second annealing
temperature, which is high stringent conditions, comprising at
least one cycle of primer annealing, primer extending and
denaturing, using the same primers as used in step (a) or a primer
pair each comprising a pre-selected arbitrary nucleotide sequence
corresponding to each 5'-end portion of the primers used in step
(a), under conditions in which each primer anneals to the 3'- and
5'-ends of the amplification product, respectively, whereby the
amplification product is re-amplified.
[0141] Where the template for amplification is mRNA, the production
of cDNA is required prior to amplification. Therefore, in still
further aspect of this invention, there is provided a method for
selectively amplifying a target nucleic acid sequence from an mRNA,
wherin the method comprises reverse transcribing the mRNA and
performing an amplification reaction using primers, characterized
in that at least one primer is derived from the ACP described
above. Preferably, the primer according to the structure of ACP is
one having at its 3'end portion a hybridizing sequence
substantially complementary to a region of the target nucleic acid
sequence to hybridize therewith.
[0142] In a specific embodiment of this invention, there is
provided a method using two stage amplifications for selectively
amplifying a target nucleic acid sequence from an mRNA which
comprises:
[0143] (a) contacting the mRNA with an oligonucleotide dT primer
which is hybridized to polyA tail of the mRNA under conditions
sufficient for template driven enzymatic deoxyribonucleic acid
synthesis to occur;
[0144] (b) reverse transcribing the mRNA to which the
oligonucloetide dT pirmer hybridizes to produce a first DNA strand
that is complementary to the mRNA to which the oligonucloetide dT
pirmer hybridizes;
[0145] (c) performing a first-stage amplification of the target
nucleic acid sequence from the first DNA strand obtained from step
(b) at a first annealing temperature comprising at least two cycles
of primer annealing, primer extending and denaturing, using the
primer pair of ACP described above having at its 3'end portion a
hybridizing sequence substantially complementary to a region of the
target nucleic acid sequence to hybridize therewith, under
conditions in which each primer anneals to its target nucleotide
sequence, whereby the amplification product of the target
nucleotide sequence is generated; and
[0146] (d) performing a second-stage amplification of the
amplification product generated from step (c) at a second annealing
temperature, which is high stringent conditions, comprising at
least one cycle of primer annealing, primer extending and
denaturing, using the same primers as used in step (c) or a primer
pair each comprising a pre-selected arbitrary nucleotide sequence
corresponding to each 5'-end portion of the primers used in step
(c), under conditions in which each primer anneals to the 3'- and
5'-ends of the amplification product, respectively, whereby the
amplification product is re-amplified.
[0147] Since the amplification methods of this invention employs
the ACP of this invention, the common descriptions between them are
omitted in order to avoid the complexity of this specification
leading to undue multiplicity.
[0148] This application using ACP of the subject invention can
provide an improved method for selectively amplifying a target
nucleic acid sequence from a nucleic acid or a mixture of nucleic
acids (DNA or mRNA) by performing nucleic acid amplifications,
preferably, PCR. Since the effect of ACP provides the conventional
primers with primer annealing specificity regardless of "primer
search parameters" for primer design such as primer length,
annealing temperature, GC content and product length, it is
particularly recommended to use the ACP when the conventional
primers used to amplify a target nucleic acid fragment are too
sensitive to such parameters to generate specific nucleic acid
amplification products.
[0149] A schematic representation for selectively amplifying a
target nucleic acid of double-stranded DNA using novel ACP system
as described above is illustrated in FIG. 1A. FIG. 1B illustrates a
schematic representation for selectively amplifying a target
nucleic acid of mRNA using novel ACP system. Referring to FIGS. 1A
and 1B, the present methods will be described in more detail.
[0150] The present methods for amplifying a nucleic acid sequence
may be carried out in accordance with various primer-based nucleic
acid amplifications known in the art. Preferably, the methods are
carried out according to the two stage amplifications developed by
the present inventor, more preferably, the amplification is
performed by polymerase chain reaction known in the art and most
preferably, hot start PCR method.
[0151] The methods of the present invention, for amplifying a
nucleic acid sequence can be used to amplify any desired nucleic
acid molecule. Such molecules may be either DNA or RNA. The
molecule may be in either a double-stranded or single-stranded
form, preferably, double-stranded. Where the nucleic acid as
starting material is double-stranded, it is preferred to render the
two strands into a single-stranded, or partially single-stranded,
form. Methods known to separate strands includes, but not limited
to, heating, alkali, formamide, urea and glycoxal treatment,
enzymatic methods (e.g., helicase action) and binding proteins. For
instance, strand separation can be achieved by heating at
temperature ranging from 80.degree. C. to 105.degree. C. General
methods for accomplishing this treatment are provided by Joseph
Sambrook, et al., Molecular Cloning, A Laboratory Manual, Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.(200
1).
[0152] Where a mRNA is employed as starting material for
amplification, a reverse transcription step is necessary prior to
amplification, details of which are found in Joseph Sambrook, et
al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y.(2001); and Noonan, K. F.
et al., Nucleic Acids Res. 16:10366 (1988)). For reverse
transcription, an oligonucleotide dT primer hybridizable to poly A
tail of mRNA is used. The oligonucleotide dT primer is comprised of
dTMPs, one or more of which may be replaced with other dNMPs so
long as the dT primer can serve as primer. Reverse transcription
can be done with a reverse transcriptase that has RNase H activity.
If one uses an enzyme having RNase H activity, it may be possible
to omit a separate RNase H digestion step, by carefully choosing
the reaction conditions.
[0153] The present methods do not require that the molecules to be
amplified have any particular sequence or length. In particular,
the molecules which may be amplified include any naturally
occurring procaryotic, eukaryotic (for example, protozoans and
parasites, fungi, yeast, higher plants, lower and higher animals,
including mammals and humans) or viral (for example, Herpes
viruses, HIV, influenza virus, Epstein-Barr virus, hepatitis virus,
polio virus, etc.) or viroid nucleic acid. The nucleic acid
molecule can also be any nucleic acid molecule which has been or
can be chemically synthesized. Thus, the nucleic acid sequence may
or may not be found in nature. The ACP used for the present
invention is hybridized or annealed to a region on template so that
double-stranded structure is formed. Conditions of nucleic acid
hybridization suitable for forming such double stranded structures
are described by Joseph Sambrook, et al., Molecular Cloning, A
Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, N.Y.(2001) and Haymes, B. D., et al., Nucleic Acid
Hybridization, A Practical Approach, IRL Press, Washington, D.C.
(1985). The sequence of the 3'-end portion of ACP needs not to
exhibit precise complementarity, but need only to be substantially
complementary in sequence to be able to form a stable
double-stranded structure. Thus, departures from complete
complementarity are permissible, so long as such departures are not
sufficient to completely preclude hybridization to form a
double-stranded structure. Hybridization of ACP to a region on
template nucleic acid is a prerequisite for its template-dependent
polymerization with polymerases. Factors (see Joseph Sambrook, et
al., Molecular Cloning, A Laboratory Manual, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y.(2001); and Haymes, B.
D., et. al., Nucleic Acid Hybridization, A Practical Approach, IRL
Press, Washington, D.C.(1985)) which affect the base pairing of ACP
to its complementary nucleic acids subsequently affect priming
efficiency. The nucleotide composition of ACP can affect the
temperature at which annealing is optimal and therefore can affect
its priming efficiency.
[0154] A variety of DNA polymerases can be used in the
amplification step of the present methods, which includes "Klenow"
fragment of E. coli DNA polymerase I, a thermostable DNA polymerase
and bacteriophage T7 DNA polymerase. Preferably, the polymerase is
a thermostable DNA polymerase such as may be obtained from a
variety of bacterial species, including Thermus aquaticus (Taq),
Thermus thermophilus (Tth), Thermus fliformis, Thermis flavus,
Thermococcus literalis, and Pyrococcus furiosus (Pfu). Many of
these polymerases may be isolated from bacterium itself or obtained
commercially. Polymerase to be used with the subject invention can
also be obtained from cells which express high levels of the cloned
genes encoding the polymerase. When a polymerization reaction, is
being conducted, it is preferable to provide the components
required for such reaction in excess in the reaction vessel. Excess
in reference to components of the amplification reaction refers to
an amount of each component such that the ability to achieve the
desired amplification is not substantially limited by the
concentration of that component. It is desirable to provide to the
reaction mixture an amount of required cofactors such as Mg.sup.2+,
and dATP, dCTP, dGTP and dTTP in sufficient quantity to support the
degree of amplification desired.
[0155] All of the enzymes used in this amplification reaction may
be active under the same reaction conditions. Indeed, buffers exist
in which all enzymes are near their optimal reaction conditions.
Therefore, the amplification process of the present invention can
be done in a single reaction volume without any change of
conditions such as addition of reactants.
[0156] It would be understood that the 5'-end portions of a set of
ACPs used in the step of the first-stage amplification could
comprise identical or different sequences; if they are identical,
one primer corresponding to the sequence of 5'-end portion will be
used in the step of the second-stage amplification, whereas if they
are different, two primers each corresponding to the sequence of
each 5'-end portion of ACPs will be used in the step of the
second-stage amplification.
[0157] The present invention includes an alternative process for
selectively amplifying a target nucleic acid fragment from a
nucleic acid or a mixture using ACP, wherein a set of primers
comprising an ACP and a conventional primer can be used in the
first amplification step, instead of a set of ACP. The term
"conventional primer" used herein refers to any primer having a
structure different from ACP, especially, in terms of the presence
of the regulator portion containing universal base. In this case,
the conventional primer is added only the first amplification step
with the ACP and only one pre-selected arbitrary primer
corresponding to the 5'-end portion sequence of the ACP is added in
the second amplification step. In preferred embodiment, the
alternative process can be used when each 3'-portion of a pair of
ACP to be used in the first amplification step has different
melting temperature (T.sub.m). "T.sub.m" refers to the temperature
at which half the primers are annealed to the target region.
[0158] Two amplification steps of the present methods (in case of
amplification from mRNA, including reverse transcritptation) are
separated only in time. The first-stage amplification should be
followed by the second-stage amplification. It would be understood
that the first-stage amplification reaction mixture could include
the primers corresponding to the 5'-end portion which will be used
to anneal to the sequences of the 5'-end portions of the ACPs in
the second-stage amplification, which means that the primers
corresponding to the 5'-end portion can be added to the reaction
mixture at the time of or after the first-stage amplification
step.
[0159] As an alternative process, in the second-stage amplification
step the complete sequences of the ACPs used in the first-stage
amplification step, instead of the primers corresponding to the
5'-end portions of the ACPs, can be used as primers at the high
stringent conditions for re-amplifying the product generated from
the first-stage amplification step, wherein the 3'- and 5'- ends of
the product from the first amplification step which is generated
from annealing and extension of the 3'-end portion sequence of the
set of ACP to the template nucleic acid at the low stringent
conditions comprise the sequence or complementary sequence of ACP
and also serve as perfect paring sites to the set of ACP. In this
view, this alternative process is preferred because this need not
further add the primers corresponding to the 5'-end portions of the
ACPs to the reaction mixture at the time of or after the
first-stage amplification step. FIG. 1A also illustrates a
schematic representation for selectively amplifying a target
nucleic acid by the alternative process stated above.
[0160] Annealing or hybridization in the present methods is
performed under stringent conditions that allow for specific
binding between a nucleotide sequence and ACP. Such stringent
conditions for annealing will be sequence-dependent and varied
depending on environmental parameters. In the present methods, the
second-stage amplification is generally performed under higher
stringent conditions than the first-stage amplification.
[0161] In a preferred embodiment, the first annealing temperature
ranges from about 30.degree. C. to 68.degree. C. for the
first-stage amplification step, more preferably, 40.degree. C. to
65.degree. C. It is preferred that the second annealing temperature
ranges from about 50.degree. C. to 72.degree. C. for the
second-stage amplification. According to a more preferred
embodiment, the first annealing temperature is equal to or lower
than the second annealing temperature. The length or melting
temperature (T.sub.m) of the 3'-end portion sequence of ACP will
determine the annealing temperature for the first-stage
amplification. For example, in case that ACP comprises 10 arbitrary
nucleotides at the 3'-end portion, preferably, the annealing
temperature will be about between 45.degree. C. and 55.degree. C.
for the first-stage amplification.
[0162] According to the present methods, the first-stage
amplification under low stringent conditions is carried out for at
least 2 cycles of annealing, extending and denaturing to improve
the specificity of primer annealing during the first-stage
amplification, and through the subsequent cycles, the second-stage
amplification is processed more effectively under high stringent
conditions. The first-stage amplification can be carried out up to
30 cycles. In a preferred embodiment, the first-stage amplification
is carried out for 2 cycles. In another embodiment, the
second-stage amplification under high stringent conditions is
carried out for at least one cycle (preferably, at least 5 cycles)
and up to 45 cycles to amplify the first-stage product. In a more
preferred embodiment, the second-stage amplification is carried out
for 25-35 cycles. High and low stringent conditions may be readily
determined from the standard known in the art. "Cycle" refers to
the process which results in the production of a copy of target
nucleic acid. A cycle includes a denaturing step, an annealing
step, and an extending step.
[0163] In the most preferable embodiment, the amplification is
performed in accordance with PCR which is disclosed in U.S. Pat.
Nos. 4,683,195, 4,683,202, and 4,800,159.
[0164] According to a preferred embodiment, when the first-stage
amplification is carried out, the 3'-end portion of the primer pair
of ACP is involved in annealing at the first annealing temperature
and when the second-stage amplification is carried out, the 5'-end
portion of the primer pair serves as a priming site. Such
alteration of the portion to involve in annealing is mainly
ascribed to the ACP itself, in particular, the regulator portion of
ACP. In the present methods, the regulator portion of ACP is
capable of restricting the annealing portion of ACP to its 3'-end
portion at the first annealing temperature, responsible for
improving annealing specificity to a target sequence.
[0165] The present methods may be combined with many other
processes known in the art to achieve a specific aim. For example,
the isolation (or purification) of amplified product may follow the
second-stage amplification. This can be accomplished by gel
electrophoresis, column chromatography, affinity chromatography or
hybridization. In addition, the amplified product of this invention
may be inserted into suitable vehicle for cloning. Furthermore, the
amplified product of this invention may be expressed in suitable
host harboring expression vector. In order to express the amplified
product, one would prepare an expression vector that carries the
amplified product under the control of, or operatively linked to a
promter. The promoter is originated from the vector itselt or the
end portion of the amplified product, which may correspond to
5'-end portion of the ACP. Many standard techniques are available
to construct expression vectors containing the amplified product
and transcriptional/translational/control sequences in order to
achieve protein or peptide expression in a variety of
host-expression systems. The promoter used for prokaryotic host
includes, but not limited to, pL.lambda. promoter, trp promoter,
lac promoter and T7 promoter. The promoter used for eukaryotic host
includes, but not limited to, metallothionein promoter, adenovirus
late promoter, vaccinia virus 7.5K promoter and the promoters
derived from polyoma, adenovirus 2, simian virus 40 and cytomegalo
virus. Certain examples of prokaryotic hosts are E. coli, Bacillus
subtilis, and other enterobacteriaceae such as Salmonella
typhimurium, Serratia marcescens, and various Pseudomonas species.
In addition to microorganisms, cultures of cells derived from
multicellular organisms may also be used as hosts. In principle,
any such cell culture is workable, whether from vertebrate or
invertebrate culture. In addition to mammalian cells, these include
insect cell systems infected with recombinant virus expression
vectors (e.g., baculovirus); and plant cell systems infected with
recombinant virus expression vectors (e.g., cauliflower mosaic
virus, tobacco mosaic virus) or transformed with recombinant
plasmid expression vectors (e.g., Ti plasmid) containing one or
more coding sequences. The expressed polypeptide from the amplified
product may be generally purified with a variety of purposes in
accordance with the method known in the art.
[0166] In another aspect of this invention, there is provided a kit
for nucleic acid amplification of the instant invention described
previously, which comprises the annealing control primer or
annealing control primer set indicated above.
[0167] In still another aspect of this invention, there is provided
a kit for selective amplification of a target nucleic acid sequence
from DNA described previously, which comprises the annealing
control primer or annealing control primer set indicated above.
[0168] In further aspect of this invention, there is provided a kit
for selective amplification of a target nucleic acid sequence from
mRNA described previously, which comprises the annealing control
primer or annealing control primer set indicated above.
[0169] According to one embodiment of this invention, these kits
further comprises a primer or a primer pair each having a
nucleotide sequence corresponding to the 5'-end portion of the ACP;
in case that the 5'-end portion comprises universal primer
sequence, it is more preferred that the kit comprises the universal
primers. The present kits may optionally include the reagents
required for performing PCR reactions such as buffers, DNA
polymerase, DNA polymerase cofactors, and
deoxyribonucleotide-5'-triphosphates. Optionally, the kits may also
include various polynucleotide molecules, reverse transcriptase,
various buffers and reagents, and antibodies that inhibit DNA
polymerase activity. The kits may also include reagents necessary
for performing positive and negative control reactions. Optimal
amounts of reagents to be used in a given reaction can be readily
determined by the skilled artisan having the benefit of the current
disclosure. The kits, typically, are adapted to contain in separate
packaging or compartments the constituents afore-described.
[0170] II. Application to Multiplex DNA Amplification
[0171] This application using ACP of the subject invention can also
provide an improved method for amplifying more than one target
sequence using more than one pair of primers in the same reaction.
In general, it is extremely difficult to set up PCR conditions to
amplify more than 10 targets in parallel because an optimal PCR
reaction is required to amplify even one specific locus without any
unspecific by-products, so that those researchers who have achieved
multiplex PCR have had to work hard to optimize their systems.
Since annealing needs to take place at a sufficiently high
temperature to allow the perfect DNA-DNA matches to occur in the
reaction, the ACP of the subject invention is ideal in the
optimization of multiplex DNA amplification due to its function of
improving the specificity of amplification. "Multiplex PCR" as used
herein refers to the simultaneous amplification of multiplex DNA
targets in a single polymerase chain reaction (PCR) mixture.
[0172] In still further aspect of this invention, there is provided
a method for amplifying more than one target nucleotide sequence
simultaneously using more than one pair of primers in the same
reaction, wherein the method comprises performing an amplification
reaction using primers, characterized in that at least one primer
is derived from any one of ACP described above. Preferably, the
primer according to the structure of ACP is one having at its 3'end
portion a hybridizing sequence substantially complementary to a
region of the target nucleic acid sequence to hybridize
therewith.
[0173] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0174] (a) performing a first-stage amplification of more than one
target nucleotide sequence at a first annealing temperature
comprising at least two cycles of primer annealing, primer
extending and denaturing, using the primer pairs of any one of ACP
above in which its 3'end portion each of the primer pairs has a
hybridizing nucleotide sequence substantially complementary to a
region of the target nucleic acid sequence to hybridize therewith,
under conditions in which each of each primer pair anneals to its
target nucleotide sequence, whereby the amplification products of
target nucleotide sequences are generated; and
[0175] (b) performing a second-stage amplification of the
amplification products generated from step (a) at a second
annealing temperature, which is high stringent conditions,
comprising at least one cycle of primer annealing, primer extending
and denaturing, using the same primer pairs as used in step (a) or
primer pairs each comprising a pre-selected arbitrary nucleotide
sequence corresponding to each 5'-end portion of the primer pairs
used in step (a), under conditions in which each of each primer
pair anneals to the 3'- and 5'-end sequences of the amplification
products generated from step (a), respectively, whereby the
amplification products are re-amplified in the same reaction.
[0176] Since this application using the ACP of this invention is
carried out in accordance with the present methods for
amplification of nucleic acid sequence previously discussed, except
for using more than one target nucleotide sequence and primer
pairs, the common descriptions between them are omitted in order to
avoid the complexity of this specification leading to undue
multiplicity.
[0177] For instance, tjie composition and structure of ACP used and
the conditions for amplification, are common between this process
and the present methods for amplification of nucleic acid sequence
previously discussed.
[0178] In a preferred embodiment, the amplified products from each
of target nucleotide sequences are different in size for subsequent
analysis.
[0179] According to a preferred embodiment, the amplification
products of multiplex target nucleotide sequences may be analyzed
through size separation. The size separation comparison is
performed using a variety of method known in the art, such as
electrophoresis through a polyacrylamide gel matrix or agarose gel
matrix and nucleotide sequencing. The nucleotide sequencing may be
rapidly carried out with an automatic sequencer available from
various manufacturer.
[0180] As exemplified in Example below, the ACP of this invention
permits the final amplified products to be free from the background
problems as well as non-specificity arising from the conventional
primers used in multiplex nucleic acid amplification methods known
in the art.
[0181] The advantage of the multiplex amplification is that
numerous diseases or specific nucleotide sequence alterations
(e.g., single nucleotide polymorphism or point mutation) can be
assayed in the same reaction.
[0182] The number of analyses that can be run simultaneously is
unlimited; however, the upper limit is probably about 20 and is
likely to be dependent on the size difference required for
resolution and methods that are available to resolve the amplified
product.
[0183] In another aspect of this invention, there is provided a kit
for amplifying more than one target nucleotide sequence
simultaneously in the same reaction, which comprises the annealing
control primer or annealing control primer set described above.
According to one embodiment of this invention, these kits further
comprises a primer or a primer pair having a nucleotide sequence
corresponding to the 5'-end portion of the ACP; in case that the
5'-end portion comprises universal primer sequence, it is more
preferred that the kit comprises the universal primers. The present
kits may optionally include the reagents required for performing
PCR reactions such as buffers, DNA polymerase, DNA polymerase
cofactors, and deoxyribonucleotide-5'-triphosphates. Optionally,
the kits may also include various polynucleotide molecules, reverse
transcriptase, various buffers and reagents, and antibodies that
inhibit DNA polymerase activity. The kits may also include reagents
necessary for performing positive and negative control reactions.
Optimal amounts of reagents to be used in a given reaction can be
readily determined by the skilled artisan having the benefit of the
current disclosure. The kits, typically, are adapted to contain in
separate packaging or compartments the constituents
afore-described.
[0184] The method and kit of the present invention may be applied
to the diagnosis of genetic and infectious diseases, gender
determination, genetic linkage analysis, and forensic studies.
[0185] III. Application to Identification of Differentially
Expressed Genes
[0186] This application using ACP of the subject invention can also
provide an improved method for detecting and cloning cDNAs
complementary to differentially expressed mRNAs in two or more
nucleic acid samples.
[0187] In still further aspect of this invention, there is provided
a method for detecting DNA complementary to differentially
expressed mRNA in two or more nucleic acid samples, wherein the
method comprises reverse transcribing the mRNA and performing an
amplification reaction using primers, characterized in that at
least one primer is derived from any one of ACP described above.
Preferably, the primer according to the structure of ACP is one
having at its 3'end portion a hybridizing sequence (more
preferably, arbitrary sequence) substantially complementary to a
region of cDNA strands generated from reverse transcription.
[0188] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0189] (a) providing a first sample of nucleic acids representing a
first population of mRNA transcripts and a second sample of nucleic
acids representing a second population of mRNA transcripts;
[0190] (b) separately contacting each of the first nucleic acid
sample and the second nucleic acid sample with a first primer of
any one of ACP described above, in which the 3'-end portion of the
first primer comprises a hybridizing nucleotide sequence
substantially complementary to a first site in the differentially
expressed mRNA to hybridize therewith, under conditions sufficient
for template driven enzymatic deoxyribonucleic acid synthesis to
occur;
[0191] (c) reverse transcribing the differentially expressed mRNA
to which the first primer hybridizes to produce a first population
of first cDNA strands that are complementary to the differentially
expressed mRNA in the first nucleic acid sample to which the first
primer hybridizes, and a second population of first cDNA strands
that are complementary to the differentially expressed mRNA in the
second nucleic acid sample to which the first primer
hybridizes;
[0192] (d) purifying and quantifying each of the first and second
populations of first cDNA strands;
[0193] (e) performing a first-stage amplification of each of the
first and second population of first DNA strands obtained from step
(d) at a first annealing temperature comprising at least one cycle
of primer annealing, primer extending and denaturing, using a
second primer of any one of ACP described above having at its 3'
end portion a hybridizing sequence substantially complementary to a
second site in the first and second populations of first cDNA
strands, under conditions in which the second primer anneals to the
second site in each population of the first cDNA strands, whereby
first and second populations of second cDNA strands are
generated;
[0194] (f) performing a second-stage amplification of each second
cDNA strand generated from step (e) at a second annealing
temperature, which is high stringent conditions, comprising at
least two cycles of primer annealing, primer extending and
denaturing, using the same first and second primers as used in
steps (b) and (e), respectively, or a primer pair each comprising a
pre-selected arbitrary nucleotide sequence corresponding to each
5'-end portion of the first and second primers used in steps (b)
and (e), respectively, under conditions in which each primer
anneals to the 3'- and 5'-end sequences of each second cDNA strand,
respectively, whereby amplification products of the second cDNA
strands are generated, and
[0195] (g) comparing the presence or level of individual
amplification products in the first and second populations of
amplification products obtained from step (f).
[0196] Since this application using the ACP of this invention
employs the present methods for amplification of nucleic acid
sequence previously discussed, the common descriptions between them
are omitted in order to avoid the complexity of this specification
leading to undue multiplicity.
[0197] A schematic representation for identifying differentially
expressed genes using novel ACP is illustrated in FIG. 2A.
[0198] In the present method, the nucleic acid sample representing
a population of mRNA transcripts can be obtained from a wide
variety of biological materials. In general, the first nucleic acid
sample comprises mRNA expressed in a first cell and the second
nucleic acid sample comprises mRNA expressed in a second cell. In
particular, the first nucleic acid sample comprises mRNA expressed
in a cell at a first developmental stage and the second nucleic
acid sample comprises mRNA expressed in a cell at a second
developmental stage. In addition, the first nucleic acid sample
comprises mRNA expressed in a tumorigenic cell and the second
nucleic acid sample comprises mRNA expressed in a normal cell.
[0199] Steps (e) and (f) of the subject application may occur in a
single tube using the same reaction mixture except for primers,
which means that steps (e) and (f) are separated only in time. It
would be understood that the primers corresponding to the 5'-end
portion could be added to the reaction mixture at the time of or
after the second cDNA strand synthesis. In a preferred embodiment,
the primers corresponding to the 5'-end portion are added to the
reaction mixture right after step (e) is completed, followed by
subsequent PCR amplification of second cDNA strands.
[0200] It would be also understood that the 5'-end portion
sequences of the first and second ACPs used in steps (b) and (e),
respectively, could be identical or different sequences; if they
are identical, one primer corresponding to the sequence of 5'-end
portion will be used in the step (f), whereas if they are
different, two primers each corresponding to the sequence of each
5'-end portion of ACPs will be used in the step (f). In a preferred
embodiment, the 5'-end portion sequences of the first and second
ACPs used in steps (b) and (e) are different and thus, two primers
each corresponding to the sequence of each 5'-end portion of ACPs
are used in step (f).
[0201] As an alternative process, in step (f) the complete
sequences of the first and second ACPs used in steps (b) and (e),
respectively, instead of the primers corresponding to the 5'-end
portions of the ACPs, can be used as primers at the high stringent
conditions for amplifying each second DNA strand obtained from step
(e), wherein the 3'- and 5'-ends of the second DNA strands which
are initially synthesized using the second ACP comprise the
sequence of the first ACP and the complementary sequence of the
second ACP, respectively, and also serve as perfect pairing sites
to the first and second ACPs. In this view, this alternative
process is preferred because there is no need to add the primers
corresponding to the 5'-end portions of the ACPs to the reaction
mixture at the time of or after first-stage PCR reaction. FIG. 2B
illustrates a schematic representation for identifying
differentially expressed genes by the alternative process stated
above.
[0202] The method of the subject application for detecting
differences in gene expression uses only a single cDNA synthesis
primer (the first ACP) to react with mRNA, unlike conventional
Differential Display PCR which requires multiple cDNA synthesis
anchor primers. In the original differential display method
outlined by Liang and Pardee in 1992, twelve anchor primers have
been introduced. The anchor primers for example, having a sequence
of T.sub.12 MN, where M is A, C, or G and N is A, C, G or T,
produced twelve separate cDNA populations. Recently, modified
anchor primers have been proposed by altering the number of
nucleotides such as one or three instead of two at the 3'-end which
can hybridize to a sequence that is immediately 5' to the poly A
tail of mRNAs or by extending additional nucleotides at the 5'-end
while retaining the Oligo (dT).sub.9-12 MN tail resulting in at
least 21 nucleotides in length (Villeponteau et al., 1996, Combates
et al., 2000).
[0203] The subject invention concerns the embodiments of the ACP
used in this method for the identification of differentially
expressed genes, wherein the first ACP used in step (b) is
represented by the following general formula (2):
5'-dX.sub.p-dY.sub.q-dT.sub.r-3' wherein dX is one of the four
deoxyribonucleotides, A, C, G, or T; dY is a regulator portion
comprising universal bases responsible for the main function of the
ACP associated with alteration of annealing temperature during PCR;
dT is a T deoxyribonucleotide; p, q, and r represent an integer,
respectively; dX.sub.p represents the 5'-end portion and contains a
pre-selected arbitrary nucleotide sequence; dY.sub.q contains at
least 2 universal bases; dT.sub.r represents the 3'-end portion;
the nucleotide sequence of the 3'-end portion should have lower
T.sub.m than that of the 5'-end portion. The formula (2) basically
follows the rule of formula (1). The 3 '-end portion of formula (2)
consists of the sequences capable of annealing to the poly A tail
of mRNA and serves as a cDNA synthesis primer for reverse
transcription of mRNA.
[0204] In a preferred embodiment, the 3'-end portion of the first
ACP used in step (b) contains at least 6 T nucleotides in length,
which is considered a minimal requirement of length for primer
annealing. More preferably, the 3'-end portion sequence is from 10
to 20 T nucleotides and can be up to 30 T nucleotides in length.
Most preferably, the 3'-end portion sequence is about 15 T
nucleotides in length. This primer is named dT.sub.15 annealing
control primer (dT.sub.15-ACP). In a preferred embodiment, the
first primer has a general formula of
5'-dX.sub.15-30-dY.sub.2-10-dT.sub.10-20-3', wherein dX represents
a deoxyribonucleotide and comprises a pre-selected arbitrary
nucleotide sequence not substantially complementary to the first
and second populations of mRNAs; dY represents the regulator
portion comprising 2-10 universal bases or non-discriminatory base
analogs; and dT represents a contiguous deoxythymidine capable of
annealing to the first site in the first and second populations of
mRNAs.
[0205] In one embodiment, the 3'-end portion of the first ACP used
in step (b) may contain at least one additional nucleotide at the
3'-end that can hybridize to an mRNA sequence which is immediately
upstream of the polyA tail. The additional nucleotides at the 3'
end of the first ACP may be up to 3 in length. For example, dT may
further comprise 3'-V at its 3'-end; in which V is one selected
from the group consisting of deoxyadenosine, deoxycytidine and
deoxyguanosine. In addition, dT may further comprise 3'-NV at its
3'-end; in which V is one selected from the group consisting of
deoxyadenosine, deoxycytidine and deoxyguanosine and N is one
selected from the group consisting of deoxyadenosine,
deoxythymidine, deoxycytidine and deoxyguanosine. Most preferably,
the 3'-end portion sequence of the first ACP used in step (b)
contains dT.sub.15 only.
[0206] In a preferred embodiment, the first entire ACP is about
40-45 nucleotides in length and comprises dT.sub.15 at the 3'-end
portion, dX.sub.20-25 at the 5'-end portion and dY.sub.5 between
the 3'- and 5'-end portions. The first entire ACP can be up to 100
nucleotides in length. The first primer is exemplified by SEQ ID
NOs: 30, 39, 57 and 61-63.
[0207] The first ACP described herein is hybridized to the poly A
tail of the mRNA, which is present on all mRNAs, except for a small
minority of mRNA. The use of the first ACP used in this invention
results in only one reaction and produces only one cDNA population,
in contrast to at least 3 to 64 separate cDNA populations generated
by the conventional anchor primers of Differential Display
technique. This greatly increases the efficiency of the method by
generating a substantially standard pool of single-stranded cDNA
from each experimental mRNA population.
[0208] In the step (d), the standard pools of cDNAs synthesized by
the first ACP should be purified and then quantitated by techniques
well known to those of ordinary skill in the art such as
spectrophotometry. This step is necessary to precisely control
their inputs into the amplification step and then compare the final
amplified poducts between two or more samples Preferably, the
amount of cDNA produced at this point in the method is measured. It
is more preferred that this determination is made using ultraviolet
spectroscopy, although any standard procedure known for quantifying
cDNA known to those of ordinary skill in the art is acceptable for
use for this purpose. When using the UV spectroscopy procedure, an
absorbance of about 260 nm of UV light advantageously is used. By
the measurement of cDNA quantity at this step, therefore, the cDNA
quantity can be standardized between or among samples in the
following amplification reaction.
[0209] After synthesis of the first cDNA strands using the first
ACP, the second cDNA strands are synthesized using the second ACP
primer under low stringent conditions, by at least one cycle
comprising denaturing, annealing and primer extension, wherein the
resultant first cDNA strands are used as templates.
[0210] The second ACP basically follows the rule of formula (1) and
its 3'-end portion comprises a short arbitrary sequence, which
preferably has lower T.sub.m than that of the 5'-end portion. This
primer is named an arbitrary annealing control primer (AR-ACP). In
a preferred embodiment, the 3'-end portion of the second ACP can
have from 8 to 15 nucleotides in length. Most preferably, the
3'-end portion of the second ACP contains about 10 nucleotides in
length.
[0211] According to a preferred embodiment, the second ACP has the
general formula of 5'-dX.sub.15-30-dY.sub.2-10-dZ.sub.8-15-3',
wherein dX represents a deoxyribonucleotide and comprises a
pre-selected arbitrary nucleotide sequence not substantially
complementary to the first and second populations of the first cDNA
strands; dY represents the regulator portion comprising 2-10
universal bases or non-discriminatory base analogs; dZ represents a
hybridizing arbitrary nucleotide sequence capable of annealing to
the second site in the first and second populations of DNA strands.
More preferably, the entire second ACP is about 40-45 nucleotides
in length comprising dZ.sub.10 at the 3'-end portion, dX.sub.20-25
at the 5'-end portion and dY.sub.5 between the 3'- and 5'-end
portions. The second entire ACP can be up to 100 nucleotides in
length. The second primer is exemplified by SEQ ID NOs: 1-9, 13-18
and 20-23.
[0212] The second ACP described herein is different from a
so-called long arbitrary primer, as used in the known modified
Differential Display technique. For example, the conventional long
arbitrary primers as described by Villeponteau et al. (1996) and
Diachenko et al. (1996), having at least 21 or 25 nucleotides in
length, comprise of only arbitrary nucleotides in the entire
sequences. These conventional long arbitrary primers will hybridize
in a non-predictable way under the low annealing temperature (about
40.degree. C.) which is required to achieve arbitrary priming in
the early PCR cycle, such that it is impossible to design a
representative set of primers rationally. Furthermore, many of the
bands represent the same mRNA due to the "Stickiness" of long
primers when used under such a low stringency.
[0213] The advantages of the present method for detecting
differentially expressed genes are predominantly ascribed to the
use of the second ACP. Since the second ACP is designed to limit
the annealing of the second ACP to its 3'-end portion sequence, not
to its 5'-end portion sequence, in association with annealing
temperature, the resultant annealing will come out in a predictable
way, such that it is possible to design a representative set of
primers rationally. In addition, the use of the second ACP allows
avoiding false positive problems caused by the "Stickiness" of the
conventional long primers under low stringent conditions as used in
the previous Differential Display technique.
[0214] The annealing temperature used for the synthesis of second
DNA strands under low stringency conditions used in step (e) is
preferably about between 40.degree. C. to 65.degree. C., more
preferably, about between 45.degree. C. and 55.degree. C. and the
most preferably, about 50.degree. C. However, unlike Differential
Display, which uses annealing temperatures between 35.degree. C.
and 45.degree. C., the annealing temperature of low stringency
conditions used in the subject application is relatively higher
than those used in the known classical or enhanced Differential
Display techniques with arbitrary primers.
[0215] Another unique and significant features of the subject
application for detecting differentially expressed genes is to
amplify only the initially synthesized second DNA strands by the
subsequent amplification, wherein the 3'- and 5'-ends of the second
DNA strands which have been initially synthesized using the second
ACP comprise the complementary sequence of the first ACP and the
sequence of the second ACP, respectively and thus, the entire
sequences of the first and second ACPs, or only their 5'-end
portion sequences of the first and second ACPs, are used as 3' and
5' primer sequences for the amplification of the second DNA
strands.
[0216] Since the ACP in the subject application leads to the
amplification of specific products, it can be possible to
fundamentally eliminate the cause of major bottleneck problems,
such as false products and poor reproducibility, which result from
non-specific annealing of the conventional arbitrary and dT primers
to first and second DNA strands as well as to amplified products
during PCR in the known Differential Display methods.
[0217] In a preferred embodiment, the synthesis of second DNA
strands in step (e) is carried out by at least 1 cycle of
amplification under low stringent conditions to achieve arbitrary
priming, and through the subsequent cycles, the amplification is
processed more effectively for the amplification of the resultant
second DNA strands under high stringent conditions used in step
(f). Most preferably, the synthesis of second DNA strands in step
(e) is carried out by one cycle of amplification under low
stringent conditions.
[0218] In a preferred embodiment, the amplification of the
resultant second DNA strands synthesized by the step (e) is carried
out under high stringent conditions using the complete sequences of
the first and second ACPs used in steps (b) and (e), respectively,
as primer sequences, wherein the 3'- and 5'-ends of the resultant
second DNA strands provide perfect pairing sites to the first and
second ACPs. However, it is interesting that the first and second
ACPs are not involved in any other annealing to the template
nucleic acid, except the annealing and extension of the 3'- and 5'-
ends of the second DNA strands as a reaction unit at such a high
stringent condition because their 3'-end portions require
relatively low annealing temperature and the high stringent
conditions do not allow them to anneal to any site of the template,
except the 3'- and 5'-ends of the second DNA strands. Consequently,
owing to this function of ACP, which is capable of selectively
annealing to the template in associated with annealing temperature,
the amplified products can be free from the problems of the high
false positive rate, poor reproducibility and possible
under-representation of minor mRNA fractions in the analysis which
are the main problems of the known Differential Display. In this
view, there is a significant difference between this subject method
and the conventional Differential Display methods despite the fact
that they are in common to use the same primers for high stringent
conditions as well as for low stringent conditions.
[0219] In a preferred embodiment, the annealing temperature of the
amplification for high stringent conditions used in step (f) is
preferably about between 55.degree. C. and 72.degree. C. Most
preferably, the annealing temperature used for the high stringent
conditions is about 65-68.degree. C.
[0220] In a preferred embodiment, the amplification under high
stringent conditions used step (f) is carried out by at least 10
cycles and up to 50 cycles to amplify the resultant second DNA
strands synthesized by step (e) during PCR. Most preferably, the
PCR amplification is carried out by 40-45 cycles.
[0221] The second-strand cDNA is preferably synthesized by PCR,
more preferably, hot start PCR method in which the procedure is to
set up the complete reactions without the DNA polymerase and
incubate the tubes in the thermal cycler to complete the initial
denaturation step at >90.degree. C. Then, while holding the
tubes at a temperature above 70.degree. C., the appropriate amount
of DNA polymerase can be pipetted into the reaction. In a preferred
embodiment, the addition of the primers for the second-stage
amplification into the reaction mixture after the complete reaction
of the second-strand cDNA synthesis is also carried out under
denaturation temperature such as >90.degree. C. Then, while
holding the tubes at a temperature about 90.degree. C., the
appropriate amount of the primers for the second-stage
amplification can be pipetted into the reaction.
[0222] An example of the second DNA strand synthesis and the
subsequent amplification of the resultant second DNA strands in a
single tube using the pre-selected arbitrary sequence of the 5'-end
portions of the first and second ACPs is conducted under the
following conditions: the second DNA strands are synthesized under
low stringent conditions by one cycle of the first-stage
amplification comprising annealing, extending and denaturing
reaction; the reaction mixture containing the first-strand cDNA,
PCR reaction buffer (e.g., available from Roche), dNTP, and the
second ACP is pre-heated at about 94.degree. C., while holding the
tube containing the reaction mixture at about 94.degree. C., Taq
polymerase (e.g., available from Roche) is added into the reaction
mixture; the PCR reactions are as follows: one cycle of 94.degree.
C. for 1 min, 50.degree. C. for 3 min, and 72.degree. C. for 1 min;
followed by denaturing the amplification product at 94.degree. C.;
after the complete reaction of the second DNA strand synthesis in
step (e), 5' pre-selected arbitrary primer and 3' pre-selected
arbitrary primer are added to the reaction mixture and then the
second stage amplification is conducted as follows: 40 cycles of
94.degree. C. for 40 sec, 68.degree. C. for 40 sec, and 72.degree.
C. for 40 sec; followed by a 5 min final extension at 72.degree.
C.
[0223] An alternative example of the second DNA strand synthesis
and the subsequent amplification of the resultant second DNA
strands in a single tube using the complete sequences of the first
and second ACPs used in steps (b) and (e), respectively, instead of
the pre-selected arbitrary sequences of the 5'-end portions of the
first and second ACPs, is conducted under the following conditions:
the second DNA strands are synthesized under low stringent
conditions by one cycle of the first-stage amplification comprising
annealing, extending and denaturing reaction; the reaction mixture
containing the first-strand cDNA, PCR reaction buffer (e.g.,
available from Roche), dNTP, the first ACP (dT.sub.15-ACP), and the
second ACP (AR-ACP) is pre-heated at about 94.degree. C., while
holding the tube containing the reaction mixture at about
94.degree. C., Taq polymerase (e.g., available from Roche) is added
into the reaction mixture; the PCR reactions are as follows: one
cycle of 94.degree. C. for 1 min, 50.degree. C. for 3 min, and
72.degree. C. for 1 min; followed by the second-stage PCR
amplification comprising annealing, extending and denaturing
reaction; the PCR reactions are as follows: 40 cycles of 94.degree.
C. for 40 sec, 65.degree. C. for 40 sec, and 72.degree. C. for 40
sec; followedc by a 5 min final extension at 72.degree. C.
[0224] It should be noted that a proper concentration of arbitrary
ACP (the second ACP) is used to synthesize the second-strand cDNAs
by one cycle of the first-stage amplification. If the amount of the
second ACP used in the step (e) is too low, the resultant amplified
products are not reproducible. In contrast, the excess amount of
the second ACP used in the step (e) generates backgrounds such as
DNA smear during PCR. In a preferred embodiment, the concentration
of the second ACP used in the step (e) is about between 0.1 .mu.M
and 1.0 .mu.M. Most preferably, the concentration of the second ACP
as well as the first ACP is about 0.2 .mu.M. In a preferred
embodiment, the concentration of the primers used in the step (f)
is about between 0.1 .mu.M and 1 .mu.M, most preferably, about 0.4
.mu.M.
[0225] Another significant feature of the subject application to
the identification of differences in gene expression is the use of
high annealing temperature in a method. High annealing temperature
used in step (f) increases the specificity of primer annealing
during PCR, which results in eliminating false positive products
completely and increasing reproducibility. Freedom from false
positives which is one major bottleneck remaining for the previous
Differential Display technique is especially important in the
screening step for the verification of the cDNA fragments
identified by Differential Display.
[0226] The step of comparing the presence or level of amplification
products obtained from step (f) may be performed in accordance with
various methods known in the art. In a preferred embodiment, each
of the first and second populations of amplification products of
step (f) are resolved by electrophoresis to identify differentially
expressed mRNAs. More preferably, the resultant PCR cDNA fragments
are detected on an ethidium bromide-stained agarose gel. Another
prominent feature of this subject application is the use of
ethidium bromide-stained agarose gel to identify differentially
expressed mRNAs. In general, the conventional Differential Display
methods use radioactive detection techniques using denaturing
polyacrylamide gels. However, according to the present method, the
significant amount of the amplified cDNA fragments obtained through
two stage amplifications allows to use an ethidium bromide-stained
agarose gel to detect the amplified cDNAs, which results in
increasing the speed and avoiding the use of radioactivity.
[0227] Alternatively, the resulting cDNA fragments can be also
detected on a denaturing polyacrylamide gel by autoradiography or
non-radioactive detection methods such as silver staining
(Gottschlich et al., 1997; Kociok et al., 1998), the use of
fluoresenscent-labelled oligonucleotides (Bauer et al. 1993; Ito et
al. 1994; Luehrsen et al., 1997; Smith et al., 1997), and the use
of biotinylated primers (Korn et al., 1992; Tagle et al., 1993;
Rosok et al., 1996).
[0228] In another embodiment, it might be useful for diagnostic
purposes to use an automatic system such as an automatic DNA
sequencer together with any distinct labeling of the ACPs to detect
or analyze the amplified products (Bauer, et al., 1993).
[0229] Considering the features of ACP in this subject application,
the present method for detecting and cloning differentially
expressed genes differs fundamentally from the previous
Differential Display techniques as described above.
[0230] In conclusion, the use of the ACP in this method makes it
possible to allow the amplification of only second DNA strands and
the use of the sufficient amount of starting materials as well as
the high concentration of dNTP, resulting in the following
benefits: a) increasing primer annealing specificity, b)
eliminating the problem of false positives which requires the
subsequent labor-intensive work to verify true positives, c)
improving reliability and reproducibility, d) detecting rare mRNAs,
e) generating long-distance PCR products ranging in size from 150
bp to 2.0 kb, f) allowing the use of ethidium bromide-stained
agarose gel to detect products, g) increasing the speed of
analysis, h) particularly, not requiring well-trained hands to
conduct this method, and i) allowing the rational design of a
representative set of primers.
[0231] In further aspect of this invention, there is provided a kit
for detecting DNA complementary to differentially expressed mRNA,
which comprises the annealing control primer or annealing control
primer set described above (the first and second primer). According
to one embodiment of this invention, these kits further comprises a
primer or a primer pair having a nucleotide sequence corresponding
to the 5'-end portion of the ACPs; in case that the 5'-end portion
comprises universal primer sequence, it is more preferred that the
kit comprises the universal primers. The present kits may
optionally include the reagents required for performing PCR
reactions such as buffers, DNA polymerase, DNA polymerase
cofactors, and deoxyribonucleotide-5'-triphosphates. Optionally,
the kits may also include various polynucleotide molecules, reverse
transcriptase, various buffers and reagents, and antibodies that
inhibit DNA polymerase activity. The kits may also include reagents
necessary for performing positive and negative control reactions.
Optimal amounts of reagents to be used in a given reaction can be
readily determined by the skilled artisan having the benefit of the
current disclosure. The kits, typically, are adapted to contain in
separate packaging or compartments the constituents
afore-described.
[0232] IV. Application to Rapid Amplification of cDNA Ends
(RACE)
[0233] This application using the ACP of the subject invention can
provide an improved method for rapidly amplifying cDNA ends, so
called RACE technologies. To be specific, the ACP of the subject
application is adapted to the RACE technologies related to either
of 3 '- and 5'-end, and eliminates the background problems
resulting from the primers used in the conventional RACE
technologies.
[0234] In still further aspect of this invention, there is provided
a method for rapidly amplifying a target cDNA fragment comprising a
cDNA region corresponding to the 3'-end region of an mRNA, wherein
the method comprises reverse transcribing said mRNA and performing
an amplification reaction using primers, characterized in that at
least one primer is derived from any one of ACPs described above.
Preferably, the primer according to the structure of ACP is one
having at its 3'-end portion a gene-specific hybridizing nucleotide
sequence substantially complementary to a site in cDNA generated
from reverse transcription and/or one having at its 3'-end portion
a hybridizing nucleotide sequence substantially complementary to
poly A tails of the mRNAs.
[0235] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0236] (a) contacting mRNAs with a first primer of any one of the
ACP described above, in which the 3'-end portion of the primer
comprises a hybridizing nucleotide sequence substantially
complementary to poly A tails of the mRNAs to hybridize therewith,
under conditions sufficient for template driven enzymatic
deoxyribonucleic acid synthesis to occur;
[0237] (b) reverse transcribing the mRNAs to which the first primer
hybridizes to produce a population of first cDNA strands that are
complementary to the mRNAs to which the first primer
hybridizes;
[0238] (c) performing a first-stage amplification of the first cDNA
strands at a first annealing temperature comprising at least one
cycle of primer annealing, primer extending and denaturing, using a
second primer of any one of the ACP described above having at its
3'-end portion a gene-specific hybridizing nucleotide sequence
substantially complementary to a site in one of the first cDNA
strands to hybridize therewith, under conditions in which the
second primer anneals to a gene-specific site on one of the first
cDNA strands, whereby a gene-specific second cDNA strand is
generated; and
[0239] (d) performing a second-stage amplification of the
gene-specific second cDNA strand generated from step (c) at a
second annealing temperature, which is high stringent conditions,
comprising at least two cycles of primer annealing, primer
extending and denaturing, using the same first and second primers
as used in steps (a) and (c), respectively, or a primer pair each
comprising a pre-selected arbitrary nucleotide sequence
corresponding to each 5'-end portion of the first and second
primers used in steps (a) and (c), respectively, under conditions
in which each primer anneals to the 3'- and 5'-end sequences of a
gene-specific second cDNA strand, respectively, whereby an
amplification product of a gene-specific cDNA strand is
generated.
[0240] Since this application using the ACP of this invention
employs the present methods for amplification of nucleic acid
sequence previously discussed, the common descriptions between them
are omitted in order to avoid the complexity of this specification
leading to undue multiplicity.
[0241] A schematic representation for amplifying a target cDNA
fragment comprising 3'-end region corresponding to the 3 -end of
mRNA using novel ACP system, called as ACP-based 3' RACE, is
illustrated in FIG. 3.
[0242] Steps (c) and (d) of the subject application may occur in a
single tube using the same reaction mixture except for primers,
which means that steps (c) and (d) are separated only in time. It
would be understood that the primers corresponding to the 5'-end
portion could be added to the reaction mixture at the time of or
after second cDNA strand synthesis. In a preferred embodiment, the
primers corresponding to the 5'-end portion are added to the
reaction mixture right after step (2) is completed, followed by
subsequent amplification of second cDNA strands.
[0243] As an alternative process, in step (d) the complete
sequences of the first and second ACPs, instead of the primers
corresponding to the 5'-end portions of the first and second ACPs,
can be used as 3' and 5' primers for amplifying the second-strand
cDNA obtained from step (c), wherein the 3'- and 5'-ends of the
second-strand cDNA which are initially synthesized using the second
ACP comprise the complementary sequence of the first ACP and the
sequence of the second ACP, respectively, and also serve as perfect
pairing sites to the first and second ACPs. FIG. 3 also illustrates
a schematic representation for amplifying a target cDNA fragment
comprising 3'-end region corresponding to the 3'-end of mRNA by the
alternative process stated above.
[0244] One of significant features of the present invention for
3'-RACE is that the first ACP comprising nucleotide sequence
substantially complementary to poly A tail of mRNA is used as a
cDNA synthesis primer and then the resultant cDNAs are directly
used as templates for subsequent amplification without any
additional purification steps to remove the cDNA synthesis
primer.
[0245] The annealing of the first ACP to the templates will be
interrupted during subsequent by the effect of the regulator
portion on the 3'- and 5'-end portions of the ACP under relatively
high stringent conditions as described in the principle of ACP. As
a result, the subject application to 3'-RACE simplifies the
conventional RACE methods by reducing the step of purification and
also, the ACP used in the subject application does not involve the
background problems because the annealing of the 3'-end portion is
specified by the presence of the regulator portion positioned
between the 3'-and 5'-end portions in the ACPs, whereas the
conventional cDNA synthesis primers such as Oligo-dT primers for
3'-RACE generate backgrounds during PCR, which is non-specific
products. According to a preferred embodiment, the formula of the
first ACP for the cDNA synthesis may be identical to the formula
(2).
[0246] When a gene-specific primer is used as 5' primer, the first
amplification of a target cDNA fragment containing a 3'-end
sequence in step (c) is carried out in accordance with conventional
PCR methods as known in the art. The term "gene-specific" in
reference sequence used herein refers to a partial sequence of a
specific gene or complement thereof that has been generally known
or available to one skilled in the art. Therefore, the
gene-specific primer means one comprising the gene-specific
sequence.
[0247] The generated second cDNA strand is amplified by the
second-stage amplification which is used in the application of the
present invention for amplifying a target nucleic acid sequence
above. Since the ACP described in this invention can generate
stable T.sub.m in a primer and also tolerate "primer search
parameters" for primer design such as primer length, annealing
temperature, GC content, and PCR product length, it is useful when
the gene-specific primer sequences have low T.sub.m or are too
sensitive to such parameters to generate specific products.
[0248] In another aspect of this invention, there is provided a
method for rapidly amplifying a target DNA fragment comprising a
cDNA region corresponding to the 5'-end region of an niRNA, wherein
the method comprises reverse transcribing the mRNA and performing
an amplification reaction using primers, characterized in that at
least one primer is derived from any one of ACPs described above.
Preferably, the primer according to the structure of ACP is one
having at its 3'-end portion a gene-specific hybridizing nucleotide
sequence substantially complementary to a site in cDNA generated
from reverse transcription.
[0249] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0250] (a) contacting mRNAs with an oligonucleotide dT primer or
random primer as a cDNA synthesis primer under conditions
sufficient for template driven enzymatic deoxyribonucleic acid
synthesis to occur, in which the cDNA synthesis primer comprises a
hybridizing nucleotide sequence substantially complementary to a
region of an mRNA to hybridize therewith;
[0251] (b) reverse transcribing the mRNAs, using a reverse
transcriptase, to which the cDNA synthesis primer hybridizes to
produce a population of first cDNA strands that are complementary
to the mRNAs to which the cDNA synthesis primer hybridizes, whereby
mRNA-cDNA intermediates are generated;
[0252] (c) permitting cytosine residues to be tailed at the 3'-ends
of the first cDNA strands in the form of the mRNA-cDNA
intermediates by the terminal transferase reaction of reverse
transcriptase;
[0253] (d) contacting the cytosine tails at the 3'-ends of the
first cDNA strands generated from step (c) with an oligonucleotide
which comprises a 3'-end portion and a 5'-end portion separated by
a group of universal base or non-discriminatory base analog,
wherein the 3'-end portion comprises at least three guanine
residues at its 3'-end to hybridize with the cytosine tails at the
3'-ends of the first cDNA strands and the 5'-end portion comprises
a pre-selected arbitrary nucleotide sequence, under conditions in
which the 3-end portion of the oligonucleotide is hybridized to the
cytosine tails;
[0254] (e) extending the tailed 3'-ends of the first cDNA strands
to generate an additional 30 sequence complementary to the
oligonucleotide using reverse transcriptase, in which the
oligonucleotide serves as a template in the extension reaction,
whereby full-length first cDNA strands are extended;
[0255] (f) performing a first-stage amplification of the
full-length first cDNA strands obtained from step (e) at a first
annealing temperature comprising (i) and (ii) as follows:
[0256] (i) at least one cycle of primer annealing, primer extending
and denaturing using a first primer comprising a nucleotide
sequence substantially complementary to the 3'-end sequences of the
full-length first cDNA strands under conditions in which the first
primer anneals to the full-length first cDNA strands, under
conditions in which the first primer anneals to the 3'- ends of the
full-length first cDNA strands, whereby full-length second cDNA
strands are generated;
[0257] (ii) at least one cycle of primer annealing, primer
extending and denaturing using a 10 second primer of any one of
claims 1-25 having at its 3'-end portion a gene-specific
hybridizing sequence substantially complementary to a region on one
of the full-length second cDNA strands to hybridize therewith,
under conditions in which the second primer anneals to a
gene-specific site on one of the full-length second cDNA strands,
whereby a gene-specific cDNA strand is generated; and
[0258] (g) performing a second-stage amplification of the
gene-specific cDNA strand at a second annealing temperature, which
is high stringent conditions, comprising at least two cycles of
primer annealing, primer extending and denaturing, using the same
first and second primers as used in steps (f)-(i) and (f)-(ii),
respectively, or a primer pair each comprising a nucleotide
sequence corresponding to each 5'-end portion of the first and
second primers as used in steps (f)-(i) and (i)-(ii), respectively,
under conditions in which each primer anneals to the 3'- and 5'-end
sequences of a gene-specific cDNA strand, respectively, whereby an
amplification product of a gene-specific cDNA strand is
generated.
[0259] The schematic representations for amplifying a target cDNA
fragment comprising 5'-end region corresponding to the 5'-end of
mRNA using novel ACP system, called as ACP-based 5' RACE, is
illustrated in FIGS. 4A (using oligonucleotide dT primer) and 4B
(using random primer).
[0260] The descriptions of the oligonucleotide dT primer used in
step (a) is identical to those used in the present method for
amplification of a target nucleic acid sequence from an mRNA.
[0261] Alternatively, when the size of a target mRNA is so large
that the reverse transcriptase falls off before reaching the 5'
complete sequences, the random primer is used as cDNA synthesis
primer.
[0262] According to a preferred embodiment, the step (c),
permitting cytosine residues to be tailed is performed in the
presence of manganese ion.
[0263] Steps (f) and (g) of the subject application may occur in a
single tube using the same reaction mixture except for primers,
which means that steps (f) and (g) are separated only in time. It
would be understood that the primer(s) used in each step (f) and
(g) can be added to the reaction mixture at the time of or after
each step. In a preferred embodiment, the primer(s) is(are) added
to the reaction mixture right after each step is completed,
followed by subsequent PCR amplification of second cDNA
strands.
[0264] When a gene-specific primer is used as 5' primer, the
amplification of a target cDNA fragment containing a 5'-end
sequence in step (f) is carried out under high stringent conditions
in accordance with conventional PCR methods as known in the
art.
[0265] In a preferred embodiment, a target cDNA fragment containing
a 5'-end sequence in step (f) is amplified using a second ACP
comprising a gene-specific sequence at the 3'-end portion, by two
stage PCR amplifications which are used in the application of the
present invention for amplifying a target nucleic acid sequence
above. Since the ACP described in this invention can generate
stable T.sub.m in a primer and also tolerate "primer search
parameters" such as primer design, comprising primer length,
annealing temperature, GC content, and PCR product length, it is
particularly useful when the gene-specific primer sequences have
low T.sub.m or are too sensitive to such parameters to generate
specific products. The formula of the second ACP is identical to
the formula (1) in which the 3'-end portion contains a
gene-specific sequence.
[0266] The oligonucleotide for the step (d) is similar to CapFinder
primer (Chenchik et al., 1998; Chenchik et al. U.S. Pat. Nos.
5,962,271 and 5,962,272) in the senses both of them comprise at
least three guanine residues at its 3'-end and use them as a
template switching primer for the 3'-end extension of the first
cDNA strand by reverse transcriptase, whereas they are clearly
different from each other in terms of the function of a switch in
controlling primer annealing to a template nucleic acid in
associated with annealing temperature during PCR. CapFinder primer
does not comprise univeasl base residue group which is responsible
for regulating primer annealing in ACP, so that the CapFinder PCR
method for 5'-RACE (Chenchik et al., 1998) can not be free from a
high background such as DNA spear arising from contamination of the
primers such as the CapFinder and Oligo-dT primers used in cDNA
synthesis during PCR. On the other hand, the universal base resiude
group of the first ACP plays a key role in regulating primer
annealing, so that the subject method does not provide any cause
for the background problems during subsequent PCR amplification;
this is a key feature of the ACP application to 5'-RACE.
[0267] Furthermore, when the ACP of the present invention is used
in 5'-RACE technology, it is unnecessary to conduct the process of
physical separation such as a solid-phase cDNA synthesis and
procedures which has been introduced as an alternative method to
remove all contaminants used in cDNA synthesis (Schramm et al.,
2000).
[0268] In a preferred embodiment, the oligonucleotide to form a
base-pair(s) with the cytosine tail for 5'-RACE which has a similar
structure to ACP, wherein the oligonucleotide is represented by the
following general formula (3):
5'-dX.sub.15-30dY.sub.2-10-dZ.sub.1-10-G.s- ub.3-5-3', in which dX
represents a deoxyribonucleotide and comprises a pre-selected
arbitrary sequence; dY represents a regulatory portion comprising
2-10 universal bases or non-discriminatory base analogs; dZ
represents a deoxyribonucleotide and comprises a pre-selected
arbitrary sequence; and G.sub.3-5 represents three to five
guanines.
[0269] Most preferably, the 3'-end portion sequence dZ is about 2-3
nucleotides in length. Further, in one embodiment, the 5'-end
portion dX can include a sequence that is recognized by a
restriction endonuclease.
[0270] The G.sub.3-5 may be three to five riboguanines or
deoxyguanines, or a combination of riboguanine and
deoxyriboguanine. In more preferred embodiment, the G.sub.3-5
comprises two riboguanines and one deoxyriboguanine
(r(G).sub.2-d(G)-3'), most preferably, three riboguanines.
[0271] When the gene-specific primer in step (f) is used as 3'
primer for 5'-RACE, a target cDNA fragment containing a 5'-end
sequence is amplified under high stringency conditions by
conventional PCR methods as known in the art.
[0272] In a preferred embodiment, a target cDNA fragment containing
a 5'-end sequence is amplified using a second ACP which comprises a
gene-specific sequence at the 3'-end portion, by two stage PCR
amplifications which is conducted in the application for amplifying
a target nucleic acid sequence in the present invention. Since the
ACP described in this invention can provide stable T.sub.m in a
primer and also tolerate "primer search parameters" for primer
design such as primer length, annealing temperature, GC content,
and PCR product length, it is useful when the gene-specific primer
sequences have low T.sub.m or are too sensitive to such parameters
to generate specific products. The formula of the second ACP is
identical to the formula (1) in which the 3'-end portion contains a
gene-specific sequence. p The use of ACP in RACE technology
significantly simplifies and improves the conventional RACE
technologies with regard to the amplification of cDNA ends as
described above. The vital feature of the subject method is to be
free from the background problems arising from the primers used in
conventional RACE methods. Consequently this method described
herein can be more effective, easier, less labor-intensive, and
more reproducible than conventional RACE methods.
[0273] In still another aspect of this invention, there is provided
a kit for rapidly amplifying a target cDNA fragment comprising
3'-end region of mRNA, which comprises the annealing control primer
or annealing control primer set described previously (including the
first and second primer). According to one embodiment of this
invention, these kits further comprises a primer or a primer pair
having a nucleotide sequence corresponding to the 5'-end portion of
the ACPs; in case that the 5'-end portion comprises universal
primer sequence, it is more preferred that the kit comprises the
universal primers. The present kits may optionally include the
reagents required for performing PCR reactions such as buffers, DNA
polymerase, DNA polymerase cofactors, and
deoxyribonucleotide-5'-triphosphates. Optionally, the kits may also
include various polynucleotide molecules, reverse transcriptase,
various buffers and reagents, and antibodies that inhibit DNA
polymerase activity. The kits may also include reagents necessary
for performing positive and negative control reactions. Optimal
amounts of reagents to be used in a given reaction can be readily
determined by the skilled artisan having the benefit of the current
disclosure. The kits, typically, are adapted to contain in separate
packaging or compartments the constituents afore-described.
[0274] In further aspect of this invention, there is provided a kit
for rapidly amplifying a target cDNA fragment comprising 5'-end
region of mRNA, which comprises the annealing control primer or
annealing control primer set described above (including the
oligonucleotide dT primer and random primer for cDNA synthesis, the
oligonucleotide to form a base-pair(s) with the cytosine tail, the
first primer and the second primer). According to one embodiment of
this invention, these kits further comprises a primer pair each
comprising a nucleotide sequence corresponding to each 5'-end
portion of the first and second primers as used in steps (f)-(i)
and (f)-(ii); in case that the 5'-end portion comprises universal
primer sequence, it is more preferred that the kit comprises the
universal primers.
[0275] V. Application to Amplifying Full-length cDNA
[0276] In further aspect of this invention, there is provided a
method for amplifying a population of full-length double-stranded
cDNAs complementary to mRNAs, wherein the method comprises reverse
transcribing the mRNA and performing an amplification reaction
using primers, characterized in that at least one primer is derived
from any one of ACP described above. Preferably, the primer having
the structure of ACP is one having a hybridizing nucleotide
sequence substantially complementary to poly A tails of mRNAs.
[0277] In a specific embodiment of this invention, there is
provided the method comprises:
[0278] (a) contacting the mRNAs with a first primer of any one of
ACP described above, in which the 3'-end portion of the first
primer has a hybridizing nucleotide sequence substantially
complementary to poly A tails of the mRNAs to hybridize therewith,
under conditions sufficient for template driven enzymatic
deoxyribonucleic acid synthesis to occur;
[0279] (b) reverse transcribing the mRNAs, using a reverse
transcriptase, to which the first primer hybridizes to produce the
population of first cDNA strands that are complementary to the
mRNAs to which the primer hybridizes, whereby mRNA-cDNA
intermediates are generated;
[0280] (c) permitting cytosine residues to be tailed at the 3'-ends
of the first cDNA strands in the form of the mRNA-cDNA
intermediates by the terminal transferase reaction of reverse
transcriptase;
[0281] (d) contacting the cytosine tails at the 3'-ends of the
first cDNA strands generated from step (c) with an oligonucleotide
which comprises a 3'-end portion and a 5'-end portion separated by
a group of universal base or non-discriminatory base analog,
wherein the 3'-end portion comprises at least three guanine
residues at its 3'-end to hybridize with the cytosine tails at the
3'-ends of the first cDNA strands and the 5'-end portion comprises
a pre-selected arbitrary nucleotide sequence, under conditions in
which the 3-end portion of the oligonucleotide is hybridized to the
cytosine tails;
[0282] (e) extending the tailed 3'-ends of the first cDNA strands
to generate an additional sequence complementary to the
oligonucleotide using reverse transcriptase, in which the
oligonucleotide serves as a template in the extension reaction,
whereby full-length first cDNA strands are extended; and
[0283] (f) performing an amplification of the full-length first
cDNA strands generated from step (e) comprising at least two cycles
of primer annealing, primer extending and denaturing, using a
primer pair each comprising a nucleotide sequence corresponding to
the same first primer and oligonucleotide as used in steps (a) and
(d), respectively, or a primer pair each comprising a nucleotide
sequence corresponding to each 5'-end portion of the first primer
and oligonucleotide used in steps (a) and (d), respectively, under
conditions in which each primer anneals to the 3'- and 5'-end
sequences of the full-length first cDNA strands, respectively,
whereby amplification products of full-length cDNA strands
complementary to the mRNAs are generated.
[0284] Since this application using the ACP of this invention
employs in principle the present methods for amplification of
nucleic acid sequence previously discussed, the common descriptions
between them are omitted in order to avoid the complexity of this
specification leading to undue multiplicity. In addition, the ACP
described above in which the 3'-end portion has a hybridizing
nucleotide sequence substantially complementary to poly A tails is
in principle identical to the first primer for the present method
for 3'-RACE. Furthermore, the oligonucleotide to form a
base-pair(s) with the cytosine tail and the primer pair used in the
step (f) are in principle identical to those for 5'-RACE of this
invention discussed above.
[0285] A schematic representation for amplifying full-length cDNA
molecules of the present invention is illustrated in FIG. 5.
[0286] The use of ACP significantly simplifies and improves the
conventional technologies with regard to the amplification of
full-length cDNAs as described above. The vital feature of the
subject method is to be free from the background problems arising
from the primers used in conventional methods. Consequently this
method described herein can be more effective, easier, less
labor-intensive, and more reproducible than conventional
methods.
[0287] In still further aspect of this invention, there is provided
a kit for amplifying a full-length double stranded cDNA
complementary to mRNA, which comprises the annealing control primer
or the annealing control primer set described above (including the
oligonucleotide dT primer, the oligonucleotide to form a
base-pair(s) with the cytosine tail, the primer(s) used in the step
(f)). According to one embodiment of this invention, these kits
further comprises a primer pair each comprising a nucleotide
sequence corresponding to each 5'-end portion of the primer and
oligonucleotide used in steps (a) and (d), respectively; in case
that the 5'-end portion comprises universal primer sequence, it is
more preferred that the kit comprises the universal primers. The
present kits may optionally include the reagents required for
performing PCR reactions such as buffers, DNA polymerase, DNA
polymerase cofactors, and deoxyribonucleotide-5'-triphosphates.
Optionally, the kits may also include various polynucleotide
molecules, reverse transcriptase, various buffers and reagents, and
antibodies that inhibit DNA polymerase activity. The kits may also
include reagents necessary for performing positive and negative
control reactions. Optimal amounts of reagents to be used in a
given reaction can be readily determined by the skilled artisan
having the benefit of the current disclosure. The kits, typically,
are adapted to contain in separate packaging or compartments the
constituents afore-described.
[0288] VI. Application to Amplifying 5'-Enriched cDNA
[0289] In another aspect of this invention, there is provided a
method for amplifying a population of 5' -enriched double-stranded
cDNAs comprising cDNA regions corresponding to the 5'-end regions
of mRNAs, wherein the method comprises reverse transcribing the
mRNA and performing an amplification reaction using primers,
characterized in that at least one primer is derived from any one
of ACP described above. Preferably, the primer having the structure
of ACP used for cDNA synthesis is one having at its 3'-end portion
at least six random nucleotide sequences.
[0290] In a specific embodiment of this invention, there is
provided the method comprises:
[0291] (a) contacting the mRNAs with a first primer of any one of
ACP described above under conditions sufficient for template driven
enzymatic deoxyribonucleic acid synthesis to occur, wherein the
3'-end portion of the first primer has at least six random
nucleotide sequences;
[0292] (b) performing the steps (b)-(e) of the method for
amplifying a population of full-length double-stranded cDNAs,
whereby 5'-enriched first cDNA strands are extended;
[0293] (c) performing an amplification of the 5'-enriched first
cDNA strands generated from step (b) comprising at least two cycles
of primer annealing, primer extending and denaturing, using a
primer pair each comprising a nucleotide sequence corresponding to
each 5'-end portion of the primer and oligonucleotide used in steps
(a) and (b), respectively, under conditions in which each primer
anneals to the 3'- and 5'-end sequences of the 5'-enriched first
cDNA strands, respectively, whereby amplification products of
5'-enriched cDNA strands are generated.
[0294] Since this application using the ACP of this invention
employs in principle the present methods for amplification of
nucleic acid sequence previously discussed, the common descriptions
between them are omitted in order to avoid the complexity of this
specification leading to undue multiplicity. In addition, the
oligonucleotide to form a base-pair(s) with the cytosine tail and
the primer pair used in the step (c) are in principle identical to
those for 5'-RACE of this invention discussed above. A schematic
representation for the method for amplifying 5'-enriched
double-stranded cDNAs complementary to mRNAs is illustrated in FIG.
6.
[0295] "5' enriched cDNAs" refers to a significant portion of the
cDNA constituents which contain the nucleotide sequence information
of the 5'-end of the mRNAs from which the cDNAs are derived.
[0296] The formula of the first primer is identical to the formula
(1) in which the 3'-end portion comprises a random nucleotide
sequence. In a preferred embodiment, the 3'-end portion of the
first primer used in step (a) contains at least six random
deoxyribonucleotides. In a preferred embodiment, the 5'-end portion
of the first primer used in step (a) can includes a sequence that
is recognized by a restriction endonuclease. The conventional
methods require more steps to amplify 5' enriched cDNA molecules
complementary to the mRNA molecules than the subject method because
the conventional methods use the conventional primers which do not
have the function of controlling primer annealing. In contrast,
this subject method is considerably a simple and effective approach
due to the function of regulating primer annealing generated by the
effect of a universal base residue group in ACP.
[0297] In still another aspect of this invention, there is provided
a kit for amplifying 5'-enriched double-stranded cDNAs
complementary to mRNAs, which comprises the annealing control
primer or the annealing control primer set described above (the
first primer, the oligonucleotide to form a base-pair(s) with the
cytosine tail). According to one embodiment of this invention,
these kits further comprises a primer pair each comprising a
nucleotide sequence corresponding to each 5'-end portion of the
primer and oligonucleotide used in steps (a) and (b),
respectively;
[0298] in case that the 5'-end portion comprises universal primer
sequence, it is more preferred that the kit comprises the universal
primers. The present kits may optionally include the reagents
required for performing PCR reactions such as buffers, DNA
polymerase, DNA polymerase cofactors, and
deoxyribonucleotide-5'-triphosphates. Optionally, the kits may also
include various polynucleotide molecules, reverse transcriptase,
various buffers and reagents, and antibodies that inhibit DNA
polymerase activity. The kits may also include reagents necessary
for performing positive and negative control reactions. Optimal
amounts of reagents to be used in a given reaction can be readily
determined by the skilled artisan having the benefit of the current
disclosure. The kits, typically, are adapted to contain in separate
packaging or compartments the constituents afore-described.
[0299] VII. Application to DNA or RNA Fingerprinting
[0300] This application using ACP of the subject invention can
provide an improved method for detecting polymorphisms in genomic
DNA (DNA fingerprinting) or for detecting differential gene
expression in mRNA (RNA fingerprinting).
[0301] In further aspect of this invention, there is provided a
method for producing a DNA fingerprint of gDNA, wherein the method
comprises performing an amplification reaction using primers,
characterized in that at least one primer is derived from any one
of ACPs described above. Preferably, the primer having the
structure of ACP is one having at its 3'-end portion an arbitrary
nucleotide sequence substantially complementary to sites on the
gDNA.
[0302] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0303] (a) performing a first-stage amplification of the DNA
fingerprint, which is a set of discrete DNA segments characteristic
of genome, from the gDNA at a first annealing temperature
comprising at least two cycles of primer annealing, primer
extending and denaturing, using the primer or the primer pair of
any one of ACPs described above, wherein each primer has at its
3'-end portion an arbitrary nucleotide sequence substantially
complementary to sites on the gDNA to hybridize therewith, under
conditions in which the primer or the primer pair anneals to the
gDNA, whereby the set of discrete DNA segments characterized as a
DNA fingerprint is produced; and
[0304] (b) performing a second-stage amplification of the set of
discrete DNA segments generated from step (a) at a second annealing
temperature, which is high stringent conditions, comprising at
least one cycle of primer annealing, primer extending and
denaturing, using the same primer or primer pair as used in step
(a) or a primer or a primer pair each comprising a nucleotide
sequence corresponding to each 5'-end portion of the primer or
primer pair used in step (a), under conditions in which the primer
or each of the primer pair anneals to the 3'- and 5'-end sequences
of the set of discrete DNA segments generated from step (a),
respectively, whereby the set of discrete DNA segments is
re-amplified.
[0305] In still further aspect of this invention, there is provided
a method for producing a RNA fingerprint of an mRNA sample, wherein
the method comprises reverse transcribing and performing an
amplification reaction using primers, characterized in that at
least one primer is derived from any one of ACPs. Preferably, the
primer according to the structure of ACP is one having at its
3'-end portion an arbitrary nucleotide sequence substantially
complementary to sites on cDNA strands generated from reverse
transcription and/or one having at its 3'-end portion a hybridizing
nucleotide sequence substantially complementary to poly A tails of
the mRNAs.
[0306] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0307] (a) contacting the mRNA sample with a first primer of any
one of ACPs described above, in which the first primer has a
hybridizing nucleotide sequence substantially complementary to poly
A tails of the mRNA sample to hybridize therewith, under conditions
sufficient for template driven enzymatic deoxyribonucleic acid
synthesis to occur;
[0308] (b) reverse transcribing the mRNA sample to which the first
primer hybridizes to produce a population of first cDNA strands
that are complementary to the mRNA sample to which the first primer
hybridizes;
[0309] (c) performing a first-stage amplification of the population
of first cDNA strands generated from step (b) at a first annealing
temperature comprising at least one cycle of primer annealing,
primer extending and denaturing, using a second primer or primer
pair of any one of ACPs described above, wherein each primer has at
its 3'-end portion an arbitrary nucleotide sequence substantially
complementary to sites on the first cDNA strands to hybridize
therewith, under conditions in which the primer or primer pair
anneals to the mRNA sample, whereby a set of discrete cDNA segments
characterized as a RNA fingerprint is produced; and
[0310] (d) performing a second stage amplification of the set of
discrete cDNA segments generated from step (c) at a second
annealing temperature which is high stringent conditions,
comprising at least one cycle of primer annealing, primer extending
and denaturing, using the same primer or primer pair as used in
step (c) or a primer or primer pair each comprising a nucleotide
sequence corresponding to each 5'-end portion of the primer or
primer pair used in step (c), under conditions in which the primer
or each of the primer pair anneals to the 3'- and 5' -end sequences
of the set of discrete cDNA segments generated from step (c),
respectively, whereby the set of discrete cDNA segments is
re-amplified.
[0311] Since this application using the ACP of this invention
employs in principle the present methods for amplification of
nucleic acid sequence previously discussed, the common descriptions
between them are omitted in order to avoid the complexity of this
specification leading to undue multiplicity. In addition, the RNA
fingerprinting in principle follows the present method for
detecting DNA complementary to differentially expressed mRNA.
[0312] The term "genomic DNA" as used herein refers to a population
of DNA that comprises the complete genetic component of a species.
Thus genomic DNA comprises the complete set of genes present in a
pre-selected species. The complete set of genes in a species is
also referred to as genome. The term DNA or RNA "fingerprinting" as
used herein refers to a set of discrete DNA amplification products
characteristic of a genome or a set of discrete cDNA segments
characteristic of a sample of mRNA, respectively.
[0313] In the previous arbitrarily primed PCR fingerprints, called
AP-PCR, short or long arbitrary primers have been used under
non-stringent conditions for early 2-5 cycles of PCR amplification
because a low annealing temperature is required to achieve
arbitrary priming, such that a significant portion of isolated
fragments is not still reproducible although effective
amplification proceeds in the following cycles under high stringent
condition.
[0314] In contrast to AP-PCR, the ACP-based PCR for fingerprinting
increases the specificity of primer annealing during PCR due to the
function of a universal base residue group positioned between the
3'- and 5'-end portions of ACP, wherein the universal base residue
group restricts the annealing site to the 3'-end portion of the ACP
and also allows this 3'-end portion to anneal at a relatively high
annealing temperature. Thus, the ACP-based PCR for fingerprinting
completely eliminates false positive products and significantly
increases reproducibility.
[0315] In a preferred embodiment, the ACP contains an arbitrary
sequence at the 3'-end portion with at least 6 nucleotides in
length. More preferably, the 3'-end portion contains 8-15
nucleotides in length, most preferably, about 10 nucleotides in
length.
[0316] A single ACP or a pair of ACPs can be used for detecting
polymorphisms in DNA fingerprinting. Preferably, a pair of ACPs is
used for DNA fingerprinting because a pair of ACPs produces more
products than a single arbitrary ACP does.
[0317] An example of the DNA fingerprinting using ACP is conducted
by two stages of PCR amplifications under the following conditions:
amplification reactions are performed under low stringent
conditions by two cycles of the first-stage PCR comprising
annealing, extending and denaturing reaction; the reaction mixture
containing genomic DNA, PCR reaction buffer, MgCl.sub.2, dNTPs
(dATP, dCTP, dGTP and dTTP), a pair of ACPs is pre-heated, Taq
polymerase is added into the reaction mixture; the PCR reactions
are performed, followed by denaturing the amplification product;
after the complete reaction of the first-stage PCR, the
pre-selected arbitrary primer JYC4 corresponding to the 5'-end
portion of the ACPs are added to the reaction mixture and then the
second stage PCR amplification is conducted.
[0318] It should be noted that a proper concentration of ACP is
used to produce DNA fingerprinting. If the amount of the ACP is too
low, the resultant amplified PCR products are not reproducible. In
contrast, the excess amount of the ACP generates backgrounds such
as DNA smear during PCR. In a preferred embodiment, the
concentration of the ACP is about between 0.1 .mu.M and 2 .mu.M.
Most preferably, the concentration of the ACP is about 1.4
.mu.M.
[0319] In a preferred embodiment, the concentration of the primer
corresponding to the 5'-end portion of the ACPs is about between
0.1 .mu.M and 2 .mu.M, most preferably, about 0.8 .mu.M.
[0320] The genomic DNA and mRNA samples may be obtained from a wide
variety of biomaterials and conditions. For example, they may be
obtained from plants, animal (human) and microbes and from
different individual organisms.
[0321] The amplified products can be analyzed by gel
electrophoresis. In one embodiment, the resulting PCR products can
be also detected on a denaturing polyacrylamide gel by
autoradiography or non-radioactive detection methods such as silver
staining (Gottschlich et al., 1997; Kociok et al., 1998), the use
of fluoresenscent-labelled oligonucleotides (Bauer et al. 1993; Ito
et al. 1994; Luehrsen et al., 1997; Smith et al., 1997), and the
use of biotinylated primers (Korn et al., 1992; Tagle et al., 1993;
Rosok et al., 1996).
[0322] In still further aspect of this invention, there is provided
a kit for producing a DNA fingerprint by use of gDNA or mRNA, which
comprises the annealing control primer or annealing control primer
set described above. The descriptions of the kits for the
amplification of nucleic acid sequence and for detecting DNA
complementary to differentially expressed mRNA of this invention
can be applied to the present kit.
[0323] VIII. Application to Identification of Conserved Homology
Segments in Multigene Families
[0324] This application using ACP of the subject invention can also
provide an improved method for the identification of conserved
homology segments in multigene families.
[0325] In another aspect of this invention, there is provided a
method for identifying conserved homology segments in a multigene
family from an mRNA sample, wherein the method comprises reverse
transcribing and performing an amplification reaction using
primers, characterized in that at least one primer is derived from
any one of ACPs described above. Preferably, the primer having the
structure of ACP is one having at its 3'-end portion a hybridizing
sequence substantially complementary to a consensus sequence or a
degenerate sequence encoding amino acid sequence of a conserved
homology segment on cDNA strands generated from reverse
transcription and/or one having at its 3'-end portion a hybridizing
nucleotide sequence substantially complementary to poly A tails of
the mRNAs.
[0326] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0327] (a) contacting the mRNA sample with a first primer of any
one of claims 1-29, in which the first primer has a hybridizing
nucleotide sequence substantially complementary to poly A tails of
the mRNA sample to hybridize therewith, under conditions sufficient
for template driven enzymatic deoxyribonucleic acid synthesis to
occur;
[0328] (b) reverse transcribing the mRNA sample to which the first
primer hybridizes to produce a population of first cDNA strands
that are complementary to the mRNA sample to which the first primer
hybridizes;
[0329] (c) performing a first-stage amplification of the population
of first cDNA strands generated from step (b) at a first annealing
temperature comprising at least one cycle of primer annealing,
primer extending and denaturing, using a second primer of any one
of claims 1-25 having at its 3' end portion a hybridizing sequence
substantially complementary to a consensus sequence or a degenerate
sequence encoding amino acid sequence of a conserved homology
segment on the first cDNA strands to hybridize therewith, under
conditions in which the second primer anneals to the consensus
sequence or degenerate sequence of first cDNA strands, whereby
3'-end cDNA segments having the consensus sequence or degenerate
sequence are generated; and
[0330] (d) performing a second stage amplification of the 3'-end
cDNA segments generated from step (c) at a second annealing
temperature which is high stringent conditions, comprising at least
two cycles of primer annealing, primer extending and denaturing,
using the same first and second primers as used in steps (a) and
(c) or a primer pair each comprising a nucleotide sequence
corresponding to each 5'-end portion of the first and second
primers used in steps (a) and (c), respectively, under conditions
in which each primer anneals to the 3'- and 5'-end sequences of the
3'-end cDNA segments, respectively, whereby the 3'-end conserved
homology cDNA segments are amplified.
[0331] This specific embodiment follows in principle, the present
method for 3' RACE as discussed previously except for the second
primer used.
[0332] In another specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0333] (a) performing steps of (a)-(e) of the method for amplifying
a population of full-length double-stranded cDNA, whereby
full-length cDNA strands are generated;
[0334] (b) performing a first-stage amplification of the
full-length first cDNA strands obtained from step (a) at a first
annealing temperature, which comprises the steps of:
[0335] (i) at least one cycle of primer annealing, primer extending
and denaturing using a first primer comprising a nucleotide
sequence substantially complementary to the 3'-end sequences of the
full-length first cDNA strands under conditions in which the first
primer anneals to the full-length first cDNA strands, under
conditions in which the first primer anneals to the 3'- ends of the
full-length first cDNA strands, whereby full-length second cDNA
strands are generated; and
[0336] (ii) at least one cycle of primer annealing, primer
extending and denaturing using a second primer of any one of claims
1-25 having at its 3' end portion a hybridizing sequence
substantially complementary to a consensus sequence or a degenerate
sequence encoding amino acid sequence of a conserved homology
segment on the full-length second cDNA strands to hybridize
therewith, under conditions in which the second primer anneals to
the consensus sequence or degenerate sequence of full-length second
cDNA strands, whereby 5'-end cDNA segments having the consensus
sequence or degenerate sequence are generated; and
[0337] (c) performing a second stage amplification of the 5'-end
cDNA segments generated from step (b) at a second annealing
temperature which is high stringent conditions, comprising at least
two cycles of primer annealing, primer extending and denaturing,
using the same first and second primers as used in steps (b)-(i)
and (b)-(ii), respectively, or a primer pair each comprising a
nucleotide sequence corresponding to each 5'-end portion of the
first and second primers used in steps (b)-(i) and (b)-(ii),
respectively, under conditions in which each primer anneals to the
3'- and 5'-end sequences of the 5'-end cDNA segments, respectively,
whereby the 5'-end conserved homology cDNA segments are
amplified.
[0338] This specific embodiment follows in principle, the present
method for 5' RACE as discussed previously except for the second
primer used.
[0339] In further aspect of this invention, there is provided a
method for identifying conserved homology segments in a multigene
family from gDNA, wherein the method comprises performing an
amplification reaction using primers, characterized in that at
least one primer is derived from any one of ACPs described above.
Preferably, the primer having the structure of ACP is one having at
its 3 '-end portion a hybridizing sequence substantially
complementary to a consensus sequence or a degenerate sequence
encoding amino acid sequence of a conserved homology segment on the
gDNA.
[0340] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0341] (a) performing a first-stage amplification of the conserved
homology segments from the gDNA at a first annealing temperature
comprising at least two cycles of primer annealing, primer
extending and denaturing, using the primer or the primer pair of
any one of ACPs described above, wherein each primer has at its 3'
end portion a hybridizing sequence substantially complementary to a
consensus sequence or a degenerate sequence encoding amino acid
sequence of a conserved homology segment on the gDNA to hybridize
therewith, under conditions in which the primer or the primer pair
anneals to the consensus sequence or degenerate sequence of gDNA,
whereby genomic DNA segments having the consensus sequence or
degenerate sequence are generated; and
[0342] (b) performing a second-stage amplification of the genomic
DNA segments generated from step (a) at a second annealing
temperature, which is high stringent conditions, comprising at
least one cycle of primer annealing, primer extending and
denaturing, using the same primer or primer pair as used in step
(a) or a primer or a primer pair each comprising a nucleotide
sequence corresponding to each 5 -end portion of the primer or
primer pair used in step (a), under conditions in which the primer
or each of the primer pair anneals to the 3'- and 5'-end sequences
of the genomic DNA segments generated from step (a), respectively,
whereby the conserved homology genomic segments are amplified.
[0343] The present method follows in principle, the present method
for amplifying a target nucleic acid sequence from a DNA as
discussed previously except for the primer used.
[0344] Since this application using the ACP of this invention
employs in principle the present methods for amplification of
nucleic acid sequence previously discussed, the common descriptions
between them are omitted in order to avoid the complexity of this
specification leading to undue multiplicity. In addition, where an
mRNA is used as starting material, the present methods for 3' or 5'
RACE are in principle applied to the present methods for the
identification of conserved homology segments in multigene
families.
[0345] The formula of ACP for the identification of conserved
homology segments in multigene families is identical to the formula
(1) in which the 3'-end portion of ACP has a hybridizing sequence
substantially complementary to a consensus sequence in a gene
family or a degenerate sequence encoding amino acid sequence of a
conserved homology.
[0346] There are two principle approaches to the design of
degenerate primer: (a) using peptide sequence data obtained from a
purified protein; and (b) using consensus protein sequence data
from alignments of gene families. If orthologs of the gene of
interest have been cloned from other organisms, or if the gene is a
member of a gene family, it will be possible to generate protein
sequence alignments.
[0347] These may reveal appropriate regions for the design of
degenerate primers, for example, from consensus sequence of highly
conserved regions. Amplifications using degenerate primers can
sometimes be problematic and may require optimization. The first
parameter is annealing temperature. It is important to keep the
annealing temperature as high as possible to avoid extensive
nonspecific amplification and a good rule of thumb is to use
55.degree. C. as a starting temperature. In general, it is
difficult to keep this rule because degenerate primers should be
designed based on amino acid sequences as a precondition. However,
the ACP of the present invention does not have to satisfy this
requirement because it allows a high annealing temperature such as
65.degree. C. at the second stage of PCR amplification regardless
of primer design.
[0348] According to a preferred embodiment, the second primer is a
pool of primers each comprising a degenerate sequence selected from
a plurality of the nucleotides coding for amino acid sequence of
the consensus sequence.
[0349] The term "conserved region" and more specifically "conserved
region of a gene in a multigene family" as used herein refers to a
segment of nucleotide sequence of a gene or amino acid sequence of
a protein that is significantly similar between members of gene
families. The degree of similarity can vary. In some cases the
conserved regions will be identical between family members. In some
cases the nucleotide sequence may vary significantly but still
encode for amino acid segments that are conserved between family
members. The term "consensus sequence" as used herein refers to the
bases most often found at any given position when comparing a large
number of similar nucleotide sequences.
[0350] Alternatively, the present methods for the identification of
conserved homology segments can be also combined with that for
detecting differentially expressed mRNAs.
[0351] In still further aspect of this invention, there is provided
a kit for identifying a conserved homology segment in a multigene
family by use of mRNA or gDNA, which comprises the annealing
control primer or annealing control primer set described above. The
descriptions of the kits for the amplification of nucleic acid
sequence, 3' RACE and 5' RACE of this invention can be applied to
the present kit.
[0352] IX. Application to Identification of a Nucleotide
Variation
[0353] This application using ACP system of the subject invention
can also provide an improved method for identifying a nucleotide
variation in a target nucleic acid.
[0354] In another aspect of this invention, there is provided a
method for identifying a nucleotide variation in a target nucleic
acid, wherein the method comprises performing an amplification
reaction using primers, characterized in that at least one primer
is derived from any one of ACPs described above. Preferably, the
primer having the structure of ACP is (a) a first primer one having
at its 3'-end portion a hybridizing sequence substantially
complementary to a pre-selected sequence at a first site of target
nucleic acid, wherein each of the first primer and the first site
comprises an interrogation position corresponding to the nucleotide
variation, and/or (b) a second primer having a hybridizing sequence
substantially complementary to a pre-selected sequence at a second
site of target nucleic acid.
[0355] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0356] (a) performing a first-stage amplification to produce a
first DNA strand complementary to the target nucleic acid including
the nucleotide variation at a first annealing temperature
comprising at least one cycle of primer annealing, primer extending
and denaturing, using a first primer of any one of ACPs described
above having at its 3'-end portion a hybridizing sequence
substantially complementary to a pre-selected sequence at a first
site of the target nucleic acid to hybridize therewith, wherein
each of the first primer and the first site comprises an
interrogation position corresponding to the nucleotide variation,
whereby the first DNA strand complementary to the target nucleic
acid including the nucleotide variation is generated when the
interrogation position is occupied by the complementary nucleotide
of the first primer to its corresponding nucleotide of the first
site; and
[0357] (b) performing a second-stage amplification of the first DNA
strand generated from step (a) at a second annealing temperature,
which is high stringent conditions, comprising the steps:
[0358] (i) at least one cycle of primer annealing, primer extending
and denaturing using a second primer of any one of ACPs decribed
above having at its 3'-end portion a hybridizing sequence
substantially complementary to a pre-selected sequence at a second
site of the target nucleic acid to hybridize therewith under
conditions in which the second primer anneals to the second site of
the target nucleic acid, whereby a second DNA strand complementary
to the first DNA strand including the nucleotide variation is
generated; and
[0359] (ii) at least one cycle of primer annealing, primer
extending and denaturing using the same first and second primers as
used in steps (a) and (b)-(i) or a primer pair each having a
hybridizing sequence complementary or corresponding to the 3'- and
5'-ends of the second DNA strand generated from step (b)-(i) to
hybridize therewith, under conditions in which each primer anneals
to the 3'- and 5'-end sequences of the second DNA strand,
respectively, whereby the second DNA strand which comprises the
first and second sites of the target nucleic acid at its 3'-and
5'-ends is amplified so that a short target nucleotide segment
corresponding to the second DNA strand containing the nucleotide
variation is generated.
[0360] Since this application using the ACP of this invention
employs in principle the present methods for amplification of
nucleic acid sequence previously discussed, the common descriptions
between them are omitted in order to avoid the complexity of this
specification leading to undue multiplicity.
[0361] A schematic representation of this specific embodiment for
single nucleotide polymorphism (SNP) genotyping using novel ACP is
illustrated in FIG. 7A.
[0362] The formula of ACP for the detection of a nucleotide
variation, is identical to the formula (1) in which its 3'-end
portion comprises a hybridizing sequence substantially
complementary to a pre-selected sequence at a site of the target
nucleic acid to hybridize therewith which contains the nucleotide
variation, wherein the nucleotide corresponding to the nucleotide
variation and its complementary nucleotide of the ACP occupy an
interrogation position. The process for this application is carried
out by two stage PCR amplifications using the genomic DNA obtained
from samples such as patient blood or a short segment of the sample
DNA, which includes a target nucleotide variation. The interesting
nucleotide sample may be obtained from human nucleic acid and an
organism that can cause an infectious disease.
[0363] The method using two-stage PCR amplifications for detecting
single nucleotide polymorphism (SNP) genotyping basically follows
the process used for amplifying a target nucleic acid sequence
using genomic DNA as a starting material. In addition, the process
for multiplex DNA amplification can be adapted to this application.
To use a short segment of the sample DNA including a target
nucleotide variation as a starting material for the above process,
it is preferable that the target short segment is pre-amplified
prior to step (a) using a primer pair in which each has a
hybridizing sequence substantially complementary to the sample DNA
to hybridize therewith. Furthermore, more than one target
nucleotide segment each including a SNP can be prepared by the
multiplex DNA amplification as described in Application II to be
used as a starting material in the subject invention for multiple
SNP screening.
[0364] The first ACP used in step (a) for the detection of a
polymorphic base is an allele-specific ACP which contains an
interrogation position within its 3'-end portion occupied by a
complementary nucleotide to the corresponding nucleotide of the
nucleotide variation in a target nucleic acid. Preferably, the
interrogation position of the first primer is in the middle of its
3'-end portion. In a more preferred embodiment, the interrogation
position of the allele-specific ACP is within about 10 bases of the
3'-end nucleotide. More advantageously, the interrogation position
of the allele-specific ACP is within about 6 bases of the 3'-end
nucleotide of the allele-specific ACP. In another preferred
embodiment, the interrogation position of the allele-specific ACP
is located within positions 4 and 6 from the 3'-end nucleotide.
Most preferably, the interrogation position of the allele-specific
ACP is located in position 5 from the 3'-end nucleotide. The term
"3 -end nucleotide" used herein refers to a nucleotide which is
positioned at the 3'-end of ACP.
[0365] In another embodiment, the 3'-end portion of the
allele-specific ACP used in step (a) contains at least 6
nucleotides in length, which is a minimal requirement of length for
primer annealing. Preferably, the 3 -end portion sequence is about
8 to 20 nucleotides in length. Most preferably, the 3'-end portion
sequence is about 10 nucleotides in length including an
interrogation position.
[0366] In one embodiment, at least one artificial mismatch can be
also placed within the 3'-end portion of ACP using universal base
or non-discriminatory analog that hydrogen-bonds minimally with all
four bases without steric disruption of the DNA duplex. Although
the position of the artificial mismatch can vary depending on
experimental designs, it is preferred that the mismatch nucleotide
is substantially adjacent the interrogation position of the first
primer.
[0367] In a preferred embodiment, the first or second primers
comprise at least one nucleotide with a label for detection or
isolation.
[0368] According to a preferred embodiment, the first DNA strand
including nucleotide variation in step (a) is generated by one
cycle of primer annealing, primer extending, and denaturing. It is
preferred that the second DNA strand including nucleotide variation
in step (b)-(i) is generated by one cycle of primer annealing,
primer extending, and denaturing. Preferably, the second DNA strand
including nucleotide variation in step (b)-(ii) is amplified by at
least 5 cycles of primer annealing, primer extending, and
denaturing.
[0369] In another specific embodiment of this invention using
amplified short DNA strand fragment containing the nucleotide
variation, there is provided the method using two individual
amplifications of a first and a second amplifications in which the
second amplification is performed using two stage amplifications,
which comprises:
[0370] (a) performing the first amplification to produce a short
DNA strand fragment containing the nucleotide variation between its
ends comprising at least two cycles of primer annealing, primer
extending and denaturing, using a primer pair each primer
comprising a hybridizing sequence substantially complementary to a
pre-selected sequence at a site of the target nucleic acid under
conditions that the nucleotide variation is positioned between the
pre-selected sequences, in which at least one primer of the primer
set is any one of ACPs described above having at its 3'-end portion
the hybridizing sequence, whereby the short DNA strand fragment
containing the nucleotide variation between its ends is
amplified;
[0371] (b) performing a first-stage amplification of the second
amplification to produce a first DNA strand complementary to the
short DNA strand fragment including the nucleotide variation at a
first annealing temperature comprising at least one cycle of primer
annealing, primer extending and denaturing, using a first primer of
any one of ACPs described above having at its 3'-end portion a
hybridizing sequence substantially complementary to a pre-selected
sequence at a first site of the target nucleic acid to hybridize
therewith, wherein each of the first primer and the first site
comprises an interrogation position corresponding to the nucleotide
variation, whereby the first DNA strand complementary to the target
nucleic acid including the nucleotide variation is generated when
the interrogation position is occupied by the complementary
nucleotide of the first primer to its corresponding nucleotide of
the first site; and
[0372] (c) performing a second-stage amplification of the second
amplification of the first DNA strand generated from step (a) at a
second annealing temperature, which is high stringent conditions,
comprising at least one cycle of primer annealing, primer extending
and denaturing using a primer pair in which amongst the primer pair
one is the same as the primer of any one of ACPs used in step (a)
the other is the same as the first primer used in step (b), or a
primer pair each having a hybridizing sequence complementary or
corresponding to the 3'- and 5'-ends of the first DNA strand
generated from step (b) to hybridize therewith, under conditions in
which each primer anneals to the 3'- and 5'-end sequences of the
first DNA strand, respectively, whereby the first DNA strand is
amplified so that a short target nucleotide segment corresponding
to the first DNA strand containing the nucleotide variation is
generated.
[0373] A schematic representation of another specific embodiment
for single nucleotide polymorphism (SNP) genotyping using novel ACP
is illustrated in FIG. 7B. Since this specific embodiment is
carried out in a similar manner to above embodiment, the common
descriptions between them are omitted in order to avoid the
complexity of this specification leading to undue multiplicity.
[0374] The present method can be applied to a variety of nucleotide
variations including single nucleotide polymorphism and point
mutation (substitution, deletion and insertion).
[0375] The amplified products can be analyzed by gel
electrophoresis. In one embodiment, the resulting PCR products can
be also detected on a denaturing polyacrylamide gel by
autoradiography or non-radioactive detection methods such as silver
staining (Gottschlich et al., 1997; Kociok et al., 1998), the use
of fluoresenscent-labelled oligonucleotides (Bauer et al. 1993; Ito
et al. 1994; Luehrsen et al., 1997; Smith et al., 1997), and the
use of biotinylated primers (Korn et al., 1992; Tagle et al., 1993;
Rosok et al., 1996).
[0376] The amplified products generated by multiplex DNA
amplification for multiple SNP screening can be compared through
the size separation of the products. The size separation comparison
is also performed by electrophoresis through an agarose gel matrix
or polyacrylamide gel matrix or sequencing. The products can be
also detected by the use of fluoresenscent-labelled oligonucleotide
primers for automatic analysis.
[0377] The term "interrogation position" as used herein refers to
the location of a specific nucleotide base of interest within a
target nucleic acid. For example, in the analysis of SNPs, the
"interrogation position" in the target nucleic acid is in position
what would be different from wild type. The interrogation position
also includes the location of nucleotide sequence of a primer which
is complementary to an interrogation position of the target nucleic
acid. The interrogation position of the target nucleic acid is
opposite the interrogation position of the primer, when the primer
is hybridized with the target nucleic acid.
[0378] The term "polymorphism" as used herein refers to the
presence of two or more alternative genomic sequences or alleles
between or among different genomes or individuals. "Polymorphic"
refers to the condition in which two or more variants of a specific
genomic sequence can be found in a population. A "polymorphic site"
is the locus at which the variation occurs. A single nucleotide
polymorphism, or SNP, is a single base-pair variant, typically the
substitution of one nucleotide by another nucleotide at the
polymorphic site. Deletion of a single nucleotide or insertion of a
single nucleotide, also give rise to single nucleotide
polymorphisms. Typically, between different genomes or between
different individuals, the polymorphic site may be occupied by two
different nucleotides. The term "allele" as used herein refers a
specific member of a collection of naturally occurring sequence
variants (detectable within a population of individuals) at a
specific genomic locus or marker.
[0379] In still another aspect of this invention, there is provided
a kit for identifying a nucleotide variation in a target nucleic
acid, which comprises the annealing control primer or annealing
control primer set (including the first and second primers)
described above. The descriptions of the kits for the amplification
of nucleic acid sequence of this invention can be applied to the
present kit.
[0380] X. Application to Mutagenesis
[0381] This application using ACP of the subject invention can also
provide an improved method for mutagenesis. The ACP-based PCR
provides an excellent tool for mutagenesis, including deletion, or
insertion of sequences, the alteration of one or a few specific
nucleotides, and the random mutation of nucleotide sequence.
[0382] In further aspect of this invention, there is provided a
method for mutagenesis in a target nucleic acid, comprising
performing an amplification reaction using primers, characterized
in that at least one primer is derived from any one of ACPs
described above. Preferably, the primer having the structure of ACP
is one having at its 3'-end portion a hybridizing sequence
substantially complementary to a region of target nucleic acid
sequence, wherein the hybridizing sequence has a nucleotide
sequence responsible for mutagenesis.
[0383] In a specific embodiment of this invention, there is
provided the method using two stage amplifications, which
comprises:
[0384] (a) performing a first-stage amplification of the target
nucleic acid sequence at a first annealing temperature comprising
at least two cycles of primer annealing, primer extending and
denaturing, using a primer pair of any one of ACPs described above
each having at its 3'end portion a hybridizing sequence
substantially complementary to a region of the target nucleic acid
sequence to hybridize therewith, wherein the hybridizing sequence
has at least one mismatch nucleotide to generate site-directed
mutation, under conditions in which the primer or primer pair
anneals to its target nucleotide sequence, whereby an amplification
product containing site-directed mutation site is generated;
and
[0385] (b) performing a second-stage amplification of the
amplification product generated from step (a) at a second annealing
temperature, which is high stringent conditions, comprising at
least one cycle of primer annealing, primer extending and
denaturing, using the same primers as used in step (a) or a primer
pair each comprising a pre-selected arbitrary nucleotide sequence
corresponding to each 5'-end portion of the primers used in step
(a), under conditions in which each primer anneals to the 3'- and
5'-ends of the amplification product, respectively, whereby the
amplification product containing site-directed mutation site is
re-amplified.
[0386] This specific embodiment relates to site-directed
mutagenesis.
[0387] Since this application using the ACP of this invention
employs in principle the present methods for amplification of
nucleic acid sequence previously discussed, the common descriptions
between them are omitted in order to avoid the complexity of this
specification leading to undue multiplicity.
[0388] The formula of ACP for PCR mutagenesis is identical to the
formula (1) in which the 3'-end portion comprises a sequence for
site-directed mutagenesis or for random mutation.
[0389] In still further aspect of this invention, there is provided
a kit for mutagenesis in a target nucleic acid, which comprises the
annealing control primer or annealing control primer set described
above. The descriptions of the kits for the amplification of
nucleic acid sequence of this invention can be applied to the
present kit.
[0390] XI. Other Applications
[0391] The ACP of the subject invention can be also useful in a
variety of processes involving nucleic acid amplifications,
particularly, PCR. For example, the processes include mixed
oligonucleotide-primed amplification of cDNA, long-range PCR,
linear PCR, inverse PCR, quantitative PCR, touchdown PCR,
sequencing, in situ PCR, vectorette PCR and thermal asymmetric
interlaced PCR. The general procedures for these methods can be
found in Joseph Sambrook, et al., Molecular Cloning, A Laboratory
Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y.(2001) and M. J. McPherson, et al., PCR, Springer-Verlag New
York Inc., N.Y.(2000).
[0392] Therfore, the present invention encompasses all uses of the
primer according to ACP for process involving nucleic acid
amplification, particularly PCR.
[0393] The ACP of this invention is significantly effective and
widely accessible to nucleic acid amplification-based applications.
Also, various problems related to primer annealing specificity
remained in the previous nucleic acid amplification techniques can
be fundamentally solved by the ACP and the methods of the present
invention. The main benefits to be obtained from the use of the ACP
during nucleic acid amplification are as follows:
[0394] (a) since the presence of a regulator portion positioned
between the 3'- and 5'-end portions restricts primer annealing
portion to the 3'-end portion under such conditions that the 3'-end
portion anneals to the template, the annealing sequence of a primer
can be precisely controlled, which makes it possible to design a
primer caplable of having only a desired number of sequence
annealed (or possible to design a primer capable of controlling an
annealing portion thereof). It is particularly useful when an
annealing portion of a primer has to be limited (e.g., SNP
genotyping, DNA microarrary screening, and detection of
differentially expressed genes);
[0395] (b) since the presence of a regulator portion positioned
between the 3'- and 5'-end portions interrupts the annealing of the
5'-end portion to the template under such conditions that the
3'-end portion anneals to the template, eventually the 5'-end
portion not involved in the annealing provides the 3'-end portion
with primer annealing specificity;
[0396] (c) the specificity of primer annealing is highly sensitive
enough to detect even a single-base mismatching. It is particularly
useful for single nucleotide polymorphisms(SNPs) genotyping;
[0397] (d) the ACP is capable of providing a primer with a high
tolerance in "primer search parameters" for primer design such as
primer length, annealing temperature, GC content, and PCR product
length;
[0398] (e) the ACP provides two-stage nucleic acid amplifications
which allow the amplified products to be excluded from non-specific
amplification;
[0399] (f) the efficiency of nucleic acid amplification is
increased, which makes it easier to detect rare mRNAs; and
[0400] (g) the reproducibility of nucleic acid amplification
products is increased, which saves a great amount of time and
cost.
[0401] As much as the nucleic acid amplification technology such as
PCR has influenced the biotechnological field, the use of ACP
fundamentally alter the principles of the current existing nucleic
acid amplification methods, as mentioned above, by exhibiting
unlimited applicability, and have them significantly upgraded at
one time. In consequence, the ACP and its various applications
described herein provide a turning point to open a new
biotechnological era since the introduction of nucleic acid
amplification technology.
[0402] The following specific examples are intended to be
illustrative of the invention and should not be construed as
limiting the scope of the invention as defined by appended
claims.
EXAMPLES
[0403] In the experimental disclosure which follows, the following
abbreviations apply to: M (molar), mM (millimolar), .mu.M
(micromolar), g (gram), .mu.g (micrograms), ng (nanograms), l
(liters), ml (milliliters), .mu.l (microliters), .degree. C.
(degree Centigrade); Promega (Promega Co., Madison, U.S.A.);
Clontech (CLONTECH Laboratories, Palo Alto, U.S.A.); Roche (Roche
Diagnostics, Mannheim, Germany); QIAGEN (QIAGEN GmbH, Hilden,
Germany). The primers used in the subject invention are shown in
Table 1.
EXAMPLE 1
Evaluation of Universal Base Effect in ACP
[0404] The effect of universal base residues positioned between the
3'- and 5 -end portions of ACP was evaluated by RT-PCR using mouse
conceptus tissues.
[0405] Total RNA was isolated from the entire conceptuses of mouse
strain ICR at the day of 4.5, 11.5 and 18.5 during gestation period
using either Tri-reagent (Sigma), or the LiCl/Urea method (Hogan et
al., 1994) as previously described (Chun et al., 1999; Hwang et
al., 2000). Two individual experiments of cDNA amplifications using
ACP were performed to examine the effect of universal base,
particularly, deoxyinosine residues positioned between the 3'- and
5'-end portions of ACP as follows: A. The effect of deoxyinosine
residues positioned between the 3 '- and 5'-end portions of ACP in
comparison with ACP and the conventional primer not containing a
dexoyinosine group; B. The effect of deoxyinosine residues
positioned between the 3'- and 5'-end portions of ACP in
association with the alteration of number of dexoyinosine.
[0406] These experiments were conducted based on the following
assumptions:
[0407] (i) the presence of universal base residues which have lower
T.sub.m than other portions in ACP due to their weaker hydrogen
bonding interactions in base pairing would not be involved in
annealing to the template nucleic acid under the conditions that
the 3'-end portion of ACP anneals to a site of the template at a
first annealing temperature.
[0408] (ii) the presence of at least one universal base residue
between the 3'- and 5'-end portions of ACP would be capable of
interrupting the annealing of the 5'-end portion and restricting a
primer annealing portion to the 3'-end.
[0409] (iii) the 3'-end portion of ACP would act only as a
annealing portion to the template during PCR.
[0410] (iv) the 3'-end portion of dT-ACP which is dT.sub.10
comprising 10 T nucleotides also has too low T.sub.m to bind the
template nucleic acid.
[0411] (v) consequently, the dT.sub.10-ACP does not produce any PCR
products under high annealing temperature.
[0412] A. The effect of deoxyinosine residues positioned between
the 3'- and 5'-end portions of ACP in comparison with ACP with the
primer not containing a dexoyinosine group
[0413] (a) First-strand cDNA synthesis
[0414] dT.sub.10-JYC2 5'-GCTTGACTACGATACTGTGCGATTTTTTTTTT-3' (SEQ
ID NO:29) or dT.sub.10-ACP1
5'-GCTTGACTACGATACTGTGCGAIIIIITTTTTTTTTT-3' (SEQ ID NO:30) was used
as a cDNA synthesis primer.
[0415] Three micrograms of total RNA and 2 .mu.l of 10 .mu.M
dT.sub.10-JYC2 or 10 .mu.M dT.sub.10-ACP1 were combined in a 20
.mu.l final volume. The solution was heated at 65.degree. C. for 10
minutes, quenched on ice, and microcentrifuged to collect solvent
at the bottom. The following components were added sequentially to
the annealed primer/template on ice: 0.5 .mu.l (40 units/.mu.l) of
RNasin ribonuclease inhibitor (Promega), 4 .mu.l of 5.times.
reaction buffer (250 mM Tris-HCl, pH 8.3, 375 mM KCl, 15 mM
MgCl.sub.2, 50 mM DTT; Promega), 5 .mu.l of 2 mM each
deoxynucleotide mix (dATP, dCTP, dGTP, dTTP), and 1 .mu.l of
Moloney-murine leukemia virus (M-MLV) reverse transcriptase (200
units/.mu.l; Promega). The 20 .mu.l of reaction mixture was
incubated at 37.degree. C. for 90 min, microcentrifuged, and placed
on ice for 2 min. The reaction was stopped by incubation at
94.degree. C. for 2 min.
[0416] (b) cDNA amplification using ACPs
[0417] The dT.sub.10-ACP1 was used to examine the effect of a
deoxyinosine group positioned between the 3'- and 5'-end portions
during PCR. The dT.sub.10-JYC2 not containing a deoxyinosine group
was used as a control.
[0418] The ACP10 5'- GTCTACCAGGCATTCGCTTCATIIIIIGCCATCGACC-3' (SEQ
ID NO: 13) was used as 5' primer for this experiment.
[0419] The PCR amplification was conducted in a 50 .mu.l volume
containing 50 ng of the first-strand cDNA, 5 .mu.l of 10.times. PCR
buffer, 1 .mu.l of 10 .mu.M 5'primer (ACP10), 1 .mu.l of 10 .mu.M
3'primer (dT.sub.10-JYC2 or dT.sub.10-ACP1), 3 .mu.l of 25 mM
MgCl.sub.2, 5 .mu.l of 2 mM dNTP, 0.5 .mu.l of Taq polymerase (5
units/.mu.l). The PCR reactions were conducted under the following
conditions: 5 min at 94.degree. C. followed by 30 cycles of
94.degree. C. for 1 min, 54.degree. C. for 1 min, and 72.degree. C.
for 1 min; followed by a 5 min final extension at 72.degree. C.
Amplified products were analyzed by electrophoresis in a 2% agarose
gel followed by ethidium bromide staining.
[0420] As a result, FIG. 8 shows that the dT.sub.10-ACP1 containing
a deoxyinosine group produced almost no products (lanes 4-6),
whereas the dT.sub.10-JYC2 not containing a deoxyinosine group
produced a plurality of amplified cDNA products (lanes 1-3).
Consistent with our assumption, the results clearly indicate that
the deoxyinosine group positioned between the 3'-and 5'-end
portions affects the annealing of the 3'- and 5'-end portions of
the dT.sub.10-ACP to the template cDNA under such high annealing
temperature, resulting in no product as stated in the above
assumption.
[0421] B. The effect of deoxyinosine residues positioned between
the 3'- and 5'-end portions of ACP in association with the
alteration of number of dexoyinosine
[0422] (a) First-strand cDNA synthesis
[0423] The first-strand cDNA was synthesized from total RNA of
mouse concentues using dT.sub.10-JYC2 as a cDNA synthesis primer as
the above.
[0424] (b) cDNA amplification using ACPs
[0425] This experiment used four ACPs each comprising different
number of deoxyinosine residues as follows, to examine the effect
of deoxyinosine residues positioned between the 3'- and 5'-end
portions in association with the alteration of number of
deoxyinosine, under a particular stringency conditions.
[0426] ACP16 5'-GTCTACCAGGCATTCGCTTCATIIGCCATCGACC-3' (SEQ ID
NO:20);
[0427] ACP17 5'-GTCTACCAGGCATTCGCTTCATIIIIGCCATCGACC-3' (SEQ ID
NO:21);
[0428] ACP18 5'-GTCTACCAGGCATTCGCTTCATIIIIIIGCCATCGACC-3' (SEQ ID
NO:22);
[0429] ACP19 5'-GTCTACCAGGCATTCGCTTCATIIIIIIIIGCCATCGACC-3' (SEQ ID
NO:23); and
[0430] CRP2I0 5'-GTCTACCAGGCATTCGCTTCATGCCATCGACC-3' (SEQ ID NO:19)
not containing a deoxyinosine group was used as a control.
[0431] The resultant first-strand cDNA generated from step (A),
which comprises the pre-selected arbitrary sequence of the
dT.sub.10-ACP at its 5'-end, was used as a template and the primer
JYC2 5'-GCTTGACTACGATACTGTGCGA-3' (SEQ ID NO:10) corresponding to
the 5'-end portion of the dT.sub.10-ACP was used as 3' primer.
[0432] The PCR amplification was conducted in a 50 .mu.l volume
containing 50 ng of the first-strand cDNA, 5 .mu.l of 10.times. PCR
buffer, 1 .mu.l of 10 .mu.M 5'primer (ACP16, 17, 18, 19, or
CRP2I0), 1 .mu.l of 10 .mu.M 3'primer (JYC2), 3 .mu.l of 25 mM
MgCl.sub.2, 5 .mu.l of 2 mM dNTP, 0.5 .mu.l of Taq polymerase (5
units/.mu.l). The PCR reactions were comprised of: 5 min at
94.degree. C., followed by 30 cycles of 94.degree. C. for 1 min,
57.degree. C. for 1 min, and 72.degree. C. for 1 min; followed by a
5 min final extension at 72.degree. C. Amplified products were
analyzed by electrophoresis in a 2% agarose gel followed by
ethidium bromide staining.
[0433] As a result, FIG. 9 shows that the CRP2I0 not containing any
deoxyinosine residues produced a plurality of amplified cDNA
products, whereas the ACPs containing at least two deoxyinosine
residues generated the significant reduction of amplified cDNA
products, and even more, the ACP containing eight deoxyinosine
residues produced almost no products. Consistent with our
assumption, the results clearly indicates that the annealing of the
3'-end portion of ACP to the template could be separated from the
5'-portion since a group of contiguous deoxyinosine residues
separates the annealing of the 3'-end and 5'-end portions under
high stringent conditions due to the property of deoxyinosine such
as its weaker hydrogen bonding interaction in base pairing.
EXAMPLE 2
Method for Amplifying a Target Nucleic Acid Sequence Using ACP
[0434] The ACP of the subject invention was applied to amplify
target nucleotide sequences of mouse placenta-specific homeobox
gene Esxl cDNA. The process and results for the amplification of
the target nucleotide sequences of Esxl cDNA using ACPs are
described herein. Total RNA (3 .mu.g) obtained from mouse
18.5-day-old placenta was used as a starting material. First-strand
cDNAs were prepared under the same conditions as used in the cDNA
synthesis of Example 1, except that Oligo-dT.sub.15 was used as the
first-strand cDNA synthesis primer.
[0435] Oligo-dT.sub.15 5'-TTTTTTTTTTTTTTT-3' (SEQ ID NO:54)
[0436] The resultant first-strand cDNAs were used as templates to
amplify target cDNA fragments of Esxl using ACPs. These experiments
conducted two stage PCR amplifications, which is one of unique
features of the present invention.
[0437] The conventional primers of Esxl used in the Example
are:
1 EsxN7 5'-GCCGGTTGCAGAAGCACC-3'; (SEQ ID NO:44) EsxC6
5'-GAACCATGTTTCTGAATGCC-3'; (SEQ ID NO:45) EsxN1
5'-GAATCTGAAACAACTTTCTA-3'; (SEQ ID NO:48) EsxC2
5'-GATGCATGGGACGAGGCACC-3'; (SEQ ID NO:49) EsxN3
5'-CGCCGCAACCCCTGCCCGCA-3'; and (SEQ ID NO:51) EsxC5
5'-GATGCATGGGACGAGGCA-3'. (SEQ ID NO:52)
[0438] Three primer sets, EsxN7 and EsxC6, EsxN1 and EsxC2, and
EsxN3 and EsxC5, were used in the Example because they are known as
the primer sets which generate high backgrounds as well as
non-specific products in conventional PCR methods as known in the
art.
[0439] According to single-target PCR systems, primers with similar
melting temperatures (T.sub.m ) should be chosen. However, a primer
set of EsxN1 (T.sub.m 50.7.degree. C.) and EsxC2 (T.sub.m
71.9.degree. C.) shows about 20.degree. C. of different melting
temperatures between them, and a primer set of EsxN3 (T.sub.m
86.9.degree. C.) and EsxC5 (T.sub.m 66.2.degree. C.) both has high
melting temperatures. Also, a primer set of EsxN7 (T.sub.m
68.2.degree. C.) and EsxC6 (T.sub.m 61.2.degree. C.), which has
relatively similar melting temperature, are selected to observe the
effect of ACP.
[0440] The ACP of the subject invention was applied to these three
conventional primer sets to demonstrate if the ACP system can
overcome the main problems arising from these conventional primer
sets, such as background and non-specific products.
[0441] The following ACPs comprise the sequences of the above
conventional primers at their 3'-end portions and were used as Esxl
gene-specific primers for the first-stage PCR amplification:
2 EsxN7-ACP 5' primer
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCCGGTTGCAGAAGC- ACC-3'; (SEQ ID
NO:46) EsxC6-ACP 3' primer
5'-GCTTGACTACGATACTGTGCGAIIIIIGAACCATGTTTCTGAATGCC-3'; (SEQ ID
NO:47) EsxN1-ACP 5' primer
5'-GTCTACCAGGCATTCGCTTCATIIIIIGAATCTGAAAC- AACTTTCTA-3'; (SEQ ID
NO:50) EsxC2-ACP 3' primer
5'-GCTTGACTACGATACTGTGCGAIIIIIGATGCATGGGACGAGGCACC-3'; (SEQ ID
NO:55) EsxN3-ACP 5' primer
5'-GTCTACCAGGCATTCGCTTCATIIIIICGCCGCAACCC- CTGCCCGCA-3'; and (SEQ
ID NO:53) EsxC5-ACP 3' primer
5'-GCTTGACTACGATACTGTGCGAIIIIIGATGCATGGGACGAGGCA-3'. (SEQ ID
NO:56)
[0442] The 5'-end portion sequences of the ACPs were served as
pre-selected arbitrary primer sequences only for the second-stage
PCR amplification: JYC2 and JYC4 5'-GTCTACCAGGCATTCGCTTCAT-3' (SEQ
ID NO:12).
[0443] During the first-stage PCR amplification, the primer set of
EsxN7-ACP and EsxC6-ACP was used as 5' and 3' primers,
respectively, to generate the 520-bp fragment of the Esxl cDNA, the
primer set of EsxN1-ACP and EsxC2-ACP was used as 5' and 3'
primers, respectively, to generate the 784-bp fragment of the Esxl
cDNA, and the primer set of EsxN3-ACP and EsxC5-ACP was used as 5'
and 3' primers, respectively, to generate the 483-bp fragment of
the Esxl cDNA.
[0444] During the second-stage PCR amplification, JYC4 and JYC2
were used as pre-selected arbitrary 5' and 3' primers, respectively
(PROTOCOL A). As an alternative, the complete sequences of the
ACPs, instead of the pre-selected arbitrary primers such as JYC4
and JYC2, can be used as 5' and 3' primers for the second-stage PCR
amplification at the high stringent conditions. In this case, it is
not necessary to add the pre-selected arbitrary primers to the
reaction mixture at the time of or after the first-stage PCR
reaction (PROTOCOL B).
[0445] PROTOCOL A: One-stop two-stage PCR Amplifications
[0446] (A) First-stage PCR Amplification
[0447] The first-stage PCR amplification was performed by hot start
PCR method in which the procedure is to set up the complete
reactions without the DNA polymerase and incubate the tubes in the
thermal cycler to complete the initial denaturation step at
>90.degree. C. Then, while holding the tubes at a temperature
above 70.degree. C., the appropriate amount of DNA polymerase can
be pipetted into the reaction.
[0448] The first-stage PCR amplification was conducted by two
cycles of PCR consisting of annealing, extending and denaturing
reaction; the reaction mixture in a final volume of 49.5 .mu.l
containing 50 ng of the first-strand cDNA, 5 .mu.l of 10.times. PCR
reaction buffer (Promega), 5 .mu.l of 25 mM MgCl.sub.2, 5 .mu.l of
dNTP (2 mM each dATP, dCTP, dGTP, dTTP), 1.35 .mu.l of 5' ACP (1
.mu.M) and 1.35 .mu.l of 3' ACP (1 .mu.M) is pre-heated at
94.degree. C., while holding the tube containing the reaction
mixture at the 94.degree. C., 0.5 .mu.l of Taq polymerase (5
units/.mu.l; Promega) is added into the reaction mixture; the PCR
reactions comprise two cycles of 94.degree. C for 40 sec,
60.degree. C. for 40 sec, and 72.degree. C. for 40 sec; followed by
denaturing the amplification product at 94.degree. C.
[0449] (B) Second-Stage PCR Amplification
[0450] The resultant cDNA product generated by the first-stage PCR
amplification using Esxl gene-specific ACPs was then amplified by
the following second-stage PCR amplification under higher annealing
temperature. After the completion of the first-stage PCR
amplification, each 1 .mu.l of 10 .mu.M pre-selected arbitrary
primers, JYC4 and JYC2, was added into the reaction mixture
obtained from the first-stage PCR amplification, under denaturing
temperature such as at 94.degree. C. The second stage-PCR reaction
was as follows: 35 cycles of 94.degree. C. for 40 sec, 68.degree.
C. for 40 sec, and 72.degree. C. for 40 sec; followed by a 5 min
final extension at 72.degree. C.
[0451] The amplified products were analyzed by electrophoresis in a
2% agarose gel and detected by staining with ethidium bromide. The
resulting PCR products can be also detected on a denaturing
polyacrylamide gel by autoradiography or non-radioactive detection
methods such as silver staining (Gottschlich et al., 1997; Kociok
et al., 1998), the use of fluoresenscent-labelled oligonucleotides
(Bauer et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith
et al., 1997), and the use of biotinylated primers (Korn et al.,
1992; Tagle et al., 1993; Rosok et al., 1996).
[0452] As shown in FIGS. 10A-C, the one-stop two-stage PCR
amplifications for Esxl using each primer set of EsxN7-ACP and
EsxC6-ACP, EsxN1-ACP and EsxC2-ACP, and EsxN3-ACP and EsxC5-ACP
generated a single band which corresponds to the expected size,
520-bp (FIG. 10A, lane 2), 784-bp (FIG. 10B, lane 4), and 483-bp
(FIG. 10C, lane 3) of Esxl cDNA fragments, respectively. Subsequent
cloning and sequence analysis of the clones confirm that the band
is Esxl cDNA fragments. In contrast, the conventional primer sets,
which contain the sequences corresponding only to the 3'-end
portions of each ACP sets, produced non-specific products as well
as high backgrounds such as DNA smear (FIG. 10A, lane 1; FIG. 10B,
lane 3; FIG. 10C, lanes 1 and 2). Since the PCR products using a
ACP set comprise the pre-selected arbitrary sequences at their 5'-
and 3'-ends, additional 54-bp sequences corresponding to the
pre-selected arbitrary sequences and deoxyinosine residues were
found.
[0453] FIG. 10A shows the amplified cDNA products generated by the
following sets of primers; a set of EsxN7 and EsxC6 (lane 1), and a
set of EsxN7-ACP and EsxC6-ACP (lane 2). PCR reactions using the
conventional primer set EsxN7 and EsxC6 were as follows: 5 min at
94.degree. C. followed by 30 cycles of 94.degree. C. for 40 sec,
60.degree. C. for 40 sec, and 72.degree. C. for 40 sec; followed by
a 5 min final extension at 72.degree. C.
[0454] FIG. 10B shows the amplified cDNA products generated by a
single primer or a primer pair as follows: the primers, EsxN1 and
EsxC2, were used in lanes 1 and 2, respectively; a combination of
EsxN1-ACP and conventional primer EsxC2 was used in lanes 3; two
ACPs EsxN1-ACP and EsxC2-ACP were used in lane 4. When a
conventional primer set, EsxN1 and EsxC2, was used under high
annealing temperature of 60.degree. C., no specific-target product
was produced. When a primer set comprising one ACP EsxN1-ACP and a
conventional primer of EsxC2 was used, a target-specific product as
well as non-specific products were amplified due to the
non-specific binding of the conventional primer EsxC2 (lane 3).
However, when a ACP set was used, only a single target-specific
product was amplified (lane 4), which indicates that the ACP of the
subject invention provides primers with tolerance to "primer design
parameter" related to melting temperatures of general primers
requested for single-target PCR systems.
[0455] FIG. 10C shows the amplified cDNA products generated by
using the following primer sets: a set of EsxN3 and EsxC5 was used
in lanes 1 and 2, and a set of EsxN3-ACP and EsxC5-ACP was used in
lane 3. PCR reactions using the conventional primer set of EsxN3
and EsxC5 were as follows: 5 min at 94.degree. C. followed by 30
cycles of 94.degree. C. for 40 sec, 58.degree. C. for 40 sec, and
72.degree. C. for 40 sec; followed by a 5 min final extension at
72.degree. C. (lane 1). The conventional primer set was also
compared with the ACP set by conducting the same two stage PCR
amplifications as used in the ACP, such that its annealing
temperature is increased from 60.degree. C. to 68.degree. C. (lane
2). These results also indicate that although the conventional
primers including ones having high T.sub.m are used in the same two
stage PCR amplification, they could not be free from the problems
of non-specific products and background, whereas the ACP of the
subject invention can help overcome such problems arising from
these conventional primers.
[0456] PROTOCOL B: Non-stop two-stage PCR Amplifications
[0457] Alternatively, the complete sequences of the ACPs, instead
of the pre-selected arbitrary primers such as JYC4 and JYC2, can be
used as primers for the second-stage PCR amplification at the high
stringent conditions. In this case, it is not necessary to add the
pre-selected arbitrary primers to the reaction mixture at the time
of or after the first-stage PCR reaction.
[0458] The process of the non-stop two-stage PCR amplifications is
basically identical to Protocol A, except that the ACPs, 1 .mu.l of
5' ACP (10 .mu.M) and 1 .mu.l of 3' ACP (10 .mu.M), are added at
the first stage PCR amplification and the second stage PCR
amplification immediately follows the first stage PCR amplification
without any delay because there is no step of adding pre-selected
arbitrary primers.
[0459] The amplified products were analyzed by electrophoresis in a
2% agarose gel and detected by staining with ethidium bromide. The
resulting PCR products can be also detected on a denaturing
polyacrylamide gel by autoradiography or non-radioactive detection
methods such as silver staining (Gottschlich et al., 1997; Kociok
et al., 1998), the use of fluoresenscent-labelled oligonucleotides
(Bauer et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith
et al., 1997), and the use of biotinylated primers (Korn et al.,
1992; Tagle et al., 1993; Rosok et al., 1996).
[0460] FIG. 10D shows the amplified cDNA products generated by the
non-stop two-stage PCR Amplifications using the following single
primer or a primer pair; the primers EsxN1 and EsxC2 were used in
lane 1 and 2, respectively; a pair of EsxN1 and EsxC2 was used in
lane 3; and a pair of EsxN1-ACP and EsxC2-ACP was used in lane 4.
When a conventional primer set, EsxN1 and EsxC2, was used, no
specific-target product was produced. However, when a ACP set was
used in non-stop two-stage PCR amplifications, only a single
target-specific product was amplified (lane 4), which is consistent
with the results of one-stop two-stage PCR Amplifications (FIG.
10B).
[0461] These examples illustrate that the ACP permits the products
to be free from the background problems as well as non-specificity
arising from the conventional primers used in PCR methods as
described in the art. It could be also understood that the ACP
allows the generation of the specific products regardless of the
design of gene-specific primers.
EXAMPLE 3
Identification and Characterization of Differentially Expressed
mRNAs during Mouse Embryonic Development Using ACP
[0462] The ACP of the subject invention has been applied to detect
differentially expressed mRNAs in embryonic developments.
Specifically, three different procedures and results using
different stages of conceptus total RNAs as starting materials are
described herein. The primers used in the subject invention are
shown in Table 1.
[0463] A1. PROCEDURE 1
[0464] Step (1): First-strand cDNA synthesis
[0465] The first-strand cDNAs were prepared under the same
conditions as used in the cDNA synthesis of Example 1 using the
dT.sub.10-ACP1 or JYC-T.sub.15-ACP as a cDNA synthesis primer. The
resultant cDNAs were purified by a spin colunm (PCR purification
Kit, QIAGEN) to remove primers, dNTP, and the above reagents. It is
necessary to perform the purification step prior to the
determination of the cDNAs concentration using the UV spectroscopy
at an absorbance of 260 nm. The same amount of cDNAs from each
sample was used for comparing their amplification patterns using
the ACP system described herein.
[0466] Step (2): First-stage PCR amplification using ACP
[0467] The following ACPs were used as arbitrary ACPs (AR-ACPs) for
the first PCR amplification:
3 ACP3 (SEQ ID NO:3) 5'-GTCTACCAGGCATTCGCTTCATIIII- IGCCATCGACS-3';
ACP5 (SEQ ID NO:5) 5'-GTCTACCAGGCATTCGCTTCATIIIIIAGGCGATGCS-3';
ACP8 (SEQ ID NO:8) 5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCGATGCS-3';
ACP10 (SEQ ID NO:13) 5'-GTCTACCAGGCATTCGCTTCAT- IIIIIGCCATCGACC-3';
ACP13 (SEQ ID NO:16) 5'-GTCTACCAGGCATTCGCTTCATIIIIIAGGCGATGCG-3';
and ACP14 (SEQ ID NO:17)
5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCGATGCC-3'- .
[0468] The 5'-end portion sequences of the dT.sub.10-ACP1 and
AR-ACPs serve as pre-selected arbitrary primer sequences only for
the second-PCR amplification. The pre-selected arbitrary primers
are JYC2 and JYC4.
[0469] The first-strand cDNAs produced from step (1) were amplified
by the following first-stage PCR amplification using one of AR-ACPs
(ACP3, ACP5, ACP8, ACP10, ACP13, or ACP14) and the dT.sub.10-ACP1
as 5' and 3' primers, respectively. The first-stage PCR
amplification was conducted in a 50 .mu.l volume containing 50 ng
of the first-strand cDNA, 5 .mu.l of 10.times. PCR reaction buffer
(Promega), 3 .mu.l of 25 mM MgCl.sub.2, 5 .mu.l of dNTP (0.2 mM
each dATP, dCTP, dGTP, dTTP), 5 .mu.l of 5' primer (1 .mu.M), 5
.mu.l of 3' primer (1 .mu.M), and 0.5 .mu.l of Taq polymerase (5
units/.mu.l; Promega). The PCR reactions were as follows: 5 min at
94.degree. C. followed by 20 cycles of 94.degree. C. for 1 min,
50.degree. C. for 1 min, and 72.degree. C. for 1 min; followed by a
5 min final extension at 72.degree. C.
[0470] The cycle of the first-stage PCR amplification can be varied
depending on the types of samples. For example, the 20 cycles of
the first PCR amplification were used for mouse conceptus
samples.
[0471] Step (3): Second-stage PCR amplification using pre-selected
arbitrary primers corresponding to the 5'-end portion sequences of
ACPs
[0472] The amplified cDNA products produced from step (2) are
re-amplified by the following second-stage PCR amplification using
two pre-selected arbitrary primers, JYC4 and JYC2, each
corresponding to the 5'-end portion sequences of AR-ACP and
dT.sub.10-ACP1, respectively. The second-stage PCR amplification
was conducted in a 50 .mu.l volume containing 5 .mu.l of the first
amplified cDNA products (50 .mu.l), 5 .mu.l of 10.times. PCR
reaction buffer (Promega), 3 .mu.l of 25 mM MgCl.sub.2, 5 .mu.l of
2 mM dNTP, 1 .mu.l of 5' primer (10 .mu.M), 1 .mu.l of 3' primer
(10 .mu.M), and 0.5 .mu.l of Taq polymerase (5 units/.mu.l). The
PCR reactions were as follows: 5 min at 94.degree. C. followed by
30 cycles of 94.degree. C. for 1 min, 65.degree. C. for 1 min, and
72.degree. C. for 1 min; followed by a 5 min final extension at
72.degree. C.
[0473] A2. PROCEDURE 2
[0474] The alternative procedure comprises the following steps
of:
[0475] (a) providing a first sample of nucleic acids representing a
first population of mRNA transcripts and a second sample of nucleic
acids representing a second population of mRNA transcripts;
[0476] (b) contacting each of the first nucleic acid sample and the
second nucleic acid sample with a first ACP, wherein the first ACP
has a hybridizing sequence substantially complementary to a region
of the first and second population of mRNA transcripts to hybridize
therewith;
[0477] (c) reverse transcribing the mRNA to which the first ACP
hybridizes to produce a first population of DNA strands that are
complementary to the mRNAs in the first nucleic acid sample to
which the first ACP hybridizes, and a second population of DNA
strands that are complementary to the mRNA in the second nucleic
acid sample to which the first ACP hybridizes;
[0478] (d) purifying and quantifying the complementary DNA strands
produced as a result of the reverse transcription step (c);
[0479] (e) synthesizing a second DNA strand complementary to each
of the first and second populations of DNA strands using a second
ACP under low stringent conditions, by at least one PCR cycle
comprising denaturing, annealing and primer extension, wherein the
second ACP has a hybridizing sequence substantially complementary
to the first and second populations of DNA strands;
[0480] (f) amplifying each second DNA strand obtained from step (e)
under high stringent conditions, by at least one PCR cycle
comprising denaturing, annealing and primer extension to generate
first and second populations of amplification products using two
pre-selected arbitrary primers each comprising a sequence
corresponding to each 5'-end portion of the first and second
annealing control primers; and
[0481] (g) comparing the amount of individual amplification
products in the first and second populations of amplification
products.
[0482] The first-strand cDNAs are synthesized using
JYC5-T.sub.15-ACP 5' -CTGTGAATGCTGC
GACTACGATIIIIIITTTTTTTTTTTTTTT-3' (SEQ ID NO:61).
[0483] The 5'-end portion sequence of the JYC5-T.sub.15-ACP serves
as a 3' pre-selected arbitrary primer sequence to be used only for
the second stage of PCR amplification:
[0484] JYC5 5'-CTGTGAATGCTGCGACTACGAT-3' (SEQ ID NO:60).
[0485] Step (1): First-strand cDNA synthesis
[0486] 1. Combine 3 .mu.g total RNA and 2 .mu.l of 10 .mu.M
JYC5-T.sub.15-ACP in a sterile 0.2 ml microcentrifuge tube.
[0487] 2. Add sterile H.sub.2O to a final volume of 9.5 .mu.l. Mix
contents and spin the tube briefly in a microcentrifuge.
[0488] 3. Incubate the tube at 80.degree. C. for 3 minutes or use a
thermocycler for the same purpose.
[0489] 4. Cool the tube on ice for 2 minutes. Spin down the
contents of the tube briefly in a microcentrifuge.
[0490] 5. To the same reaction tube add the following reagents: 4
.mu.l 5.times. First-strand buffer (Promega), 5 .mu.l dNTP (2 mM
each dATP, dCTP, dGTP, dTTP), 0.5 .mu.l RNasin inhibitor (40
units/.mu.l, Promega) and 1 .mu.l M-MLV reverse transcriptase (200
U/.mu.l).
[0491] 6. Mix contents and spin the tube briefly in a
microcentrifuge.
[0492] 7. Incubate the tube at 42 .degree. C. for 90 min.
[0493] 8. Incubate the tube at 94 .degree. C. for 2 minutes to
terminate first-strand synthesis.
[0494] 9. Place the tube on ice for 2 min.
[0495] 10. Purify the resultant cDNAs by a spin column (PCR
purification Kit, QIAGEN) to remove primers, dNTP, and the above
reagents.
[0496] 11. Next, measure the concentration of the cDNAs using the
UV spectroscopy at an absorbance of 260 nm.
[0497] 12. Process to step 2.
[0498] Step (2): Second-strand cDNA synthesis using ACP
[0499] The same amount of cDNAs from each sample was used for the
comparison of their amplification patterns using the ACPs described
herein. The second-strand cDNA was synthesized using arbitrary
ACP10 by hot start PCR method in which the procedure is to set up
the complete reactions without the DNA polymerase and incubate the
tubes in the thermal cycler to complete the initial denaturation
step at >90.degree. C. Then, while holding the tubes at a
temperature above 90.degree. C., the appropriate amount of DNA
polymerase can be pipetted into the reaction.
[0500] 1. Combine the following reagents in a sterile 0.2 ml
microcentrifuge tube: 49.5 .mu.l of the total volume containing 1
.mu.l of first-strand cDNA (50 ng/.mu.l) prepared by step 1, 5
.mu.l of 10.times. PCR buffer (Roche), 5 .mu.l of 2 mM dNTP, 1
.mu.l of 10 .mu.M arbitrary ACP (5' primer) and 37.5 .mu.l of
sterile dH.sub.2O.
[0501] 2. Mix contents and spin the tube briefly in a
microcentrifuge.
[0502] 3. Place the tube in the preheated thermal cycler at
94.degree. C.
[0503] 2 5 4. Add the 0.5 .mu.l of Taq polymerase (5 units/.mu.l;
Roche) into the reaction, while holding the tube at the temperature
94.degree. C.
[0504] 5. Conduct PCR reaction under the following conditions: one
cycle of 94.degree. C. for 5 min, 50.degree. C. for 3 min, and
72.degree. C. for 1 min; followed by denaturing the first
amplification product at 94.degree. C.
[0505] Step (3): PCR Amplification of the second-strand cDNAs using
pre-selected arbitrary primers corresponding to the 5'-end portion
sequences of ACPs
[0506] 1. After the completion of the first stage PCR
amplification, while holding the tubes at a temperature above
94.degree. C., add 2 .mu.l of 10 .mu.M JYC4 and 2 .mu.l of 10 .mu.M
JYC5, in which each corresponds to the 5'-end portion sequences of
both 5' and 3' ACPs, respectively, into the reaction mixture used
in step (2).
[0507] 2. Conduct second stage PCR reactions under the following
conditions: 40 cycles of 94.degree. C. for 40 sec, 68.degree. C.
for 40 sec, and 72.degree. C. for 40 sec; followed by a 5 min final
extension at 72.degree. C.
[0508] A3. PROCEDURE 3
[0509] As an alternative process, in the step (f) of PROCEDURE 2
the complete sequences of the first and second ACPs used in the
steps (b) and (e) of PROCEDURE 2, instead of the pre-selected
arbitrary sequences of the 5' -end portions of the first and second
ACPs, can be used as 3' and 5' primers, respectively, at the high
stringent conditions for amplifying each second DNA strand obtained
from the step (e) of PROCEDURE 2, wherein the 3'- and 5'-ends of
the second DNA strands which were initially synthesized using the
second ACP comprise the sequence of the first ACP and the
complementary sequence of the second ACP, respectively, and also
serve as perfect pairing sites to the first and second ACPs. In
this case, it is not necessary to add the pre-selected arbitrary
primers to the reaction mixture at the time of or after first-stage
PCR reaction.
[0510] Step (1): First-strand cDNA synthesis
[0511] The first-strand cDNAs were prepared under the same
conditions as used in the cDNA synthesis of PROCEDURE 2 using the
JYC5-T.sub.15-ACP as a cDNA synthesis primer.
[0512] Step (2): Second-strand cDNA synthesis and amplification
using non-stop two-stage PCR
[0513] The same amount of cDNAs from each sample was used for the
comparison of their amplification patterns using the ACPs described
herein. The second-strand cDNA was synthesized using arbitrary
ACP10 by hot start PCR method in which the procedure is to set up
the complete reactions without the DNA polymerase and incubate the
tubes in the thermal cycler to complete the initial denaturation
step at >90.degree. C. Then, while holding the tubes at a
temperature above 90.degree. C., the appropriate amount of DNA
polymerase can be pipetted into the reaction.
[0514] 1. Combine the following reagents in a sterile 0.2 ml
microcentrifuge tube: 49.5 .mu.l of the total volume containing 1
.mu.l of first-strand cDNA (50 ng/.mu.l) prepared by step 1, 5
.mu.l of 10.times. PCR buffer (Roche), 5 .mu.l of 2 mM dNTP, 1
.mu.l of 10 .mu.M arbitrary ACP10 (5' primer), 1 .mu.l of 10 .mu.M
JYC5-T.sub.15-ACP (3' primer) and 36.5 .mu.l of sterile
dH.sub.2O.
[0515] 2. Mix contents and spin the tube briefly in a
microcentrifuge.
[0516] 3. Place the tube in the preheated thermal cycler at
94.degree. C.
[0517] 4. Add the 0.5 .mu.l of Taq polymerase (5 units/.mu.l;
Roche) into the reaction, while holding the tube at the temperature
94.degree. C.
[0518] 5. Conduct PCR reaction under the following conditions: one
cycle of 94.degree. C. for 1 min, 50.degree. C. for 3 min, and
72.degree. C. for 1 min; followed by 40 cycles of 94.degree. C. for
40 sec, 65.degree. C. for 40 sec, and 72.degree. C. for 40 sec; and
followed by a 5 min final extension at 72.degree. C.
[0519] B. Separation of amplified PCR products by electrophoresis
analysis and recovery of the differentially displayed bands
[0520] The amplified products were analyzed by electrophoresis in a
2% agarose gel and detected by staining with ethidium bromide.
Several major bands differentially expressed during embryonic
development (E4.5, E11.5, and E18.5) were selected, excised and
extracted from the gels using GENECLEAN II Kit (BIO 101). The
resulting PCR products can be also detected on a denaturing
polyacrylamide gel by autoradiography or non-radioactive detection
methods such as silver staining (Gottschlich et al., 1997; Kociok
et al., 1998), the use of fluoresenscent-labelled oligonucleotides
(Bauer et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith
et al., 1997), and the use of biotinylated primers (Korn et al.,
1992; Tagle et al., 1993; Rosok et al., 1996).
[0521] C. Re-amplification of the recovered bands
[0522] The bands obtained from step B were re-amplified using the
same pre-selected arbitrary primers and PCR conditions as used in
PROCEDURE 1, 2 and 3.
[0523] D. Cloning and sequencing of the re-amplified fragments
[0524] Each amplified fragment was cloned into the pGEM-T Easy
vector (Promega) and sequenced with the ABI PRISM 310 Genetic
Analyzer (Perkin Elmer Biosystem) using BigDye Terminator cycle
sequencing kit (Perkin Elmer). Computer-assisted sequence analysis
was carried out using the BLAST search program (Basic Local
Alignment Search Tool).
[0525] E. Northern analysis
[0526] Twenty micrograms of total RNA from conceptus tissues were
resolved on denaturing 1% agarose gels containing formaldehyde,
transferred onto nylon membranes (Hybond-N, Amersham, U.S.A.), and
hybridized with a .sup.32P-labeled subcloned PCR product in QuikHyb
solution (Stratagene, U.S.A.) overnight at 58.degree. C. as
previously described (Chun et al., 1999; Hwang et al., 2000). Blots
were washed at 65.degree. C. twice for 20 min in 2.times. SSC, 0.1%
SDS, twice for 20 min in 1.times. SSC, 0.1% SDS, and twice for 20
min in 0.1.times.SSC, 0.1% SDS. The membranes were exposed to Kodak
X-Omat XK-1 film with a Fuji intensifying screen at -80.degree.
C.
[0527] FIGS. 11A-D shows the amplified cDNA products, wherein mouse
conceptus samples obtained from different stages were amplified by
PROCEDURE 1 using the primer sets as follows; a set of ACP3 and
dT.sub.10-ACP1 for the lanes 1-3 of FIG. 11A; a set of ACP5 and
dT.sub.10-ACP1 for the lanes 1-6 and of FIG. 11B and a set of ACP8
and dT.sub.10-ACP1 for the lanes 7-12 of FIG. 10B, respectively.
FIG. 11B also shows additional results of the amplified cDNA
products generated by using another ACP sets. FIGS. 11C-D shows the
amplified products generated by using two primer sets of the ACP10
and dT.sub.10-ACP1(FIG. 11C), and ACP14 and dT.sub.10-ACP1(FIG.
11D), respectively. Many differentially expressed bands in a
specific stage were obtained, subcloned into the pGEM-T Easy vector
(Promega), and sequenced. Sequence analysis reveals that all of the
clones are known genes except two novel genes (Table 2). The
expression patterns were confirmed by Northern blot analysis using
mouse conceptus stage blot (Seegene, Inc., Seoul, Korea).
[0528] FIG. 12A shows the amplified cDNA products, wherein mouse
conceptus samples (E4.5: lane 1; E11.5: lane 2; E18.5: lane 3)
obtained from different stages were amplified by PROCEDURE 2 using
a set of ACP10 and JYC5-T.sub.15-ACP. Many differentially expressed
bands in a specific stage were obtained, subcloned into the pGEM-T
Easy vector (Promega), and sequenced. Sequence analysis reveals
that all of the clones are known genes except one DEG 2 (Table 2).
The expression patterns were confirmed by Northern blot analysis
using mouse conceptus stage blot (Seegene, Inc., Seoul, Korea).
[0529] FIG. 12B shows the amplified cDNA products, wherein mouse
conceptus samples at the different stages of (E4.5: lane 3; E11.5:
lane 4; E18.5: lane 5) were amplified by non-stop two-stage PCR
amplifications using a set of ACP10 and JYC5-T.sub.15-ACP as above
mentioned in PROCEDURE 3. When a set of ACP10 and JYC5-T.sub.15-ACP
(lanes 3-5) was used, the resultant bands were identical to the
bands which were obtained by PROCEDURE 2 comprising one-stop
two-stage PCR amplifications (FIG. 12A). However, no products were
generated when a single primer, ACP10 (lane 1) or JYC5-T.sub.15-ACP
(lane 2) was used, which indicates that the amplified products were
generated only when both ACP10 and JYC5-T.sub.15-ACP as a set were
used for their specific bindings.
[0530] FIG. 13 shows the results of Northern blot hybridization for
representing six different clones using DEG1 (A; arrow 1 of FIG.
10A, FIG. 11, and FIG. 12), DEG2 (C), DEG3 (B; arrow 2 of FIG. 10A,
FIG. 11, and FIG. 12), DEG5 (E), DEG7 (F), and DEG8 (D; arrow 4 of
FIG. 10A, FIG. 11, and FIG. 12) as probes. The DEG1 probe was also
hybridized to the alternative isoform of Tropomyosin 2 (arrow 1' of
FIG. 11, and FIG. 12), which was discovered by this present
invention. Consistent with the results of agarose gel analysis,
Northern blot analysis showed that the expression patterns of the
clones are identical to the original bands on the agarose gels,
indicating that all of the clones are true positive products. Thus,
the ACP produces only positive products without any false
positives, which means that the ACP eliminates the problem of false
positives.
[0531] FIG. 14 shows the results of Northern blot hybridization for
the expression of DEG5 during mouse embryonic development. DEG5,
which is turned out as a novel gene by sequence analysis, shows an
interesting expression patterns: after a strong expression appeared
in the early pregnancy stage (E4.5), its expression was gradually
reduced in the middle stages and gradually increased again in the
late development stage (E17.5 and E18.5).
[0532] These results indicate that the method using ACP for
isolating differentially expressed genes produces only real PCR
products and completely eliminates false positive products.
[0533] Freedom from false positives which have been one major
bottleneck remaining for the previous Differential Display
technique allows avoiding the subsequent labor-intensive work
required for the verification of the cDNA fragments identified by
Differential Display.
EXAMPLE 5
Method for Rapid Amplification of 3'-Ends of cDNA (3'-RACE) Using
ACP
[0534] The present example compares the ACP-based 3'-RACE and the
conventional 3'-RACE in order to demonstrate if the ACP of the
present invention can exclude such background problems arising from
conventional oligo-dT primers used in cDNA synthesis.
[0535] In the conventional 3'-RACE, the poly(A) tail of mRNA
molecules is exploited as a priming site for PCR amplification and
thus the oligo-dT primer is used as a 3' primer for the
conventional 3'-RACE. In contrast, the ACP of the present invention
uses the poly(A) tail of mRNA as a priming site only for the cDNA
synthesis but not for the subsequent PCR amplification.
[0536] Mouse first-strand cDNAs were prepared under the same
conditions as used in the cDNA synthesis of Example 1 using Oligo
VdT.sub.15-ACP 5' -GCTTGACTACGATACTGTGCGAIIIII TTTTTTTTTTTTTTTV-3'
(SEQ ID NO:57) (V is A, C or G) as a cDNA synthesis primer and
then, directly used as templates for the subsequent PCR
amplification without the purification step for the removal of the
cDNA synthesis primer.
[0537] For the conventional 3'-RACE, the first-strand cDNAs were
synthesized using the following cDNA synthesis primer;
[0538] CDS III/3' 5'-ATTCTAGAGGCCGAGGCGGCCGACATG-(dT).sub.30-VN-3'
(SEQ ID NO:35) (V is A, C or G; and N is A, C, T or G).
[0539] This cDNA synthesis primer, CDS III/3', was used as 3'
primer for subsequent PCR amplification.
[0540] The PCR amplification was conducted in a 50 .mu.l volume
containing 50 ng of the first-strand cDNA, 5 .mu.l of 10.times. PCR
buffer (Promega), 1 .mu.l of a gene-specific 5' primer (10 .mu.M),
1 .mu.l of pre-selected arbitrary 3' primer JYC2 (10 .mu.M) or CDS
III/3' (10 .mu.M), 3 .mu.l of 25 mM MgCl.sub.2, 5 .mu.l of 2 mM
dNTP, 0.5 .mu.l Taq polymerase (5 units/.mu.l; Promega). The PCR
reactions were conducted under the following conditions: 5 min at
94.degree. C. followed by 30 cycles of 94.degree. C. for 1 min,
65.degree. C. for 1 min, and 72.degree. C. for 1 min; followed by a
5 min final extension at 72.degree. C. Amplified products were
analyzed by electrophoresis in a 2% agarose gel followed by
ethidium bromide staining. The resulting PCR products can be also
detected on a denaturing polyacrylamide gel by autoradiography or
non-radioactive detection methods such as silver staining
(Gottschlich et al., 1997; Kociok et al., 1998), the use of
fluoresenscent-labelled oligonucleotides (Bauer et al. 1993; Ito et
al. 1994; Luehrsen et al., 1997; Smith et al., 1997), and the use
of biotinylated primers (Korn et al., 1992; Tagle et al., 1993;
Rosok et al., 1996).
[0541] FIG. 15 shows the results of beta-actin 3'-RACE. The
conventional 3'-RACE (lane 1) was compared with ACP-based 3'-RACE
(lane 2). The conventional 3'-RACE method produced non-specific
products as well as DNA smear background, whereas the ACP-based
3'-RACE produced only a single band, which is the expected size of
348-bp. These results indicate that the ACP-based 3'-RACE can
exclude the background problems such as DNA smear and non-specific
products.
EXAMPLE 6
Method for Rapid Amplification of 5'-End (5'-RACE) and Full-length
cDNAs Using ACP
[0542] The ACP of the subject invention was also used to amplify
the 5'-ends of cDNA fragments. The first-strand cDNAs were
synthesized using Oligo VdT.sub.15-ACP, or Random dN.sub.6-ACP:
[0543] Oligo VdT.sub.15-ACP
5'-GCTTGACTACGATACTGTGCGAIIIIITTTTTTTTTTTTTTTV- -3'(SEQ ID NO:57),
wherein V can be A, C, or G;
[0544] Random dN.sub.6-ACP 5'-GCTTGACTACGATACTGTGCGAIIIIINNNNNN-3'
(SEQ ID NO: 58), wherein N can be A, C, G, or T.
[0545] After the complete synthesis of the first strand cDNA
sequences present in the form of mRNA-cDNA intermediates, cytosine
residues are tailed at the 3 '-end of the first strand cDNA
sequences by the terminal transferase reaction of reverse
transcriptase in the presence of manganese. The 3'-ends of the
first strand cDNAs were extended using the first strand cDNA 3'-end
extending ACP (rG3-ACP, rG2-ACP, or dG3-ACP) and then, directly
used as templates for the subsequent PCR amplification without a
purification step for the removal of the first strand cDNA 3'-end
extending ACP as well as the cDNA synthesis primer.
[0546] The sequences of the first-strand cDNA 3'-end extending ACPs
are:
[0547] rG3-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIIGGr(GGG)-3' (SEQ ID
NO:36);
[0548] rG2-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIIGGr(GG)-dG-3' (SEQ ID
NO:37);
[0549] rG1-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIIGGr(G)-d(GG)-3' (SEQ
ID NO:59); or
[0550] dG3-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIIGGd(GGG)-3' (SEQ ID
NO:38) (wherein r and d represent ribonucleotide and
deoxyribonucleotide, respectively).
[0551] A. First-strand full-length cDNA synthesis
[0552] PROTOCOL A: First-strand cDNA synthesis using the ACP of the
subject invention
[0553] 1. Combine the followings in a sterile 0.2 ml
microcentrifuge tube: 3 .mu.g of total RNA and 2 .mu.l of 10 .mu.M
of Oligo VdT.sub.15-ACP or random dN.sub.6-ACP.
[0554] 2. Add sterile H.sub.2O to a final volume of 10 .mu.l. Mix
contents and spin the tube briefly in a microcentrifuge.
[0555] 3. Incubate the tube in a 65.degree. C. water bath for 15
minutes or use a thermocycler for the same purpose.
[0556] 4. Cool the tube on ice for at least 2 minutes. Spin down
the contents of the tube briefly in a microcentrifuge.
[0557] 5. Add the following reagents to the same reaction tube: 4
.mu.l of 5.times. first-strand buffer (Invitrogen), 1 .mu.l of 0.1M
DTT, 2 .mu.l of BSA (1 mg/ml), 2 .mu.l of dNTP (10 mM each dATP,
dCTP, dGTP, dTTP), 0.4 .mu.l of 100 mM MnCl.sub.2 and 0.5 .mu.l of
RNasin inhibitor (40 units/.mu.l, Promega).
[0558] 6. Mix contents and spin the tube briefly in a
microcentrifuge.
[0559] 7. Incubate the tube at 42.degree. C. for 2 minutes in an
incubator or thermocycler.
[0560] 8. Add 1 .mu.l of SuperScript II reverse transcriptase (200
units/.mu.l; Invitrogen).
[0561] 9. Incubate the tube at 42.degree. C. for 1 hour in an
incubator or thermocycler.
[0562] 10. Add 1 .mu.l of 10 .mu.M first strand cDNA 3'-end
extending ACP (rG3-ACP, rG2-ACP, or dG3-ACP).
[0563] 11. Add 0.3 .mu.l of SuperScript II reverse transcriptase
(200 units/.mu.l; Invitrogen).
[0564] 12. Incubate the tube at 42.degree. C. for 30 minutes in an
incubator or thermocycler.
[0565] 13. Incubate the tube at 70.degree. C. for 15 minutes in an
incubator or thermocycler to terminate first-strand synthesis.
[0566] 14. Place the tube on ice or can be stored at -20.degree.
C.
[0567] PROTOCOL B: First-strand full-length cDNA synthesis by
CapFinder method
[0568] The following primers are used in the CapFinder method
(Clontech):
4 SMART IV .TM. Oligonucleotide (SEQ ID NO:33)
5'-AAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCr(GGG)-3'; and 5' PCR primer
(SEQ ID NO:34) 5'-AAGCAGTGGTATCAACGCAGA- GT-3', and CDS III/3' PCR
primer.
[0569] 1. Combine the followings in a sterile 0.2 ml
microcentrifuge tube: 3 .mu.g of total RNA, 1 .mu.l of 10 .mu.M CDS
III/3' PCR primer (Clontech) and 1 .mu.l of 10 .mu.M SMART IV
Oligonucleotide (Clontech).
[0570] 2. Add sterile H.sub.2O to a final volume of 5 .mu.l. Mix
contents and spin the tube briefly in a microcentrifuge.
[0571] 3. Incubate the tube at 72.degree. C. for 2 minutes.
[0572] 4. Cool the tube on ice for 2 minutes. Spin down the
contents of the tube briefly in a microcentrifuge.
[0573] 5. Add the following reagents to the same reaction tube: 10
.mu.l of the total volume containing 2 .mu.l of 5.times.
first-strand buffer (Clontech), 1 .mu.l of 20 mM DTT, 1 .mu.l of
dNTP (10 mM each dATP, dCTP, dGTP, dTTP) and 1 .mu.l of PowerScript
Reverse Transcriptase (Clontech).
[0574] 6. Mix contents and spin the tube briefly in a
microcentrifuge.
[0575] 7. Incubate the tube at 42.degree. C. for 1 hour
[0576] 8. Place the tube on ice or can be stored at -20.degree.
C.
[0577] B. PCR amplification
[0578] PROTOCOL C: Amnplification of a target 5'-end cDNA fragment
using ACP system or conventional 5'-RACE method
[0579] The present example compares the current CapFinder 5'-RACE
technology and ACP-based 5' RACE method, wherein the current
CapFinder 5'-RACE technology could not exclude the high background
due to residual amount of the primers during the process. In order
to demonstrate if the ACP of the present invention can eliminate
such background problems arising from primers such as the CapFinder
primer, SMART IV Oligonucleotide (Clontech), and cDNA synthesis
primer, CDS III/3' PCR primer (Clontech), used in cDNA synthesis,
both the ACP-based 5'-RACE and the CapFinder 5'-RACE for the
amplification of 5'-ends of mouse JunB and beta-actin cDNAs were
conducted in the same conditions. The mouse JunB mRNA is a
relatively rare transcript in mouse 18.5-day-old placenta RNA,
whereas mouse beta-actin is a relatively abundant.
[0580] 1. Combine the following reagents in a sterile 0.2 ml
microcentrifuge tube: 50 .mu.l of the total volume containing 1
.mu.l of first-strand cDNA prepared from Protocol A or B, 5 .mu.l
of 10.times. PCR buffer (Promega), 5 .mu.l of 25 mM MgCl.sub.2, 5
.mu.l of 2 mM dNTP, 1 .mu.l of 10 .mu.M gene-specific 5'-RACE
primer, 1 .mu.l of 10 .mu.M JYC2 or 5' PCR primer (Clontech), 0.5
.mu.l of Taq Polymerase (5 units/.mu.l; Promega) and 31.5 .mu.l of
sterile dH.sub.2O.
[0581] 2. Mix contents and spin the tube briefly in a
microcentrifuge.
[0582] 3. Conduct PCR reaction under the following conditions: 5
min at 94.degree. C., followed by 30 cycles of 94.degree. C. for 40
seconds, 58.degree. C. for 40 seconds, and 72.degree. C. for 1 min
30 sec; followed by a 5 min final extension at 72.degree. C.
[0583] 4. Analyze the amplified products by electrophoresis in a 2%
agarose gel followed by ethidium bromide staining.
[0584] The resulting PCR products can be also detected on a
denaturing polyacrylamide gel by autoradiography or non-radioactive
detection methods such as silver staining (Gottschlich et al.,
1997; Kociok et al., 1998), the use of fluoresenscent-labelled
oligonucleotides (Bauer et al. 1993; Ito et al. 1994; Luehrsen et
al., 1997; Smith et al., 1997), and the use of biotinylated primers
(Korn et al., 1992; Tagle et al., 1993; Rosok et al., 1996).
[0585] As shown in FIG. 16, the CapFinder methods for mouse JunB
and beta-actin 5' -RACE using the 5' PCR primer (Clontech) and the
gene-specific primer produced high backgrounds such as DNA smear
(lanes 1 and 3) as described by many researchers (Chenchik et al.,
1998; Matz et al., 1999; Schramm et al., 2000), whereas the
ACP-based 5'-RACE of the present invention generated only a single
band which corresponds each to the expected size 155-bp or 319-bp
of mouse JunB (lane 2) or mouse beta-actin (lane 4) 5'-end cDNA
fragment, respectively. These examples illustrate that the ACP can
be used to fundamentally eliminate such background problems arising
from contamination of primers used during cDNA synthesis, without
the purification step for the removal of primers used in the cDNA
synthesis.
[0586] FIG. 17 also shows that the ACP of the subject invention
permits the non-specific products not to be formed, which are
generated by the CapFinder method (lane 1). The first-strand cDNA
was synthesized either by CapFinder method (lane 1) or ACP method
(lanes 2, 3, and 4) and then, directly used as template in the
subsequent PCR amplification for mouse prolactin-like protein PLP-C
alpha 5'-RACE. The PLP-C alpha-specific 5'-RACE primer is: PLP-C
alpha 5'-GAGAGGATAGTTTCAGGGAC-3' (SEQ ID NO:40). The first-strand
cDNA 3'-end extending ACPs comprising either three riboguanines
(rG3-ACP; lane 2), three deoxyriboguanines (dG3-ACP; lane 4), or a
combination of two riboguanines and one deoxyriboguanine (rG2-ACP;
lane 3) at the 3'-end generated 5'-end cDNAs so that a single band
which corresponds to the expected size 506-bp of mouse PLP-C alpha
5'-end cDNA fragment was produced from the ACP-based PCR for PLP-C
alpha 5'-RACE.
[0587] PROTOCOL D: Amplification of 5' enriched cDNA fragments
using ACP
[0588] The first-strand cDNAs are synthesized using Random
dN.sub.6-ACP in Protocol A. The PCR amplification was performed by
hot start PCR method in which the procedure is to set up the
complete reactions without the DNA polymerase and incubate the
tubes in the thermal cycler to complete the initial denaturation
step at >90.degree. C. Then, while holding the tubes at a
temperature above 70.degree. C., the appropriate amount of DNA
polymerase can be pipetted into the reaction.
[0589] 1.Combine the following reagents in a sterile 0.2 ml
microcentrifuge tube: 49.5 .mu.l of the total volume containing 1
.mu.l of first-strand cDNA prepared by Random dN.sub.6-ACP in
Protocol A, 5 .mu.l of 10.times. PCR buffer (Promega), 5 .mu.l of
25 mM MgCl.sub.2, 5 .mu.l of 2 mM dNTP, 1 .mu.l of 10 .mu.M JYC2
(3'primer), 1 .mu.l of 10 .mu.M JYC4 (5'primer) and 31.5 .mu.l
sterile dH.sub.2O.
[0590] 2. Mix contents and spin the tube briefly in a
microcentrifuge.
[0591] 3. Place the tube in the preheated thermal cycler at
94.degree. C.
[0592] 4. Add the 0.5 .mu.l of Taq polymerase (5 units/.mu.l;
Promega) into the reaction, while holding the tube at the
temperature 94.degree. C.
[0593] 5. Conduct PCR reaction under the following conditions: 5
min at 94.degree. C. followed by 30 cycles of 94.degree. C. for 40
seconds, 68.degree. C. for 40 seconds, and 72.degree. C. for 1 min
30 sec; followed by a 5 min final extension at 72.degree. C.
[0594] 6. Analyze the amplified products by electrophoresis in a 2%
agarose gel followed by ethidium bromide staining.
[0595] The resulting PCR products can be also detected on a
denaturing polyacrylamide gel by autoradiography or non-radioactive
detection methods such as silver staining (Gottschlich et al.,
1997; Kociok et al., 1998), the use of fluoresenscent-labelled
oligonucleotides (Bauer et al. 1993; Ito et al. 1994; Luehrsen et
al., 1997; Smith et al., 1997), and the use of biotinylated primers
(Korn et al., 1992; Tagle et al., 1993; Rosok et al., 1996).
[0596] PROTOCOL E: Amplification of full-length enriched cDNAs
using ACP
[0597] The first-strand cDNAs are synthesized using Oligo
VdT.sub.15-ACP in Protocol A. The PCR amplification was performed
by hot start PCR method as in Protocol D.
[0598] 1. Combine the following reagents in a sterile 0.2 ml
microcentrifuge tube: 49.5 .mu.l of the total volume containing 1
.mu.l of first-strand cDNA prepared by Oligo VdT.sub.15-ACP in
Protocol A, 5 .mu.l of 10.times. PCR buffer (Promega), 5 .mu.l of
25 mM MgCl.sub.2, 5 .mu.l of 2 mM dNTP, 1 .mu.l of 10 .mu.M JYC2
(3' primer), 1 .mu.l of 10 .mu.M JYC4 (5' primer) and 31.5 .mu.l of
sterile dH.sub.2O.
[0599] 2. Mix contents and spin the tube briefly in a
microcentrifuge.
[0600] 3. Place the tube in the preheated thermal cycler at
94.degree. C.
[0601] 4. Add the 0.5 .mu.l of Taq polymerase (5 units/.mu.l;
Promega, Madison, U.S.A.) into the reaction, while holding the tube
at the temperature 94.degree. C.
[0602] 5. Conduct PCR reaction under the following conditions: 5
min at 94.degree. C. followed by 30 cycles of 94.degree. C. for 40
seconds, 68.degree. C. for 40 seconds, and 72.degree. C. for 1 min
30 sec; followed by a min final extension at 72.degree. C.
[0603] 6. Analyze the amplified products by electrophoresis in a 2%
agarose gel followed by ethidium bromide staining.
[0604] The resulting PCR products can be also detected on a
denaturing polyacrylamide gel by autoradiography or non-radioactive
detection methods such as silver staining (Gottschlich et al.,
1997; Kociok et al., 1998), the use of fluoresenscent-labelled
oligonucleotides (Bauer et al. 1993; Ito et al. 1994; Luehrsen et
al., 1997; Smith et al., 1997), and the use of biotinylated primers
(Korn et al., 1992; Tagle et al., 1993; Rosok et al., 1996).
[0605] To evaluate the efficiency of the method using ACP in the
amplification of full-length cDNAs, the full-length cDNAs amplified
by either the above procedures of ACP method or the current
CapFinder method were blotted to a Hybond-N membrane
(Amersham/United States Biochemical). The mouse
glyceraldehydes-3-phosphate dehydrogenase (GAPDH) cDNA was labeled
with [alpha-.sup.32P]dCTP using a random labeling kit (Roche
Diagnostics Co, Indianapolis, U.S.A.) and used as a probe.
[0606] As shown in FIG. 18, the GAPDH cDNA probe detected a single
band which corresponds to the expected size 1.3-kb of full-length
GAPDI cDNA. As expected, the signals of the PCR products generated
by the above ACP method (lane 2) were several fold stronger than
the ones by the CapFinder method (lane 1). This example illustrates
that the ACP method of the present invention much more effectively
amplifies full-length cDNAs than the CapFinder method does.
EXAMPLE 7
Genomic Fingerprinting Using ACP-based Arbitrarily Primed PCR
[0607] The ACP of the subject invention has been applied to detect
polymorphisms in mouse. The genomic DNAs of mouse strains C57BL/6J,
CBA, BALB/cJ, NOR, SPRETUS, PANCEVO, and Korean Wild Mouse were
used starting materials. Genomic DNA was prepared from the liver of
mice using the QIAamp Tissue Kit (QIAGEN, Hilden, Germany).
[0608] The arbitrary ACPs used in the subject invention are:
5 ACP101 (SEQ ID NO:64) 5'-GTCTACCAGGCATTCGCTTCATI-
IIIICCGGAGGATC-3'; ACP109 (SEQ ID NO:65)
5'-GTCTACCAGGCATTCGCTTCATIIIIICTGCAGGACG-3'; and ACP116 (SEQ ID
NO:66) 5'-GTCTACCAGGCATTCGCTTCATIIIIICGGAGCATCC-3- '.
[0609] A set of arbitrary ACPs, ACP101 and ACP109 (FIG. 19A), or
ACP101 and ACP116 (FIG. 19B), was used as primers for mouse genomic
fingerprinting. The PCR amplification was performed by hot start
PCR method as described in Example 2. The genomic fingerprinting
using ACP is conducted by two stages of PCR amplifications under
the following conditions:
[0610] amplification reactions are performed under low stringent
conditions by two cycles of the first-stage PCR comprising
annealing, extending and denaturing reaction; the reaction mixture
in the final volume of 49.5 .mu.l containing 50 ng of the genomic
DNA, 5 .mu.l of 10.times. PCR reaction buffer (Promega), 5 .mu.l of
25 mM MgCl.sub.2, 5 .mu.l of dNTP (2 mM each dATP, dCTP, dGTP,
dTTP), each 7 .mu.l of a pair of ACPs (each 10 .mu.M) is pre-heated
at 94.degree. C., while holding the tube containing the reaction
mixture at the 94.degree. C., 0.5 .mu.l of Taq polymerase (5
units/.mu.l; Promega) is added into the reaction mixture; the PCR
reactions are as follows: two cycles of 94.degree. C. for 40 sec,
52.degree. C. for 3 min, and 72.degree. C. for 1 min; followed by
denaturing the amplification product at 94.degree. C; after the
complete reaction of the first-stage PCR, 4 .mu.l of the
pre-selected arbitrary primer JYC4 (10 .mu.M) corresponding to the
5'-end portion of the ACPs are added to the reaction mixture and
then the second stage PCR amplification is conducted as follows: 40
cycles of 94.degree. C. for 40 sec, 68.degree. C. for 40 sec, and
72.degree. C. for 40 sec; followed by a 5 min final extension at
72.degree. C.
[0611] Amplification products were resolved and analyzed by
electrophoresis in a 2.0 agarose gel which was stained with
ethidium bromide and photographed. The resulting PCR products can
be also detected on a denaturing polyacrylamide gel by
autoradiography or non-radioactive detection methods such as silver
staining (Gottschlich et al., 1997; Kociok et al., 1998), the use
of fluoresenscent-labelled oligonucleotides (Bauer et al. 1993; Ito
et al. 1994; Luehrsen et al., 1997; Smith et al., 1997), and the
use of biotinylated primers (Korn et al., 1992; Tagle et al., 1993;
Rosok et al., 1996).
[0612] FIG. 19 shows the results of an experiment in which a pair
of arbitrary ACPs were used to amplify segments of genomic DNA from
a variety of mouse strains. To examine the reproducibility of
genomic fingerprinting, the fingerprinting of each mouse strain was
duplicated using two different sets of ACPs. The ACP -based PCR
amplification produced several DNA segments from each set of
primers and the results were reproducible. The polymorphisms were
apparent between mice stains, indicating that mice stains can be
distinguished through polymorphisms in genomic fingerprintings
generated by ACP-based arbitrarily primed PCR. Thus, the ACP of the
subject invention is useful to detect polymorphisms and construct
genetic maps.
EXAMPLE 8
Multiplex PCR Using ACP-based PCR
[0613] To demonstrate the application of ACP in multiplex PCR, the
portions containing single nucleotide polymorphisms of human
leukocyte adhesion molecule I (ELAM1) and human p53 (TP53) genes
were amplified with either conventional primers or ACP. The process
and results for the multiplex PCR amplification using ACPs are
described herein. DNA template was obtained from human
placenta.
[0614] The conventional primers for exon3 of ELAM1 (155 bp) used in
the Example are:
6 ELAM1N1 5'-TTGCACACTGTTGATTCTAA-3'; and (SEQ ID NO:67) ELAM1C1
5'-TTATTGATGGTCTCTACACA-3'. (SEQ ID NO:68)
[0615] The conventional primers for exon10 of ELAM1 (287 bp) used
in the Example are:
7 ELAM1N2 5'-CCACTGAGTCCAACATTC-3'; and (SEQ ID NO:69) ELAM1C2
5'-CTGAAACACTTCCCACAC-3'. (SEQ ID NO:70)
[0616] The conventional primers for exon4 of TP53 (349 bp) used in
the Example are:
8 P53N1 5'-CCTCTGACTGCTCTTTTCAC-3'; and (SEQ ID NO:71) P53C1
5'-ATTGAAGTCTCATGGAAGCC-3'. (SEQ ID NO:72)
[0617] The conventional primers for exons7-8 of TP53 (750 bp) used
in the Example are:
9 P53N2 5'-TGCTTGCCACAGGTCTC-3'; and (SEQ ID NO:73) P53C2
5'-GCAGTGCTAGGAAAGAGG-3'. (SEQ ID NO:74)
[0618] These conventional primers used in the Example are known as
the primers that generate non-specific products in conventional
mutiplex PCR methods as known in the art.
[0619] The ACPs of the subject invention were applied to these four
conventional primer sets to demonstrate if the ACP can overcome the
problems such as non-specific products resulting from the use of
these conventional primer sets for multiplex PCR.
[0620] The 3'-end portions of the ACPs comprise the sequences of
the above conventional primers as follows and thus the size of ACPs
is 26 bp or 27 bp bigger than that of the conventional primers:
10 ELAM1N1-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIITTGCACACTGTTTGATTCTAA-- 3'; (SEQ ID
NO:75) ELAM1C1-ACP 5'-TCACAGAAGTATGCCAAGCGAII-
IIITTATTGATGGTCTCTACACA-3'; (SEQ ID NO:76) ELAM1N2-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIICCACTGAGTCCAACATTC-3'; (SEQ ID NO:77)
ELAM1C2-ACP 5'-TCACAGAAGTATGCCAAGCGAIIIIICTGAAACACTTCCCACAC-3';
(SEQ ID NO:78) P53N1-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIICC-
TCTGACTGCTCTTTTCAC-3'; (SEQ ID NO:79) P53C1-ACP
5'-TCACAGAAGTATGCCAAGCGAIIIIIATTGAAGTCTCATGGAAGCC-3'; (SEQ ID
NO:80) P53N2-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIITGCTTGCCACAGGTCTC-3'; and (SEQ ID
NO:81) P53C2-ACP 5'-TCACAGAAGTATGCCAAGCGAIIII-
IGCAGTGCTAGGAAAGAGG-3'. (SEQ ID NO:82)
[0621] The 5'-end portion sequences of the ACPs comprise and serve
as pre-selected arbitrary primer sequences only for the
second-stage PCR amplification:
11 JYC3 5'-TCACAGAAGTATGCCAAGCGA-3' and (SEQ ID NO:11) JYC4
5'-GTCTACCAGGCATTCGCTTCAT-3'. (SEQ ID NO:12)
[0622] Multiplex PCR amplifications were conducted by one-stop or
non-stop two-stage PCR amplifications, which is a unique feature of
the present invention. The PCR amplification was performed by hot
start PCR method as described in Example 2.
[0623] PROTOCOL A: One-stop two-stage PCR amplifications
[0624] (A) First-stage PCR Amplification
[0625] The first-stage PCR amplification was conducted by two
cycles of PCR comprising of annealing, extending and denaturing
reaction; the reaction mixture in the final volume of 49.5 .mu.l
containing 50 ng of human genomic DNA, 8 .mu.l of 10.times. PCR
reaction buffer (Promega), 7 .mu.l of 25 mM MgCl.sub.2, 5 .mu.l of
dNTP (2 mM each dATP, dCTP, dGTP, dTTP), each 0.5 .mu.l of each 5'
ACP (10 .mu.M) and 3' ACP (10 .mu.M) set is pre-heated at
94.degree. C., while holding the tube containing the reaction
mixture at the 94.degree. C., 0.5 .mu.l of Taq polymerase (5
units/.mu.l; Promega) is added into the reaction mixture; the PCR
reactions are as follows: two cycles of 94.degree. C. for 40 sec,
60.degree. C. for 40 sec, and 72.degree. C. for 40 sec; followed by
denaturing the amplification product at 94.degree. C.
[0626] (B) Second-stage PCR amplification
[0627] The resultant products generated by the first-stage PCR
amplification using multiple sets of the ACPs were then amplified
by the following second-stage PCR amplification under higher
annealing temperature. After the completion of the first-stage PCR
amplification, each 2 .parallel.l of 10 .mu.M pre-selected
arbitrary primers, JYC3 and JYC4, was added into the reaction
mixture obtained from the first-stage PCR amplification, under
denaturing temperature such as at 94.degree. C. The second
stage-PCR reaction was as follows: 40 cycles of 94.degree. C. for
40 sec, 68.degree. C. for 40 sec, and 72.degree. C. for 1 min;
followed by a 5 min final extension at 72.degree. C.
[0628] The amplified products were analyzed by electrophoresis in a
2% agarose gel and detected by staining with ethidium bromide. The
resulting PCR products can be also detected on a denaturing
polyacrylamide gel by autoradiography or non-radioactive detection
methods such as silver staining (Gottschlich et al., 1997; Kociok
et al., 1998), the use of fluoresenscent-labelled oligonucleotides
(Bauer et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith
et al., 1997), and the use of biotinylated primers (torn et al.,
1992; Tagle et al., 1993; Rosok et al., 1996).
[0629] FIGS. 20 and 21 show the results of experiments in which
three or four sets of primers were used to amplify mutiplex
segments of genomic DNA at one reaction. The conventional primer
sets generated non-specific products as well as specific-target
products from three sets (FIG. 20A) or four sets (FIG. 21A) of
primers. In contrast, the three sets (FIG. 20B) or four sets (FIG.
21B) of ACPs produced only mutiplex target products. Thus, the ACP
of the subject invention can be used for the application of
multiplex PCR.
[0630] PROTOCOL B: Non-stop two-stage PCR amplifications
[0631] Alternatively, the complete sequences of each ACP set,
instead of the pre-selected arbitrary primers such as JYC3 and
JYC4, can be used as primers for the second-stage PCR amplification
at the high stringent conditions. In this case, it is not necessary
to add the pre-selected arbitrary primers to the reaction mixture
at the time of or after the first-stage PCR reaction.
[0632] The process of the non-stop two-stage PCR amplifications is
basically identical to Protocol A, except that the second stage PCR
amplification should immediately follow first stage PCR
amplification without any delay because there is no step of adding
pre-selected arbitrary primers and that the concentration of each
ACP set, each 1 .mu.l of 5' ACP (10 .mu.M) and 3' ACP (10 .mu.M)
set, is added at the first stage PCR amplification.
[0633] The amplified products were analyzed by electrophoresis in a
2% agarose gel and detected by staining with ethidium bromide. The
resulting PCR products can be also detected on a denaturing
polyacrylamide gel by autoradiography or non-radioactive detection
methods such as silver staining (Gottschlich et al., 1997; Kociok
et al., 1998), the use of fluoresenscent-labelled oligonucleotides
(Bauer et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith
et al., 1997), and the use of biotinylated primers (Korn et al.,
1992; Tagle et al., 1993; Rosok et al., 1996).
[0634] Consistent with the results of one-stop two-stage PCR
amplifications (FIG. 21B), non-stop two-stage PCR amplification
also produced only target multiplex specific products (FIG. 21C).
These examples illustrate that ACP permits the products to be free
from the background problems as well as non-specificity arising
from the conventional primers used in multiplex PCR methods as
known in the art.
EXAMPLE 9
Identification of Conserved Homology Segments in Multigene Families
Using ACP
[0635] The ACP of the subject invention was applied to detect and
clone conserved homology segments in multigene families. In the
present example, degenerate primers were designed to detect
homeobox sequences. The homeobox genes are characterized by a
conserved 180-bp nucleotide sequence known as the homeobox, which
encodes a 60-aa DNA binding homeodomain. To isolate homeobox genes
involved in mouse embryo development, total RNA obtained from three
different stages of conceptus development, mouse 4.5-, 11.5-, and
18.5-day-old conceptuses, was used as a starting material.
First-strand cDNAs were prepared under the same conditions as used
in the cDNA synthesis of Example 3, wherein JYC5-T.sub.15-ACP was
used as the first-strand cDNA synthesis primer.
[0636] The following ACPs comprise the degenerate sequences for
homeobox sequence at their 3'-end portions and were used as
degenerate homeobox-specific primers for the first-stage PCR
amplification:
12 JYC2-HD1 (SEQ ID NO:83) 5'-GCTTGACTACGATACTGTGC-
GAIIIIIGTNCRRGTGTGGTT-3'; JYC2-HD2 (SEQ ID NO:84)
5'-GCTTGACTACGATACTGTGCGAIIIIIGTNCRRGTCTGGTT-3'; and JYC2-HD3 (SEQ
ID NO:85) 5'-GCTTGACTACGATACTGTGCGAIIIIIGTNCRRGTTTGGTT-3'.
[0637] The PCR amplification was performed by hot start PCR method
as described in Example 2 and conducted by one-stop or non-stop
two-stage PCR amplifications. The following is an example of the
process of one-stop two-stage PCR amplifications.
[0638] 1. Combine the following reagents in a sterile 0.2 ml
microcentrifuge tube: 49.5 .mu.l of the total volume containing 1
.mu.l of first-strand cDNA (50 ng/.mu.l), 5 .mu.l of 10.times. PCR
buffer (Roche), 5 .mu.l of 2 mM dNTP, 1 .mu.l of one of 10 .mu.M
JYC2-HD1, JYC2-HD2, or JYC2-HD3 (5' primer), 1 .mu.l of 10 .mu.M
JYC5-T.sub.15-ACP (3' primer) and 36.5 .mu.l of sterile
dH.sub.2O.
[0639] 2. Mix contents and spin the tube briefly in a
microcentrifuge.
[0640] 3. Place the tube in the preheated thermal cycler at
94.degree. C.
[0641] 4. Add 0.5 .mu.l of Taq polymerase (5 units/.mu.l; Roche)
into the reaction while holding the tube at the temperature
94.degree. C.
[0642] 5. Conduct PCR reaction under the following conditions: one
cycle of 94.degree. C. for 1 min, 52.degree. C. for 3 min, and
72.degree. C. for 1 min; followed by 40 cycles of 94.degree. C. for
40 sec, 65.degree. C. for 40 sec, and 72.degree. C. for 40 sec; and
followed by a 5 min final extension at 72.degree. C.
[0643] The amplified products were analyzed by electrophoresis in a
2% agarose gel and detected by staining with ethidium bromide. The
resulting PCR products can be also detected on a denaturing
polyacrylamide gel by autoradiography or non-radioactive detection
methods such as silver staining (Gottschlich et al., 1997; Kociok
et al., 1998), the use of fluoresenscent-labelled oligonucleotides
(Bauer et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith
et al., 1997), and the use of biotinylated primers (Korn et al.,
1992; Tagle et al., 1993; Rosok et al., 1996).
[0644] Many differentially expressed bands in a specific stage were
obtained, subcloned into the pGEM-T Easy vector (Promega), and
sequenced. Sequence analysis reveals that some of the clones
contain homeobox sequences. Northern blot or RT-PCR analysis shows
that the clones are identical to the results of the expression
patterns observed by the electrophoresis. These results indicate
that the method using the ACP of the present invention for
isolating conserved homology segments in multigene families
produces only real PCR products. Freedom from false positives,
which is one major bottleneck remaining in the previous PCR-based
techniques for isolating conserved homology segments in multigene
families, allows avoiding the subsequent labor-intensive work
required for the verification of the amplified cDNA fragments.
EXAMPLE 10
Single Nucleotide Polymorphism Genotyping Using ACP-based PCR
[0645] To demonstrate the application of ACP in single nucleotide
polymorphism genotyping, a portion containing a single nucleotide
polymorphism (SNP) of human p53 (TP53) gene was amplified with
either conventional primer or ACP. The process and results for the
SNP genotyping using ACPs are described herein. DNA templates were
obtained from human blood samples which have a SNP in exon 4 of the
TP53 gene. This polymorphism is expressed as an Arg.fwdarw.Pro
substitution at amino acid position 72 by replacing G with C. A 349
nt sequence between nucleotide 11991 and 12339 of the TP53 gene was
amplified from each type of template by a set of the following
primers:
13 P53N (SEQ ID NO:86) 5'-CCTCTGACTGCTCTTTTCAC-3' and P53C-ACP (SEQ
ID NO:87) 5'-TCACAGAAGTATGCCAAGCGAIIIIIATTGAAGTCTCATGGAAGCC-
3'.
[0646] The amplified products containing the SNP between their ends
were used as templates for detecting the SNP using allele-specific
ACPs as follows:
14 P53N1A-ACP (SEQ ID NO:88)
5'-GTCTACCAGCATTCGCTTCATIIIIICCCCGCGTGG-3', P53N1B-ACP (SEQ ID
NO:89) 5'-GTCTACCAGGCATTCGCTTCATIIIIICCCCCCGTGG-3- ', P53N2A-ACP
(SEQ ID NO:90) 5'-GTCTACCAGGCATTCGCTTCATIIIIITCCCCGCGTG-3',
P53N2B-ACP (SEQ ID NO:91) 5'-GTCTACCAGGCATTCGCTTCATIIIIIT-
CCCCCCGTG-3', P53N3A-ACP (SEQ ID NO:92)
5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCCCGCGT-3', P53N3B-ACP (SEQ ID
NO:93) 5'-GTCTACCAGGCATTCGCTITCATIIIII- CTCCCCCCGT-3', P53N4A-ACP
(SEQ ID NO:94) 5'-GTCTACCAGGCATTCGCTTCATIIIIIGCTCCCCGCG-3',
P53N4B-ACP (SEQ ID NO:95) 5'-GTCTACCAGGCATTCGCTTCATIIIIIG-
CTCCCCCCG-3', P53N5A-ACP (SEQ ID NO:96)
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCTCCCCG-3', and P53N5B-ACP (SEQ ID
NO:97) 5'-GTCTACCAGGCATTCGCTTCATIIIIIG- CTCCCCC-3'.
[0647] The polymorphic base is underlined at the 3'-end portion of
each allele-specific ACP and the position of the polymorphic base
is considered an interrogation position. The interrogation position
is placed at several different positions from the 3'-end of
allele-specific ACPs in order to determine the most critical
position in annealing specificity for detecting the SNP.
[0648] The allele-specific ACPs were used as 5' primers. P53C-ACP
and one of P53N1A-ACP, P53N2A-ACP, P53N3A-ACP, P53N4A-ACP and
P53N5A-ACP were used for wild-type A genotyping. P53C-ACP and one
of P53N1B-ACP, P53N2B-ACP, P53N3B-ACP, P53N4B-ACP and P53N5B-ACP
were used for variant-type B genotyping. The 5'-end portion
sequences of the ACPs were served as pre-selected arbitrary primer
sequences for the second-stage PCR amplification:
15 JYC3 5'-TCACAGAAGTATGCCAAGCGA-3' and (SEQ ID NO:11) JYC4
5'-GTCTACCAGGCATTCGCTTCAT-3'. (SEQ ID NO:12)
[0649] (A) First-stage PCR Amplification
[0650] The first-stage PCR amplification was conducted by one cycle
of PCR consisting of annealing, extending and denaturing reaction;
the reaction mixture in a final volume of 49.5 .mu.l containing 1
.mu.l of the amplified target genomic segment containing the SNP in
exon 4 of the TP53 gene, 5 .mu.l of 10.times. PCR reaction buffer
(Promega), 5 .mu.l of 25 mM MgCl.sub.2, 5 .mu.l of dNTP (2 mM each
dATP, dCTP, dGTP, dTTP), and 1 .mu.l of one of allele-specific ACPs
(10 .mu.M) is pre-heated at 94.degree. C., while holding the tube
containing the reaction mixture at the 94.degree. C., 0.5 .mu.l of
Taq polymerase (5 units/.mu.l; Promega) is added into the reaction
mixture; for the allele-specific ACPs having 10 nucleotides at its
3'-end portion, the PCR reactions are as follows: one cycle of
94.degree. C. for 40 sec, 55.degree. C. for 40 sec, and 72.degree.
C. for 40 sec; followed by denaturing the amplification product at
94.degree. C; for the allele-specific ACPs having 8 nucleotides at
its 3'-end portion, the PCR reactions are as follows: one cycle of
94.degree. C. for 40 sec, 50.degree. C. for 40 sec, and 72.degree.
C. for 40 sec; followed by denaturing the amplification product at
94.degree. C. The resultant product is a first DNA strand
complementary to the target genomic segment.
[0651] (B) Second-stage PCR Amplification
[0652] The resultant product generated by the first-stage PCR
amplification was then amplified by the following second-stage PCR
amplification at a higher annealing temperature than the first
annealing temperature. After the completion of the first-stage PCR
amplification, 1 .mu.l of 10 .mu.M pre-selected arbitrary primer,
JYC3, was added into the reaction mixture obtained from the
first-stage PCR amplification, under denaturing temperature such as
at 94.degree. C. The second stage-PCR reaction was performed as
follows: 30 cycles of 94.degree. C. for 40 sec, 68.degree. C. for
40 sec, and 72.degree. C. for 40 sec; followed by a 5 min final
extension at 72.degree. C.
[0653] The amplified products were analyzed by electrophoresis in a
2% agarose gel and detected by staining with ethidium bromide. The
resulting PCR products can be also detected on a denaturing
polyacrylamide gel by autoradiography or non-radioactive detection
methods such as silver staining (Gottschlich et al., 1997; Kociok
et al., 1998), the use of fluoresenscent-labelled oligonucleotides
(Bauer et al. 1993; Ito et al. 1994; Luehrsen et al., 1997; Smith
et al., 1997), and the use of biotinylated primers (Korn et al.,
1992; Tagle et al., 1993; Rosok et al., 1996).
[0654] FIG. 22 shows the results of allele-specific amplification
using ACP. The pair of wild-type A-specific ACPs (P53N2A-ACP and
P53C-ACP) generated a specific target product only from the samples
having homozygous wild-type A (lane 1) or heterozygous genotyping
(lane 3), but not from the samples having homozygous variant-type B
genotyping (lane 5). The pair of variant-type B-specific ACPs
(P53N2B-ACP and P53C-ACP) generated a specific target product only
from the samples having homozygous variant-type B (lane 6) or
heterozygous genotyping (lane 4), but not from the samples having
homozygous wild-type A genotyping (lane 2). These results indicate
that the ACP of the subject invention can be applied as an easy and
economic method for detecting the genotype of SNPs since the use of
fluorescent DNA probe nor post-PCR processing is not required in
this approach. The allele-specific ACPs each having an
interrogation position at its 3'-end portion showed improvement of
annealing specificity. Moreover, when the allele-specific ACP has
an interrogation position at the position 5 from the 3'-end (e.g.,
P53N2A-ACP and P53N2B-ACP), the annealing specificity is most
critically accomplished.
[0655] In order to verify if the position 5 from the actual 3'-end
of the allele-specific ACP is the most appropriate for the
interrogation position, additional six experiments were conducted
using the same process as used in FIG. 22. DNA templates were
obtained from human blood samples which have a SNP. Six short
genomic fragments containing SNPs were amplified using each
different primer set as follows:
[0656] 703N 5'-ATTCTGATGGTGTGGATTGTG-3'(SEQ ID NO:98) and SM703C
5'-TCACAGAAGTATGCCAAGCGAIIIIIRACCCTGGAGTAGACGAAGA-3' (SEQ ID NO:99)
for Beta-2 adrenergic receptor (ADRB2),
[0657] 028N 5'-CCTTCTGTGCTTGATGCTTTT-3'(SEQ ID NO:102) and SM028C
5'-TCACAGAAGTATGCCAAGCGAIIIIICAGGAAGGATGAGCATTTAG-3'(SEQ ID NO:103)
for Chemokine (c-c motif) receptor 5 (CCR5),
[0658] 695N: 5'-AGAAAAACCAGAGGCAGCTT-3'(SEQ ID NO: 106) and SM695C
5'-TCACAGAAGTATGCCAAGCGAIIIIIAGCACAAACCAAAGACACAGT-3' (SEQ ID NO:
107) for Interleukin 13 receptor,
[0659] 679N 5'-CTAGCTGCAAGTGACATCTCT-3'(SEQ ID NO: 110) and SM679C
5'-TCACAGAGTATCCAAGCGIIIIITCAGTAAGAAGCCAGGAGAG-3'(SEQ ID NO: 111)
for Leukocyte adhesion molecule-1 (LAM-1),
[0660] 832N 5'-TTTTGGGTGGAGGCTAACAT-3'(SEQ ID NO: 114) and
[0661] SM832C:
5'-TCACAGAAGTATGCCAGCGAIIIIIAACGATGCAGACACCACCA-3'(SEQ ID NO: 115)
for Tachykinin receptor 3 (TACR3), and
[0662] 880N 5'-CTTCCACCAATACTCTTTTCC-3'(SEQ ID NO:118) and
[0663] SM880C : 5'-TCACAGAAGTATGCCAGCGAIIIII GCATACACACAAGAGGCAGA-3
'(SEQ ID NO: 119) for Interleukin 1, beta (IL1B).
[0664] The amplified products containing the SNP between their ends
were used as templates for detecting the SNPs wherein
allele-specific ACPs were applied as follows:
[0665] SM703 -A 5'-GTCTACCAGGCATTCGCTTCATIIIIIGGTACAGGGC-3'(SEQ ID
NO: 100) and SM703-B
5'-GTCTACCAGGCATTCGCTTCATIIIIIGGTACCGGGC-3'(SEQ ID NO: 101) for
Beta-2 adrenergic receptor (ADRB2),
[0666] SM028-A 5'-GTCTACCAGGCATTCGCTTCATIIIIITCCAAACCAA-3'(SEQ ID
NO:104) and SM028-B 5'-GTCTACCAGGCATTCGCTTCATIIIIITCCAACCCAA-3'(SEQ
ID NO:105) for Chemokine (c-c motif) receptor 5 (CCR5),
[0667] SM695-A 5'-GTCTACCAGGCATTCGCTTCATIIIII CCATTTTAGG-3'(SEQ ID
NO: 108) and SM695-B 5'-GTCTACCAGGCATTCGCTTCATIIIII
CCATTGTAGG-3'(SEQ ID NO: 109) for Interleukin 13 receptor,
[0668] SM679-A 5'-GTCTACCAGGCATTCGCTTCATIIIIICCAGAACTTT-3'(SEQ ID
NO: 112) and SM679-B
5'-GTCTACCAGGCATTCGCTTCATIIIIICCAGACCTTT-3'(SEQ ID NO:113) for
Leukocyte adhesion molecule-1 (LAM-1),
[0669] SM832-A 5'-GTCTACCAGGCATTCGCTTCATIIIIIGACTGGTAAA-3'(SEQ ID
NO: 116) and SM832-B
5'-GTCTACCAGGCATTCGCTTCATIIIIIGACTGATAAA-3'(SEQ ID NO: 117) for
Tachykinin receptor 3 (TACR3), and
[0670] SM880-A 5'-GTCTACCAGGCATTCGCTTCATIIIIIAAAGCCATAA-3'(SEQ ID
NO: 120) and SM880-B
5'-GTCTACCAGGCATTCGCTTCATIIIIIAAAGCTATAA-3'(SEQ ID NO:121) for
Interleukin 1, beta (IL1B).
[0671] FIG. 23 shows the results of allele-specific amplifications
for six additional SNPs each present in different gene such as
Beta-2 adrenergic receptor (ADRB2) (A), Chemokine (c-c motif)
receptor 5 (CCR5) (B), Interleukin 13 receptor (C), Leukocyte
adhesion molecule-1 (LAM-1) (D), Tachykinin receptor 3 (TACR3) (E),
and Interleukin 1, beta (IL1B) (F). Consistant with the results of
FIG. 22, the annealing specificity is critically accomplished when
the allele-specific ACP has an interrogation position at the
position 5 from the 3'-end. The pair of wild-type A-specific ACPs
generated a specific target product only from the samples having
homozygous wild-type A (lane 1) or heterozygous genotyping (lane
3), but not from the samples having homozygous variant-type B
genotyping (lane 5). The pair of variant-type B-specific ACPs
generated a specific target product only from the samples having
homozygous variant-type B (lane 6) or heterozygous genotyping (lane
4), but not from the samples having homozygous wild-type A
genotyping (lane 2).
[0672] Having described a preferred embodiment of the present
invention, it is to be understood that variants and modifications
thereof falling within the spirit of the invention may become
apparent to those skilled in this art, and the scope of this
invention is to be determined by appended claims and their
equivalents.
16TABLE 1 SEQ ID NO Designation Sequence Information 1 ACP1
5'-GTCTACCAGGCATTCGCTTCATIIIIIC- AGGAGTGG-3' 2 ACP2
5'-GTCTACCAGGCATTCGCTTCATIIIIIGGCGACGATS-3' 3 ACP3
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCCATCGACS-3' 4 ACP4
5'-GTCTACCAGGCATTCGCTTCATIIIIIAGATGCCCGW-3' 5 ACP5
5'-GTCTACCAGGCATTCGCTTCATTIIIIIAGGCGATGCS-3' 6 ACP6
5'-GTCTACCAGGCATTCGCTTCATIIIIITCTCCCGGTS-3' 7 ACP7
5'-GTCTACCAGGCATTCGCTTCATIIIIITTGTGGCGGS-3' 8 ACP8
5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCGATGCS-3' 9 ACP9
5'-GTCTACCAGGCATTCGCTTCATIIIIICCTGCGGGTW-3' 10 JYC2
5'-GCTTGACTACGATACTGTGCGA-3' 11 JYC3 5'-TCACAGAAGTATGCCAAGCGA-3' 12
JYC4 5'-GTCTACCAGGCATTCGCTTCAT-3' 13 ACP10
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCCATCGACC-3' 14 ACP11
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCCATCGACG-3' 15 ACP12
5'-GTCTACCAGGCATTCGCTTCATIIIIIAGGCGATGCC-3' 16 ACP13
5'-GTCTACCAGGCATTCGCTTCATIIIIIAGGCGATGCG-3' 17 ACP14
5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCGATGCC-3' 18 ACP15
5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCGATGCG-3' 19 CRP210
5'-GTCTACCAGGCATTCGCTTCATGCCATCGACC-3' 20 ACP16
5'-GTCTACCAGGCATTCGCTTCATIIGCCATCGACC-3' 21 ACP17
5'-GTCTACCAGGCATTCGCTTCATIIIIGCCATCGACC-3' 22 ACP18
5'-GTCTACCAGGCATTCGCTTCATIIIIIIGCCATCGACC-3' 23 ACP19
5'-GTCTACCAGGCATTCGCTTCATHIIIIIIGCCATCGACC-3' 24 dT-JYC3
5'-CACAGAAGTATGCCAAGCGACTCGAGTTTTTTTTTTTTTTT-3' 25 dT-JYC2
5'-GCTTGACTACGATACTGTGCGATTTTTTTTTTTTTTT-3' 26 JYC2-T13C
5'-CTTGACTACGATACTGTGCGATTTTTTTTTTTTTC-3' 27 JYC2-T13G
5'-GCTTGACTACGATACTGTGCGATTTTTTTTTTTTTG-3' 28 JYC2-T13A
5'-GCTTGACTACGATACTGTGCGATTTTTTTTTTTTTA-3' 29 dT.sub.10-JYC2
5'-GCTTGACTACGATACTGTGCGATTTTTTTTTT-3' 30 dT.sub.10-ACP1
5'-GCTTGACTACGATACTGTGCGAIIIIITTTTTTTTTT-3' 31 DEG 2
GCCATCGACCCGTTTCTCTAGCCCCATCTTCATGTGTTTTAATGAGATGATATTAATTCATTACATTCATGGA-
TAATA TGTCCCTGAGTACATTCTAATCTAGATTTAACTTCAAAAAAAAAAAAAAAAA 32 DEG 5
AGGCGATGCGGGCTGTACTCTGGGTGGCTGCCACAGTCTCATGAGAAACCAAGGGCAAAGGACC-
AAGGAAAAGGGTCT CAGGCCCCTAAAGCAGTGGCTTTCAACCATCCTAATGTTGTGACCTTTTA-
ATACAGTTCCTCATGTTGTGTGACCCCC CAACCATAAAATGATTTTTGTTTCTACTTCAAAAAA-
AAAAAAAAAAAAAAAAA 33 SMART IV
5'-AAGCAGTGGTATCAACGCAGAGTGGCCATTACGG- CCr(GGG)-3' 34 5' PCR Primer
5'-AAGCAGTGGTATCAACGCAGAGT-3' 35 CDS III/3'
5'-ATTCTAGAGGCCGAGGCGGCCGACATG-(dT).sub.30VN-3' 36 rG3-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGGr(GGG)-3' 37 rG2-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGGr(GG)d(G)-3' 38 dG3-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGGd(GGG)-3' 39 Oligo dT.sub.18-ACP
5'-GCTTGACTACGATACTGTGCGAIIIIITTTTTTTTTTTTTTTTTT-3' 40 PLP-C.alpha.
5'-GAGAGGATAGTTTCAGGGAC-3' 41 JunB3 5'-CTCCGTGGTACGCCTGCTTTCTC-3'
42 .beta.-actin 1 5'-TCGTCACCCACATAGGAGTC-3' 43 .beta.-actin 2
5'-CTAAGAGGAGGATGGTCGC-3' 44 EsxN7 5'-GCCGGTTGCAGAGCACC-3' 45 EsxC6
5'-GAACCATGTTTCTGAATGCC-3' 46 EsxN7-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCCGGTTGCAGAGCACG-3' 47 EsxC6-ACP
5'-GCTTGACTACGATACTGTGCGAIIIIIGAACCATGTTTCTGAATGCC-3' 48 EsxN1
5'-GAATCTGAAACAACTTTCTA-3' 49 EsxC2 5'-GATGCATGGGACGAGGCACC-3' 50
EsxN1-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIIGAATCTGAAACAACTTTCTA-3' 51
EsxN3 5'-CGCCGCACCCCTGCCCGCA-3' 52 EsxC5 5'-GATGCATGGGACGAGGCA-3'
53 EsxN3-ACP 5'-GTCTACCAGGCATTCGCTTCATIII- IICGCCGCACCCCTGCCCGCA-3'
54 Oligo-dT.sub.15 5'-TTTTTTTTTTTTTTT-3' 55 EsxC2-ACP
5'-GCTTGACTACGATACTGTGCGAIIIIIGATGCATGGGACGAGGCACC-3' 56 EsxC5-ACP
5'-GCTTGACTACGATACTGTGCGAIIIIIGATGCATGGGACGAGGCA-3' 57
OligoVdT.sub.15-ACP
5'-GCTTGACTACGATACTGTGCGAIIIIITTTTTTTTTTTTTTTV-- 3' 58 dN.sub.6-ACP
5'-GCTTGACTACGATACTGTGCGAIIIIINNNNN-3' 59 rG1-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGGr(G)d(GG)-3' 60 JYC5
5'-CTGTGAATGCTGCGACTACGAT-3' 61 JYC5-T.sub.15-ACP
5'-CTGTGAATGCTGCGACTACGATIIIIITTTTTTTTTTTTTTT-3' 62
JYC5-T.sub.15V-ACP 5'-CTGTGAATGCTGCGACTACGATIIIIITTTTTTTTTTTTTTV-3'
63 JYC5-T.sub.15VN-ACP
5'-CTGTGAATGCTGCGACTACGATIIIIITTTTTTTTTTTTTTTVN-3- ' 64 ACP101
5'-GTCTACCAGGCATTCGCTTCATIIIIICCGGAGGATC-3' 65 ACP109
5'-GTCTACCAGGCATFFCGCTTCATIIIIICTGCAGGACG-3' 66 ACP116
5'-GTCTACCAGGCATTCGCTTCATIIIIICGGAGCATCC-3' 67 ELAM1N1
5'-TTGCACACTGTTGATTCTAA-3' 68 ELAM1C1 5'-TTATTGATGGTCTCTACACA-3' 69
ELAM1N2 5'-CCACTGAGTCCAACATTC-3' 70 ELAM1C2
5'-CTGAAACACTTCCCACAC-3' 71 P53N1 5'-CCTCTGACTGCTCTTTTCAC-3' 72
P53C1 5'-ATTGAAGTCTCATGGAAGCC-3' 73 P53N2 5'-TGCTTGCCACAGGTCTC-3'
74 P53C2 5'-GCAGTGCTAGGAAAGAGG-3' 75 ELAM1N1-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIITTGCACACTGTTGATTCTAA-3' 76
ELAM1C1-ACP 5'-TCACAGAAGTATGCCAAGCGAIIIIITTATTGATGGTCTCTACACA-3' 77
ELAM1N2-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIICCACTGAGTCCAACATTC-3' 78
ELAM1C2-ACP 5'-TCACAGAAGTATGCCAAGCGAIIIIICTGAAACACTTCCCACAC-3' 79
P53N1-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIICCTCTGACTGCTCTTTTCAC-3' 80
P53C1-ACP 5'-TCACAGAAGTATGCCAAGCGAIIIIIATTGAAGTCTCATGGAAGCC-3' 81
P53N2-ACP 5'-GTCTACCAGGCATTCGCTTCATIIIIITGCTTGCCACAGGTCTC-3' 82
P53C2-ACP 5'-TCACAGAAGTATGCCAAGCGAIIIIIGCAGTGCTAGGAAAGAGG-3' 83
JYC2-HD1 5'-GCTTGACTACGATACTGTGCGAIIIIIGTNCRRGTGTGGTT-3' 84
JYC2-HD2 5'-GCTTGACTACGATACTGTGCGAIIIIIGTNCRRGTCTGGTT-3' 85
JYC2-HD3 5'-GCTTGACTACGATACTGTGCGAIIIIIGTNCRRGTTTGGTT-3' 86 P53N
5'-CCTCTGACTGCTCTTTTCAC-3' 87 P53C-ACP 5'-TCACAGAAGTATGCCAAGCGAIII-
IIATTGAAGTCTCATGGAAGCC-3' 88 PS3N1A-ACP
5'-GTCTACCAGGCATTCGCTTCATII- IIICCCCGCGTGG-3' 89 PS3N1B-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIICCCCCC- GTGG-3' 90 P53N2A-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIITCCCCGCGTG-3' 91 PS3N2B-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIITCCCCCCGTG-3' 92 PS3N3A-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCCCGCGT-3' 93 P53N3B-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIICTCCCCCCGT-3' 94 P53N4A-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCTCCCCGCG-3' 95 P53N4B-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCTCCCCCCG-3' 96 P53N5A-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIITGCTCCCCG-3' 97 P53NSB-ACP
5'-GTCTACCAGGCATTCGCTTCATIIIIIGCTCCCCC-3' 98 703N
5'-ATTCTGATGGTGTGGATTGTG-3' 99 SM703C 5'-TCACAGAAGTATGCCAAGCGAIIII-
IACCCTGGAGTAGACGAAGA-3' 100 SM703-A
5'-GTCTACCAGGCATTCGCCTTCATIIIII- GGTACAGGGC-3' 101 SM703-B
5'-GTCTACCAGGCATTCGCTTCATIIIIIGGTACCGGGC-- 3' 102 028N
5'-CCTTCTGTGCTTGATGCTTTT-3' 103 SM028C
5'-TCACAGAAGTATGCCAAGCGAIIIIICAGGAAGGATGAGCATTTAG-3' 104 SM028-A
5'-GTCTACCAGGCATTCGCTTCATIIIIITCCAAACCAA-3' 105 SM028-B
5'-GTCTACCAGGCATTCGCTTCATIIIIITCCAACCCAA-3' 106 695N
5'-AGAAAAACCAGAGGCAGCTT-3' 107 SM69SC 5'-TCACAGAAGTATGCCAAGCGAIIII-
IAGCACAAACCAAAGACACAGT-3' 108 SM695-A
5'-GTCTACCAGGCATTCGCTTCATIIII- ICCATTTTAGG-3' 109 SM695-B
5'-GTCTACCAGGCATTCGCTTCATIIIIICCATTGTAGG- -3' 110 679N
5'-CTAGCTGCAAGTGACATCTCT-3' 111 SM679C
5'-TCACAGAGTATCCAAGCGIIIIITCAGTAAGAAGCCAGGAGAG-3' 112 SM679-A
5'-GTCTACCAGGCATTCGCTTCATIIIIICCAGAACTTT-3' 113 SM679-B
5'-GTCTACCAGGCATTCGCTTCATIIIIICCAGACCTTT-3' 114 832N
5'-TTTTGGGTGGAGGCTAACAT-3' 115 SM832C 5'-TCACAGAAGTATGCCAGCGAIIIII-
AACGATGCAGACACCACCA-3' 116 SM832-A
5'-GTCTACCAGGCATTCGCTTCATIIIIIIG- ACTGGTAAA-3' 117 SM832-B
5'-GTCTACCAGGCATTCGCTTCATIIIIIGACTGATAAA-3- ' 118 880N
5'-CTTCCACCAATACTCTTTTCC-3' 119 SM880C
5'-TCACAGAAGTATGCCAGCGAIIIIIGCATACACACAAGAGGCAGA-3' 120 SM880-A
5'-GTCTACCAGGCATTCGCTTCATIIIIIAAAGCCATAA-3' 121 SM880-B
5'-GTCTACCAGGCATTCGCTTCATIIIIIAAAGCTATAA-3' S = G or C W = A or T V
= A, G, or C N = A, G, C, or T I is deoxyinosine r is ribose d is
deoxyribose
[0673]
17TABLE 2 Differentially Expressed cDNA Fragments Cloned by the ACP
of the Present Invention Nomenclature Identity Homology DEG 1
Tropomyosin 2 (beta) Mouse 92% DEG 2 Novel Novel DEG 3 Hypothetical
protein (Tes gene) Mouse 99% DEG 4 Protease-6 Mouse 92% DEG 5 Novel
Novel DEG 6 Cytoebrome c oxidase, subunit Vb Mouse 99% DEG 7
Hydroxylacyl-Coenzyme A dehydrogense Mouse 98% (Hadh) DEG 8
Troponin T2, cardiac (Tnnt2) Mouse 94% DEG 9 RNA binding motif
protein, X Mouse 96% chromosome DEG 10 Peroxiredoxin 6 (Prdx6)
Mouse 89% DEG 11 11 days or 13 days embryo cDNA Mouse 98%
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* * * * *