U.S. patent application number 15/069645 was filed with the patent office on 2019-01-24 for tagged oligonucleotides and their use in nucleic acid amplification methods.
The applicant listed for this patent is GEN-PROBE INCORPORATED. Invention is credited to Michael M. BECKER, Wai-Chung LAM, Kristin W. LIVEZEY.
Application Number | 20190024158 15/069645 |
Document ID | / |
Family ID | 38790699 |
Filed Date | 2019-01-24 |
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United States Patent
Application |
20190024158 |
Kind Code |
A9 |
BECKER; Michael M. ; et
al. |
January 24, 2019 |
TAGGED OLIGONUCLEOTIDES AND THEIR USE IN NUCLEIC ACID AMPLIFICATION
METHODS
Abstract
The present invention provides nucleic acid amplification
systems and methods that desirably reduce or eliminate false
positive amplification signals resulting from contaminating
biological material, e.g., nucleic acid, that may be present in one
or more reagents used in an amplification reaction and/or that may
be present in the environment in which an amplification reaction is
performed. The invention offers the further advantage of requiring
less stringent purification and/or sterility efforts than
conventionally needed in order to ensure that enzymes and other
reagents used in amplification reactions, and the environment in
which an amplification reaction is performed, are free of bacterial
or other nucleic acid contamination that may yield false positive
results.
Inventors: |
BECKER; Michael M.; (San
Diego, CA) ; LIVEZEY; Kristin W.; (Encinitas, CA)
; LAM; Wai-Chung; (Bonsall, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
GEN-PROBE INCORPORATED |
San Diego |
CA |
US |
|
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20160186249 A1 |
June 30, 2016 |
|
|
Family ID: |
38790699 |
Appl. No.: |
15/069645 |
Filed: |
March 14, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14051104 |
Oct 10, 2013 |
9284549 |
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15069645 |
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13612601 |
Sep 12, 2012 |
8580510 |
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14051104 |
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13231848 |
Sep 13, 2011 |
8278052 |
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13612601 |
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12892323 |
Sep 28, 2010 |
8034570 |
|
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13231848 |
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11810834 |
Jun 6, 2007 |
7833716 |
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12892323 |
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60871442 |
Dec 21, 2006 |
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60811581 |
Jun 6, 2006 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 15/1065 20130101;
C12Q 1/6806 20130101; C12Q 1/6895 20130101; C12Q 1/6848 20130101;
C12Q 1/689 20130101; C12Q 1/6848 20130101; C12Q 2525/155
20130101 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68 |
Claims
1. A method for the selective amplification and detection of at
least one target nucleic acid sequence from a nucleic acid sample,
said method comprising the steps of: (a) treating a nucleic acid
sample comprising a target nucleic acid sequence with a tagged
oligonucleotide comprising first and second regions, said first
region comprising a target hybridizing sequence which hybridizes to
a 3'-end of said target nucleic acid sequence and said second
region comprising a tag sequence situated 5' to said target
hybridizing sequence, wherein said second region does not stably
hybridize to a target nucleic acid containing said target nucleic
acid sequence; (b) reducing in said nucleic acid sample the
effective concentration of unhybridized tagged oligonucleotide
having an active form in which a target hybridizing sequence of
said unhybridized tagged oligonucleotide is available for
hybridization to said target nucleic acid sequence; (c) producing
amplification products in an isothermal nucleic acid amplification
reaction using first and second oligonucleotides, wherein said
first oligonucleotide comprises a hybridizing sequence which
hybridizes to a 3'-end of the complement of said target nucleic
acid sequence and said second oligonucleotide comprises a
hybridizing sequence which hybridizes to the complement of said tag
sequence, wherein said second oligonucleotide does stably hybridize
to said target nucleic acid, and wherein each of said amplification
products comprises a base sequence which is substantially identical
or complementary to the base sequence of said target nucleic acid
sequence and further comprises a base sequence which is
substantially identical or complementary to all or a portion of
said tag sequence; and (d) detecting the amplification products
generated in step (c).
2. A method for the selective amplification and detection of at
least one target nucleic acid sequence from a nucleic acid sample,
said method comprising the steps of: (a) treating a nucleic acid
sample comprising a target nucleic acid sequence with a tagged
oligonucleotide comprising first and second regions, said first
region comprising a target hybridizing sequence which hybridizes to
a 3'-end of said target nucleic acid sequence and said second
region comprising a tag sequence situated 5' to said target
hybridizing sequence, wherein said second region does not stably
hybridize to a target nucleic acid containing said target nucleic
acid sequence; (b) reducing in said nucleic acid sample the
effective concentration of unhybridized tagged oligonucleotide
having an active form in which a target hybridizing sequence of
said unhybridized tagged oligonucleotide is available for
hybridization to said target nucleic acid sequence; (c) producing
amplification products in a nucleic acid amplification reaction
using first and second oligonucleotides, wherein said first
oligonucleotide comprises a hybridizing sequence which hybridizes
to a 3'-end of the complement of said target nucleic acid sequence
and said second oligonucleotide comprises a hybridizing sequence
which hybridizes to the complement of said tag sequence, wherein
said second oligonucleotide does stably hybridize to said target
nucleic acid, and wherein each of said amplification products
comprises a base sequence which is substantially identical or
complementary to the base sequence of said target nucleic acid
sequence and further comprises a base sequence which is
substantially identical or complementary to all or a portion of
said tag sequence; and (d) detecting in a real-time detection
reaction the amplification products generated in step (c), wherein
the real-time detection reaction is a continuous reaction that
occurs during the amplification reaction.
3. A detection reaction mixture for identifying a target nucleic
acid in a sample, said reaction mixture comprising: (a) at least
one amplification product; (b) at least one polymerase; and (c) a
detection system comprising at least one labeled nucleobase;
wherein the at least one amplification product is simultaneously
generated and detected by; (i) treating the target nucleic acid
with a tagged oligonucleotide comprising first and second regions,
said first region comprising a target hybridizing sequence which
hybridizes to a 3'-end of said target nucleic acid sequence and
said second region comprising a tag sequence situated 5' to said
target hybridizing sequence, wherein said second region does not
stably hybridize to a target nucleic acid containing said target
nucleic acid sequence target nucleic acid in a sample; (ii) prior
to initiating real-time isothermal nucleic acid amplification,
reducing in the effective concentration of unhybridized tagged
oligonucleotide having an active form in which a target hybridizing
sequence of the unhybridized tagged oligonucleotide is available
for hybridization to the target nucleic acid sequence; and (iii)
simultaneously producing and detecting amplification products from
the 3'-end of the tagged oligonucleotide using the polymerase to
produce a primer extension product comprising a region
complementary to the target nucleic acid sequence.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 14/051,104, filed Oct. 10, 2013, which is a continuation of
U.S. application Ser. No. 13/612,601, filed Sep. 12, 2012, now U.S.
Pat. No. 8,580,510, which is a continuation of U.S. application
Ser. No. 13/231,848, filed Sep. 13, 2011, now U.S. Pat. No.
8,278,052, which is a continuation of U.S. application Ser. No.
12/892,323, filed Sep. 28, 2010, now U.S. Pat. No. 8,034,570, which
is a divisional application of U.S. application Ser. No.
11/810,834, filed Jun. 6, 2007, now U.S. Pat. No. 7,833,716, which
claims the benefit of U.S. Provisional Application No. 60/811,581,
filed Jun. 6, 2006, and U.S. Provisional Application No.
60/871,442, filed Dec. 21, 2006, the contents of each being
incorporated herein by reference in their entirety.
FIELD OF THE INVENTION
[0002] This invention relates to methods, compositions, reaction
mixtures and kits for the selective amplification of multiple
copies of a specific nucleic acid sequence or "target sequence"
which may be present either alone or as a component of a
homogeneous or heterogeneous mixture of nucleic acids. The mixture
of nucleic acids may be that found in a sample taken for diagnostic
testing, screening of blood products, sterility testing,
microbiological detection in food, water, beverage, industrial or
environmental samples, research studies, preparing reagents or
materials for other processes such as cloning, or for other
purposes. The selective amplification of specific nucleic acid
sequences, as described herein, is of particular value in any of a
variety of detection assays for increasing the accuracy and
reliability of such assays while at the same time reducing the
preparation, purification and/or sterilization requirements for
reagents used in the assays and for the environment in which the
assays are performed.
DESCRIPTION OF THE RELATED ART
[0003] The detection and/or quantitation of specific nucleic acid
sequences is an important technique for identifying and classifying
microorganisms, diagnosing infectious diseases, measuring response
to various types of treatment, and the like. Such procedures are
also useful in detecting and quantitating microorganisms in
foodstuffs, water, beverages, industrial and environmental samples,
seed stocks, and other types of material where the presence of
specific microorganisms may need to be monitored.
[0004] Numerous amplification-based methods for the detection and
quantitation of target nucleic acids are well known and established
in the art. The polymerase chain reaction, commonly referred to as
PCR, uses multiple cycles of denaturation, annealing of primer
pairs to opposite strands, and primer extension to exponentially
increase copy numbers of the target sequence (e.g., Mullis et al.,
"Process for Amplifying, Detecting and/or Cloning Nucleic Acid
Sequences," U.S. Pat. No. 4,683,195; Mullis, "Process for
Amplifying Nucleic Acid Sequences," U.S. Pat. No. 4,683,202; Mullis
et al., "Process for Amplifying, Detecting and/or Cloning Nucleic
Acid Sequences," U.S. Pat. No. 4,800,159; Gelfand et al., "Reaction
Mixtures for the Detection of Target Nucleic Acids," U.S. Pat. No.
5,804,375; Mullis et al. (1987) Meth. Enzymol. 155, 335-350; and
Murakawa et al. (1988) DNA 7, 287-295).
[0005] In a variation called RT-PCR, reverse transcriptase (RT) is
used to make a complementary DNA (cDNA) from RNA, and the cDNA is
then amplified by PCR to produce multiple copies of DNA (Gelfand et
al., "Reverse Transcription with Thermostable DNA Polymerases--High
Temperature Reverse Transcription," U.S. Pat. Nos. 5,322,770 and
5,310,652).
[0006] Another well known amplification method is strand
displacement amplification, commonly referred to as SDA, which uses
cycles of annealing pairs of primer sequences to opposite strands
of a target sequence, primer extension in the presence of a dNTP to
produce a duplex hemiphosphorothioated primer extension product,
endonuclease-mediated nicking of a hemimodified restriction
endonuclease recognition site, and polymerase-mediated primer
extension from the 3' end of the nick to displace an existing
strand and produce a strand for the next round of primer annealing,
nicking and strand displacement, resulting in geometric
amplification of product (e.g., Walker, G. et al. (1992), Proc.
Natl. Acad. Sci. USA 89, 392-396; Walker et al., "Nucleic Acid
Target Generation," U.S. Pat. No. 5,270,184; Walker, "Strand
Displacement Amplification," U.S. Pat. No. 5,455,166; and Walker et
al. (1992) Nucleic Acids Research 20, 1691-1696). Thermophilic SDA
(tSDA) uses thermophilic endonucleases and polymerases at higher
temperatures in essentially the same method (European Pat. No. 0
684 315).
[0007] Other amplification methods include rolling circle
amplification (RCA) (e.g., Lizardi, "Rolling Circle Replication
Reporter Systems," U.S. Pat. No. 5,854,033); helicase dependent
amplification (HDA) (e.g., Kong et al., "Helicase Dependent
Amplification Nucleic Acids," U.S. Pat. Appln. Pub. No. US
2004-0058378 A1); and loop-mediated isothermal amplification (LAMP)
(e.g., Notomi et al., "Process for Synthesizing Nucleic Acid," U.S.
Pat. No. 6,410,278).
[0008] Transcription-based amplification methods commonly used in
the art include nucleic acid sequence based amplification, also
referred to as NASBA (e.g., Malek et al., U.S. Pat. No. 5,130,238);
methods which rely on the use of an RNA replicase to amplify the
probe molecule itself, commonly referred to as Q.beta. replicase
(e.g., Lizardi, P. et al. (1988) BioTechnol. 6, 1197-1202);
transcription-based amplification methods (e.g., Kwoh, D. et al.
(1989) Proc. Natl. Acad. Sci. USA 86, 1173-1177) and self-sustained
sequence replication (e.g., Guatelli, J. et al. (1990) Proc. Natl.
Acad. Sci. USA 87, 1874-1878; Landgren (1993) Trends in Genetics 9,
199-202; and HELEN H. LEE et al., NUCLEIC ACID AMPLIFICATION
TECHNOLOGIES (1997)).
[0009] Another transcription-based amplification method is
transcription-mediated amplification, commonly referred to as TMA,
which synthesizes multiple copies of a target nucleic acid sequence
autocatalytically under conditions of substantially constant
temperature, ionic strength, and pH, in which multiple RNA copies
of the target sequence autocatalytically generate additional copies
(e.g., Kacian et al., "Nucleic Acid Sequence Amplification
Methods," U.S. Pat. No. 5,480,784; and Kacian et al., U.S. Pat. No.
5,399,491). TMA is a robust and highly sensitive amplification
system with demonstrated efficacy, which overcomes many of the
problems associated with PCR-based amplification systems. In
particular, temperature cycling is not required.
[0010] Amplification assays are particularly well suited for the
detection of microorganisms in the context of clinical laboratory
testing, bioprocess monitoring, or any other setting in which the
detection of microorganisms in a particular sample type is desired,
by offering high sensitivity and rapid time-to-result relative to
conventional microbiological techniques. In addition, amplification
methods can be used in the detection of the vast number of
microorganisms that are difficult or impossible to culture on
synthetic media. Nevertheless, there are certain limitations
associated with first-generation amplification assays that have
limited their acceptance in certain settings, such as clinical
microbiological laboratories. One inherent problem associated with
the high sensitivity of nucleic acid amplification systems is that
contaminating nucleic acid introduced into the amplification system
(e.g., from one or more reagents used during amplification, from
the technician performing the assay, from the environment in which
the amplification is performed, etc.) can result in false positive
results. For example, even extremely small amounts of nucleic acid
contamination present in reagents and/or enzymes used in an
amplification reaction, or in the environment in which the
amplification reaction is performed, can give rise to a positive
amplification signal despite the fact that the sequence of interest
is not present in the nucleic acid sample being tested. This
requires that significant effort be expended in sample preparation,
purification, sterilization, etc., of the reagents used in
amplification reactions to avoid or minimize false positive
results.
[0011] Accordingly, there remains a need in the art for a robust
nucleic acid amplification system that can selectively amplify one
or more target nucleic acid sequences of interest while reducing or
eliminating false positive results that can arise as a result of
contaminating biological material, such as contaminating nucleic
acid. There also remains a need for amplification systems that have
reduced reagent purification and/or sterility requirements. As
described further herein, the present invention meets these needs
and offers other related advantages.
SUMMARY OF THE INVENTION
[0012] The present invention is directed generally to nucleic acid
amplification methods and reaction mixtures that desirably reduce
or eliminate false positive amplification signals resulting from
contaminating biological material, e.g., nucleic acid, that may be
present in one or more reagents, components or materials that are
used in an amplification reaction or that are present in the
environment in which an amplification reaction is performed. The
invention further offers the advantage of requiring less stringent
purification and/or sterility efforts than conventionally needed in
order to ensure that enzymes and other reagents and components used
in amplification reactions are free of bacterial and other nucleic
acid contamination that may yield false positive results. Such
components or materials include, but are not limited to, water,
buffers, salts, solid supports (e.g., magnetically charged
particles or beads), and receptacles (e.g., glassware or
plasticware). Accordingly, the methods and reaction mixtures of the
invention are useful in detecting and/or quantitating
microorganisms in clinical samples, foodstuffs, water, industrial
and environmental samples, seed stocks, and other types of material
where the presence of microorganisms may need to be detected and/or
monitored. The methods and reaction mixtures of the invention have
particular advantages for the testing raw materials used in the
production of products for the biotech, pharma, cosmetics and
beverage industries, for release testing of final products, and for
sterility screening to test for a class of organisms or total
viable organisms in a material of interest (bacterial, fungal or
both). In the clinical setting, the methods and reaction mixtures
of the invention would be particularly useful for sepsis testing,
especially septicemia, which is caused by pathogenic organisms
and/or their toxins in the bloodstream.
[0013] According to one embodiment of the present invention, there
are provided methods for the selective amplification of at least
one target nucleic acid sequence, such as a DNA sequence or an RNA
sequence, where the method comprises the steps of: (a) treating a
target nucleic acid sequence in a nucleic acid sample, e.g., where
the target nucleic acid is immobilized on a solid support, with a
heterologous tag sequence to produce a tagged target nucleic acid
sequence; (b) reducing in said sample the effective concentration
of heterologous tag sequences which have not formed part of said
tagged target nucleic acid sequence and are in a form capable of
producing a tagged target nucleic acid sequence with said target
nucleic acid sequence; and (c) subjecting said tagged target
nucleic acid sequence to reagents and conditions sufficient for
detectable amplification of the target nucleic acid sequence, where
the subjecting step exposes the nucleic acid sample to a known
contaminating source of the target nucleic acid sequence after step
(b), and where detectable amplification of the target nucleic acid
sequence is substantially limited to amplification of target
nucleic acid sequence contributed by the tagged target nucleic acid
sequence of step (a) and not by the target nucleic acid sequence
contributed by the known contaminating source.
[0014] The methods of the invention are particularly useful where
one or more reagents or components used are produced with a
material known to be a contaminating source of a target nucleic
acid sequence being amplified. In one example, one or more reagents
used in the methods, such as nucleic acid polymerases, are produced
using a microorganism containing the target nucleic acid sequence.
In another example, components used in the methods, such as
reaction vessels, pipette tips and solid supports for binding the
tagged target nucleic acid sequences, may be a known contaminating
source of the target nucleic acid sequence. In addition, the
methods are useful where the environmental conditions in which
amplification is performed include a known contaminating source of
a target nucleic acid sequence, such as the ambient air, operator
or analytical instrumentation.
[0015] In a more particular aspect of this embodiment, the tagged
target nucleic acid sequence is immobilized on a solid support
during step (b).
[0016] In another particular aspect, step (b) comprises diluting or
removing heterologous tag sequences which have not formed part of
the tagged target nucleic acid sequence from the nucleic acid
sample. In an alternative aspect, step (b) comprises inactivating
heterologous tag sequences which have not formed part of said
tagged target nucleic acid sequence to produce an inactivated
heterologous tag sequence. In a related aspect, the method further
comprises removing the inactivated heterologous tag sequence from
said nucleic acid sample during step (b). The heterologous tag
sequence may be inactivated by blocking its ability to complex with
the target nucleic acid sequence, using an enzyme to digest a
component or cleave a site of a complexed portion of the
heterologous tag sequence, chemically altering the heterologous tag
sequence, or altering by other means the ability of the
heterologous tag sequence to complex with the target nucleic acid
sequence in an amplification reaction mixture.
[0017] In another aspect, the heterologous tag sequence is
contained in a tagged oligonucleotide, where the tagged
oligonucleotide comprises first and second regions, the first
region comprising a target hybridizing sequence which hybridizes to
a 3'-end of the target nucleic acid sequence and the second region
comprising a tag sequence situated 5' to the target hybridizing
sequence, and where the tag sequence does not stably hybridize to a
target nucleic acid containing the target nucleic acid
sequence.
[0018] In yet another aspect, the heterologous tag sequence has an
active form during step (a) which permits the heterologous tag
sequence to produce the tagged target nucleic acid sequence, and
where the heterologous tag sequence which has not produced the
tagged target nucleic acid sequence is converted to an inactive
form in step (b) which blocks the heterologous tag sequence from
producing a tagged target nucleic acid sequence during step
(c).
[0019] The target hybridizing sequence, in certain aspects, is a
universal oligonucleotide, such as a universal bacterial or fungal
oligonucleotide.
[0020] Step (c) comprises producing amplification products in a
nucleic acid amplification reaction using first and second
oligonucleotides, the first oligonucleotide comprising a sequence
which hybridizes to a 3'-end of the complement of the target
nucleic acid sequence and the second oligonucleotide comprising a
sequence which hybridizes to a complement of the tag sequence but
which does not stably hybridize to the target nucleic acid
sequence, wherein each of the amplification products comprises a
base sequence which is substantially identical or complementary to
the base sequence of the target nucleic acid sequence and further
comprises a base sequence which is substantially identical or
complementary to all or a portion of the tag sequence.
[0021] Various amplification methods are suitable for use in the
present invention. For example, in one aspect, the amplification
reaction is a PCR reaction. In another aspect, the target nucleic
acid sequence is amplified by a transcription-based amplification
reaction, preferably a TMA reaction, performed under isothermal
conditions.
[0022] The target nucleic acid sequence amplified according to the
methods can be any target nucleic acid sequence of interest, but
will generally be a nucleic acid sequence obtained from a
microorganism. Further, the method can be selective for the
amplification of a target nucleic acid sequence contained in the
nucleic acid of a single strain or species of microorganisms or in
multiple species of microorganisms. Alternatively, the method can
be selective for the amplification of multiple target nucleic acid
sequences contained in the nucleic acid of multiple species of
microorganisms, where, for example, the target hybridizing sequence
of a tagged oligonucleotide hybridizes to a target region present
in each of the multiple target nucleic acid sequences in step
(a).
[0023] For example, in a particular aspect, the method is selective
for the amplification of a target nucleic acid sequence contained
in each of a plurality of target nucleic acids, and wherein the
heterologous tag sequence produces a tagged target nucleic acid
sequence with the target nucleic acid sequence of each of the
plurality of target nucleic acids present in the nucleic acid
sample in step (a). In a more particular aspect, the target nucleic
acid sequence contained in each of the plurality of target nucleic
acids is the same nucleic acid sequence.
[0024] In another particular aspect, the method is selective for
the amplification of multiple bacterial or fungal target nucleic
acid sequences, e.g., wherein the multiple bacterial or fungal
target nucleic acid sequences are ribosomal nucleic acid
sequences.
[0025] In another particular aspect, the method is selective for
the amplification of target nucleic acid sequences obtained from
members of a group of bacterial species including Staphylococci
spp. (e.g., Staphylococcus aureus, Staphylococcus epidermis and
Staphylococcus haemolyticus), Streptococci spp. (e.g.,
Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus
agalactiae, Streptococcus mitis, Viridans streptococci and
beta-hemolytic streptococci), Enterococcus spp. (e.g., Enterococcus
faecium and Enterococcus faecalis), Escherichia spp. (e.g.,
Escherichia coli), Klebsiella spp. (e.g., Klebsiella pneumoniae and
Klebsiella oxytoca), Pseudomonas spp. (e.g., Pseudomonas
aeruginosa), Enterobacter spp. (e.g., Enterobacter cloacae and
Enterobacter aerogenes), Proteus spp. (e.g., Proteus mirabilis),
Bacterioides spp., Clostridium spp., Serratia spp. (e.g., Serratia
marcescens), Acinetobacter spp. (e.g., Acinetobacter baumannii) and
Stenotrophomonas spp. (e.g., Stenotrophomonas maltophilia). At
least a portion of these microorganisms would be appropriate for
detection in a sepsis test.
[0026] In another aspect, the method is selective for the
amplification of target nucleic acid sequences obtained from
members of a group of fungal species including Candida spp. (e.g.,
Candida albicans, Candida tropicalis, Candida glabrata, Candida
parapsilosis, Candida lusitaniae, Candida krusei, Candida
zeylanoides, Candida guilliermondi, Candida pseudotropicalis and
Candida famata), Histoplama capsulatum, Cryptococcus spp. (e.g.,
Cryptococcus neoformans, Cryptococcus albidus and Cryptococcus
laurentii) Coccidioides spp. (e.g., Coccidioides immitis),
Trichosporon spp. (e.g., Trichosporon cutaneum), Malassezia spp.
(e.g., Malassezia furfur), Rhodotorula spp., Nocardia spp. (e.g.,
Nocardia asteroides), Fusarium spp. and Aspergillus spp. (e.g.,
Aspergillus fumigatus). At least a portion of these microorganisms
would be appropriate for detection in a sepsis test.
[0027] In yet another aspect, at least a portion of a nucleic acid
sample used in the methods is obtained from a clinical, water,
industrial, environmental, seed, beverage or food source.
[0028] The methods are particularly well suited, in certain
aspects, for use in sterility testing or diagnostic testing for
sepsis.
[0029] According to another embodiment of the invention, there is
provided a method for the selective amplification of at least one
target nucleic acid sequence from a nucleic acid sample, the method
comprising the steps of: (a) treating a nucleic acid sample
comprising a target nucleic acid sequence with a tagged
oligonucleotide comprising first and second regions, the first
region comprising a target hybridizing sequence which hybridizes to
a 3'-end of the target nucleic acid sequence and the second region
comprising a tag sequence situated 5' to the target hybridizing
sequence, where the second region does not stably hybridize to a
target nucleic acid containing the target nucleic acid sequence;
(b) reducing in said nucleic acid sample the effective
concentration of unhybridized tagged oligonucleotide having an
active form in which a target hybridizing sequence of said
unhybridized tagged oligonucleotide is available for hybridization
to said target nucleic acid sequence; and (c) producing
amplification products in a nucleic acid amplification reaction
using first and second oligonucleotides, where the first
oligonucleotide comprises a hybridizing sequence which hybridizes
to a 3'-end of the complement of the target nucleic acid sequence
and the second oligonucleotide comprises a hybridizing sequence
which hybridizes to the complement of the tag sequence, where the
second oligonucleotide does stably hybridize to the target nucleic
acid, and where each of the amplification products comprises a base
sequence which is substantially identical or complementary to the
base sequence of the target nucleic acid sequence and further
comprises a base sequence which is substantially identical or
complementary to all or a portion of the tag sequence.
[0030] In one aspect of the above methods, at least one target
nucleic acid sequence is immobilized on a solid support during step
(b). In another aspect, step (b) does not include the use of an
enzyme having a nuclease activity.
[0031] The effective concentration of unhybridized tagged
oligonucleotide in an active form prior to amplification is
preferably reduced by diluting the nucleic acid sample or by
inactivating and/or removing the unhybridized tagged
oligonucleotide. In one aspect, step (b) comprises inactivating
unhybridized tagged oligonucleotide so that the unhybridized tagged
oligonucleotide does not stably hybridize to the target nucleic
acid sequence during step (c). In one example of inactivation, a
tagged oligonucleotide has an active form during step (a) which
permits the target hybridizing sequence to hybridize to the target
nucleic acid sequence, and where unhybridized tagged
oligonucleotide is converted to an inactive form in step (b) which
blocks or prevents the tagged oligonucleotide from hybridizing to
the target nucleic acid sequence during step (c). The tagged
oligonucleotide may be inactivated by blocking the target
hybridizing sequence from hybridizing to the target nucleic acid
sequence, using an enzyme to digest a component or cleave a site of
a duplex formed between the target hybridizing sequence and the
target nucleic acid sequence, chemically altering the target
hybridizing sequence, or altering by other means the ability of the
tagged oligonucleotide to hybridize to the target nucleic acid
sequence in an amplification reaction mixture.
[0032] In a related embodiment, the conditions of steps (b) and (c)
are less stringent than the conditions of step (a). In another
related embodiment, the temperature of the nucleic acid sample is
lowered between steps (a) and (b).
[0033] In another example where step (b) comprises inactivating
unhybridized tagged oligonucleotide, unhybridized tagged
oligonucleotide from step (a) is converted from a single-stranded
form to a duplexed form in step (b). The duplexed form may be a
hairpin tag molecule comprising a tag closing sequence joined to a
5'-end of the tagged oligonucleotide, where the tag closing
sequence hybridizes to the target hybridizing sequence under the
conditions of step (b), thereby blocking hybridization of
unhybridized tagged oligonucleotide from step (a) to the target
nucleic acid sequence in steps (b) and (c). In another aspect, the
tag closing sequence is joined to the tagged oligonucleotide by a
non-nucleotide linker For example, a 5'-end of the tag closing
sequence may be joined to a 5'-end of the tagged
oligonucleotide.
[0034] The tagged oligonucleotide can also further comprise a third
region containing a promoter for an RNA polymerase, the third
region being situated 5' to the second region.
[0035] In another aspect, the tag closing sequence is modified to
prevent the initiation of DNA synthesis therefrom.
[0036] According to another aspect, a 3'-terminal base of the
target hybridizing sequence is hybridized to a 5'-terminal base of
the tag closing sequence. In another aspect, a 3'-end of the tag
closing sequence is joined to a 5'-end of the tagged
oligonucleotide.
[0037] In still another aspect, the target hybridizing sequence is
hybridized to a tag closing oligonucleotide in step (b), the tagged
oligonucleotide and the tag closing oligonucleotide being distinct
molecules. The tag closing oligonucleotide may be modified, if
desired, to prevent the initiation of DNA synthesis therefrom.
[0038] Further, in certain aspects, a 3'-terminal base of the
target hybridizing sequence is hybridized to a 5'-terminal base of
the tag closing oligonucleotide.
[0039] In certain other aspects, the tagged oligonucleotide and the
tag closing oligonucleotide are both present in the nucleic acid
sample during step (a), and where the target hybridizing sequence
favors hybridization to the target nucleic acid sequence over the
tag closing oligonucleotide in step (a).
[0040] As noted above, the methods of the invention can employ any
of a variety of amplification techniques. In certain instances it
may be preferred that an isothermal amplification reaction is used,
such as a transcription-based amplification reaction, preferably
TMA or real-time TMA.
[0041] In a particular aspect, the first oligonucleotide comprises
a promoter for an RNA polymerase which is situated 5' to the
hybridizing sequence. In another aspect, the second oligonucleotide
comprises a promoter for an RNA polymerase which is situated 5' to
the hybridizing sequence, and where the tagged oligonucleotide
further comprises a promoter for an RNA polymerase which is
situated 5' to the second region.
[0042] The target nucleic acid sequence amplified according to the
methods can be any target nucleic acid sequence of interest, but
will generally be a nucleic acid sequence obtained from a
microorganism. Further, the method can be selective for the
amplification of a target nucleic acid sequence contained in the
nucleic acid of a single strain or species of microorganisms or in
multiple species of microorganisms. Alternatively, the method can
be selective for the amplification of multiple target nucleic acid
sequences contained in the nucleic acid of multiple species of
microorganisms, where, for example, the target hybridizing sequence
of a tagged oligonucleotide hybridizes to a target region present
in each of the multiple target nucleic acid sequences in step
(a).
[0043] In another aspect, the method is selective for the
amplification of a target nucleic acid sequence contained in each
of a plurality of target nucleic acids, and wherein the target
hybridizing sequence hybridizes to a 3'-end of the target nucleic
acid sequence of each of the plurality of target nucleic acids
present in the nucleic acid sample in step (a). In another aspect,
the target nucleic acid sequence contained in each of said
plurality of target nucleic acids is the same nucleic acid
sequence.
[0044] In a particular embodiment, the method is selective for the
amplification of multiple bacterial or fungal target nucleic acid
sequences, e.g., wherein the multiple bacterial or fungal target
nucleic acid sequences are ribosomal nucleic acid sequences.
[0045] In a more particular embodiment, the method is selective for
the amplification of target nucleic acid sequences obtained from
members of a group of bacterial species including Staphylococci
spp. (e.g., Staphylococcus aureus, Staphylococcus epidermis and
Staphylococcus haemolyticus), Streptococci spp. (e.g.,
Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus
agalactiae, Streptococcus mitis, Viridans streptococci and
beta-hemolytic streptococci), Enterococcus spp. (e.g., Enterococcus
faecium and Enterococcus faecalis), Escherichia spp. (e.g.,
Escherichia coli), Klebsiella spp. (e.g., Klebsiella pneumoniae and
Klebsiella oxytoca), Pseudomonas spp. (e.g., Pseudomonas
aeruginosa), Enterobacter spp. (e.g., Enterobacter cloacae and
Enterobacter aerogenes), Proteus spp. (e.g., Proteus mirabilis),
Bacterioides spp., Clostridium spp., Serratia spp. (e.g., Serratia
marcescens), Acinetobacter spp. (e.g., Acinetobacter baumannii) and
Stenotrophomonas spp. (e.g., Stenotrophomonas maltophilia). At
least a portion of these microorganisms would be appropriate for
detection in a sepsis test.
[0046] In another particular embodiment, the method is selective
for the amplification of target nucleic acid sequences obtained
from members of a group of fungal species including Candida spp.
(e.g., Candida albicans, Candida tropicalis, Candida glabrata,
Candida parapsilosis, Candida lusitaniae, Candida krusei, Candida
zeylanoides, Candida guilliermondi, Candida pseudotropicalis and
Candida famata), Histoplama capsulatum, Cryptococcus spp. (e.g.,
Cryptococcus neoformans, Cryptococcus albidus and Cryptococcus
laurentii) Coccidioides spp. (e.g., Coccidioides immitis),
Trichosporon spp. (e.g., Trichosporon cutaneum), Malassezia spp.
(e.g., Malassezia furfur), Rhodotorula spp., Nocardia spp. (e.g.,
Nocardia asteroides), Fusarium spp. and Aspergillus spp. (e.g.,
Aspergillus fumigatus). At least a portion of these microorganisms
would be appropriate for detection in a sepsis test.
[0047] In certain aspects, the target hybridizing sequence
hybridizes to a 3'-end of each of multiple target nucleic acid
sequences present in the nucleic acid sample in step (a). Further,
the first oligonucleotide hybridizes to a 3'-end of the complement
of each of the multiple target nucleic acid sequences present in
the nucleic acid sample in step (c).
[0048] The method can also comprise a plurality of first
oligonucleotides, each of the plurality of first oligonucleotides
hybridizing to a 3'-end of the complement of at least one but less
than all of the multiple target nucleic acid sequences present in
the nucleic acid sample in step (c).
[0049] The tagged oligonucleotide, in a particular embodiment of
the invention, is a universal bacterial oligonucleotide or a
universal fungal oligonucleotide. Such tagged oligonucleotides are
particularly well suited to methods for sterility testing, such as
methods for analyzing bioprocess materials or which are diagnostic
for sepsis.
[0050] In a more particular aspect, the target hybridizing sequence
hybridizes to a 3'-end of the target nucleic acid of each of the
plurality of target nucleic acids present in the nucleic acid
sample in step (a), the plurality of target nucleic acids belonging
to a class of microorganisms selected from the group consisting of
Eubacteria, Gram-positive bacteria, Gram-negative bacteria and
fungi. In another aspect, each of plurality of target nucleic acids
is a ribosomal nucleic acid.
[0051] In another aspect of the invention, the multiple target
nucleic acid sequences include members belonging to a class of
bacterial microorganisms selected from the group consisting of
Staphylococci spp. (e.g., Staphylococcus aureus, Staphylococcus
epidermis and Staphylococcus haemolyticus), Streptococci spp.
(e.g., Streptococcus pneumoniae, Streptococcus pyogenes,
Streptococcus agalactiae, Streptococcus mitis, Viridans
streptococci and beta-hemolytic streptococci), Enterococcus spp.
(e.g., Enterococcus faecium and Enterococcus faecalis), Escherichia
spp. (e.g., Escherichia coli), Klebsiella spp. (e.g., Klebsiella
pneumoniae and Klebsiella oxytoca), Pseudomonas spp. (e.g.,
Pseudomonas aeruginosa), Enterobacter spp. (e.g., Enterobacter
cloacae and Enterobacter aerogenes), Proteus spp. (e.g., Proteus
mirabilis), Bacterioides spp., Clostridium spp., Serratia spp.
(e.g., Serratia marcescens), Acinetobacter spp. (e.g.,
Acinetobacter baumannii) and Stenotrophomonas spp. (e.g.,
Stenotrophomonas maltophilia). At least a portion of these
microorganisms would be appropriate for detection in a sepsis
test.
[0052] In a further aspect of the invention, the multiple target
nucleic acid sequences include members belonging to a class of
fungal microorganisms selected from the group consisting of Candida
spp. (e.g., Candida albicans, Candida tropicalis, Candida glabrata,
Candida parapsilosis, Candida lusitaniae, Candida krusei, Candida
zeylanoides, Candida guilliennondi, Candida pseudotropicalis and
Candida famata), Histoplama capsulatum, Cryptococcus spp. (e.g.,
Cryptococcus neoformans, Cryptococcus albidus and Cryptococcus
laurentii) Coccidioides spp. (e.g., Coccidioides immitis),
Trichosporon spp. (e.g., Trichosporon cutaneum), Malassezia spp.
(e.g., Malassezia furfur), Rhodotorula spp., Nocardia spp. (e.g.,
Nocardia asteroides), Fusarium spp. and Aspergillus spp. (e.g.,
Aspergillus fumigatus). At least a portion of these microorganisms
would be appropriate for detection in a sepsis test.
[0053] The nucleic acid sample is often exposed to a known
contaminating source of the target nucleic acid sequence after step
(b), and, accordingly, the described methods provide that the
production of amplification products is substantially limited to
amplification of target nucleic acid sequence contributed by the
nucleic acid sample and not by the contaminating source of the
target nucleic acid sequence. For example, one or more reagents or
components used in the amplification reaction is a known
contaminating source of the target nucleic acid sequence.
Alternatively, or in addition, one or more reagents are produced
with a material known to be a contaminating source of the target
nucleic acid sequence, such as nucleic acid polymerases produced
using microorganisms known to contain the target nucleic acid
sequence. Further, the environmental conditions in which the method
is performed may include a known contaminating source of the target
nucleic acid sequence. In a particular aspect, at least a portion
of said nucleic acid is obtained from a clinical, water,
industrial, environmental, seed, beverage or food source.
[0054] According to another embodiment of the present invention,
the target nucleic acid sequence is an RNA target sequence, and
step (c) comprises: extending the tagged oligonucleotide hybridized
to the target nucleic acid sequence in a primer extension reaction
with a DNA polymerase to produce a first primer extension product
comprising a region complementary to the target nucleic acid
sequence; separating the first primer extension product from the
target nucleic acid using an enzyme which selectively degrades that
portion of the target nucleic acid hybridized to the first primer
extension product; treating the first primer extension product with
the first oligonucleotide, the first oligonucleotide being a
promoter oligonucleotide comprising first and second regions, the
first region comprising a hybridizing sequence which hybridizes to
a region of the first primer extension product that is
complementary to a 5'-end of the target nucleic acid sequence to
form a promoter oligonucleotide:first primer extension product
hybrid, and the second region comprising a promoter for an RNA
polymerase which is situated 5' to the first region; transcribing
from the promoter oligonucleotide:first primer extension product
hybrid multiple copies of a first RNA product complementary to at
least a portion of the first primer extension product using an RNA
polymerase which recognizes the promoter and initiates
transcription therefrom, where the base sequence of the first RNA
product is substantially identical to the base sequence of the
target nucleic acid sequence and the complement of the tag
sequence; treating the first RNA product with the second
oligonucleotide, the second oligonucleotide being a priming
oligonucleotide which hybridizes to the complement of the tag
sequence to form a priming oligonucleotide:first RNA product hybrid
such that a primer extension reaction can be initiated from the
priming oligonucleotide; extending the priming oligonucleotide in a
primer extension reaction with a DNA polymerase to produce a second
primer extension product complementary to the first RNA product,
the second primer extension product having a 3'-end which is
complementary to a 5'-end of the first RNA product; separating the
second primer extension product from the first RNA product using an
enzyme which selectively degrades said first RNA product; treating
the second primer extension product with the promoter
oligonucleotide to form a promoter oligonucleotide:second primer
extension product hybrid; extending a 3'-end of the second primer
extension product in the promoter oligonucleotide:second primer
extension product hybrid to add a sequence complementary to the
second region of the promoter oligonucleotide; and transcribing
from the promoter oligonucleotide:second primer extension product
hybrid multiple copies of a second RNA product complementary to the
second primer extension product using the RNA polymerase, wherein
the base sequence of the second RNA product is substantially
identical to the base sequence of the target nucleic acid sequence
and the complement of the tag sequence.
[0055] In another aspect of this embodiment of the invention, step
(a) further comprises treating the nucleic acid sample with a
binding molecule which binds to the target nucleic acid adjacent to
or near a 5'-end of the target nucleic acid sequence, and where the
first primer extension product has a 3'-end which is determined by
the binding molecule and which is complementary to the 5'-end of
the target nucleic acid sequence.
[0056] In another aspect, step (c) of the above embodiment further
comprises extending a 3'-end of the first primer extension product
in the promoter oligonucleotide:first primer extension product
hybrid to add a sequence complementary to the promoter. In yet
another aspect, the promoter oligonucleotide is modified to prevent
the initiation of DNA synthesis therefrom.
[0057] The promoter oligonucleotide hybridized to the first primer
extension product is extended with a DNA polymerase to produce a
primer extension product complementary to the first primer
extension product; and the promoter oligonucleotide hybridized to
said second primer extension product is extended with a DNA
polymerase to produce a primer extension product complementary to
the second primer extension product.
[0058] The separating steps of the described methods may be
performed with a ribonuclease activity provided by the DNA
polymerase. Alternatively, the separating steps are performed with
a ribonuclease activity provided by an enzyme other than said DNA
polymerase.
[0059] According to another embodiment of the present invention,
the target nucleic acid sequence is an RNA target sequence, and
step (c) comprises: extending the tagged oligonucleotide hybridized
to the target nucleic acid sequence in a primer extension reaction
with a DNA polymerase to produce a first primer extension product
comprising a region complementary to the target nucleic acid
sequence, where the tagged oligonucleotide further comprises a
third region situated 5' to the second region, the third region
comprising a promoter for an RNA polymerase; separating the first
primer extension product from the target nucleic acid using an
enzyme which selectively degrades that portion of the target
nucleic acid hybridized to the first primer extension product;
treating the first primer extension product with the first
oligonucleotide, the first oligonucleotide being a priming
oligonucleotide which hybridizes to a region of the first primer
extension product that is complementary to a 5'-end of the target
nucleic acid sequence to form a priming oligonucleotide:first
primer extension product hybrid such that a primer extension
reaction can be initiated from the priming oligonucleotide;
extending the priming oligonucleotide in a primer extension
reaction with a DNA polymerase to produce a second primer extension
product complementary to the first primer extension product; and
using the second primer extension product as a template to
transcribe multiple copies of a first RNA product complementary to
at least a portion of the second primer extension product using an
RNA polymerase which recognizes the promoter and initiates
transcription therefrom, where the base sequence of the first RNA
product is substantially identical to the base sequence of the tag
sequence and the complement of the target nucleic acid
sequence.
[0060] In another aspect of this embodiment, step (c) further
comprises: treating the first RNA product with the priming
oligonucleotide to form a priming oligonucleotide:first RNA product
hybrid such that a primer extension reaction can be initiated from
the priming oligonucleotide; extending the priming oligonucleotide
in a primer extension reaction with a DNA polymerase to produce a
third primer extension product complementary to the first RNA
product, the third primer extension product having a 3'-end which
is complementary to a 5'-end of the first RNA product; separating
the third primer extension product from the first RNA product using
an enzyme which selectively degrades the first RNA product;
treating the third primer extension product with the second
oligonucleotide, the second oligonucleotide being a promoter
oligonucleotide comprising first and second regions, the first
region comprising a hybridizing sequence which hybridizes to the
complement of the tag sequence to form a promoter
oligonucleotide:third primer extension product hybrid such that a
primer extension reaction can be initiated from the promoter
oligonucleotide, and the second region comprising a promoter for an
RNA polymerase which is situated 5' to the first region; extending
the promoter oligonucleotide in a primer extension reaction with
the DNA polymerase to produce a fourth primer extension product
complementary to the third primer extension product; extending the
third primer extension product to add a sequence complementary to
the promoter; transcribing from the promoter oligonucleotide:third
primer extension product hybrid multiple copies of a second RNA
product complementary to the third primer extension product using
an RNA polymerase which recognizes the promoter and initiates
transcription therefrom, where the base sequence of the second RNA
product is substantially identical to the base sequence of the tag
sequence and the complement of the target nucleic acid
sequence.
[0061] In another aspect of this embodiment, the separating steps
are performed with a ribonuclease activity provided by the DNA
polymerase. Alternatively, the separating steps are performed with
a ribonuclease activity provided by an enzyme other than the DNA
polymerase.
[0062] According to another embodiment of the present invention,
the target nucleic acid sequence is a DNA target sequence, and step
(c) comprises: extending the tagged oligonucleotide hybridized to
the target nucleic acid sequence in a primer extension reaction
with a DNA polymerase to produce a first primer extension product
comprising a region complementary to the target nucleic acid
sequence; treating the first primer extension product with the
first oligonucleotide, the first oligonucleotide being a promoter
oligonucleotide comprising first and second regions, the first
region comprising a hybridizing sequence which hybridizes to a
region of the first primer extension product that is complementary
to a 5'-end of the target nucleic acid sequence to form a promoter
oligonucleotide:first primer extension product hybrid, and the
second region being a promoter for an RNA polymerase which is
situated 5' to the first region; transcribing from the promoter
oligonucleotide:first primer extension product hybrid multiple
copies of a first RNA product complementary to at least a portion
of the first primer extension product using an RNA polymerase which
recognizes the promoter and initiates transcription therefrom,
where the base sequence of the first RNA product is substantially
identical to the base sequence of the target nucleic acid sequence
and the complement of the tag sequence; treating the first RNA
product with the second oligonucleotide, the second oligonucleotide
being a priming oligonucleotide which hybridizes to the complement
of the tag sequence to form a priming oligonucleotide:first RNA
product hybrid such that a primer extension reaction can be
initiated from the priming oligonucleotide; extending the priming
oligonucleotide in a primer extension reaction with a DNA
polymerase to give a second primer extension product comprising the
complement of the first RNA product, the second primer extension
product having a 3'-end which is complementary to a 5'-end of the
first RNA product; separating the second primer extension product
from the first RNA product using an enzyme which selectively
degrades the first RNA product; treating the second primer
extension product with the promoter oligonucleotide to form a
promoter oligonucleotide:second primer extension product hybrid;
extending a 3'-end of the second primer extension product in the
promoter oligonucleotide:second primer extension product hybrid to
add a sequence complementary to the promoter; and transcribing from
the promoter oligonucleotide:second primer extension product hybrid
multiple copies of a second RNA product complementary to the second
primer extension product using the RNA polymerase, where the base
sequence of the second RNA product is substantially identical to
the base sequence of the target nucleic acid sequence and the
complement of the tag sequence.
[0063] In one aspect of this embodiment, the promoter
oligonucleotide is modified to prevent the initiation of DNA
synthesis therefrom.
[0064] In another aspect, step (a) further comprises: treating the
nucleic acid sample with a displacer oligonucleotide which
hybridizes to the target nucleic acid upstream from the tagged
oligonucleotide such that a primer extension reaction can be
initiated from the displacer oligonucleotide; and extending the
displacer oligonucleotide in a primer extension reaction with a DNA
polymerase to produce a third primer extension product that
displaces said first primer extension product from the target
nucleic acid.
[0065] In yet another embodiment, step (a) further comprises
treating the nucleic acid sample with a binding molecule which
binds to the target nucleic acid adjacent to or near a 5'-end of
the target nucleic acid sequence, where the first primer extension
product has a 3'-end which is determined by said binding molecule
and which is complementary to the 5'-end of the target nucleic acid
sequence.
[0066] In a more particular aspect, step (c) further comprises
extending a 3'-end of the first primer extension product in the
promoter oligonucleotide:first primer extension product hybrid to
add a sequence complementary to the promoter sequence.
[0067] In another particular aspect, step (c) further comprises:
extending the promoter oligonucleotide hybridized to the first
primer extension product with a DNA polymerase to produce a primer
extension product complementary to the first primer extension
product; and extending the promoter oligonucleotide hybridized to
the second primer extension product with a DNA polymerase to
produce a primer extension product complementary to the second
primer extension product.
[0068] The separating steps, in one embodiment, are performed by a
ribonuclease activity provided by said DNA polymerase.
Alternatively, the separating steps are performed by a ribonuclease
activity provided by an enzyme other than said DNA polymerase.
[0069] Another embodiment of the present invention provides a kit
for use in the selective amplification of at least one target
nucleic acid sequence from a nucleic acid sample, the kit
comprising: a tagged oligonucleotide comprising a first region
comprising a target hybridizing sequence which hybridizes to a
3'-end of a target nucleic acid sequence under a first set of
conditions so that the first region can be extended in a
template-dependent manner in the presence of a DNA polymerase, and
a second region comprising a tag sequence situated 5' to the first
region, where the second region does not stably hybridize to a
target nucleic acid containing the target nucleic acid sequence
under the first set of conditions; a tag closing sequence which
hybridizes to the target hybridizing sequence under a second set of
conditions, thereby blocking hybridization of the tagged
oligonucleotide to the target nucleic acid sequence, where the tag
closing sequence does not stably hybridize to the target
hybridizing sequence under the first set of conditions; and a first
priming oligonucleotide which hybridizes to the complement of the
tag sequence under the second set of conditions so that the first
priming oligonucleotide can be extended in a template-dependent
manner in the presence of a DNA polymerase.
[0070] In a more particular aspect of this embodiment, the tagged
oligonucleotide further comprises a third region containing a
promoter for an RNA polymerase, the third region being situated 5'
to the second region.
[0071] In another aspect, the 3'-terminal base of the target
hybridizing sequence hybridizes to a 5'-terminal base of the tag
closing sequence when the target hybridizing sequence is not
hybridized to the target nucleic acid sequence under the second set
of conditions.
[0072] In yet another aspect, the 5'-end of the tag closing
sequence includes a moiety for stabilizing a duplex formed between
the tag closing sequence and the target hybridizing sequence when
the target hybridizing sequence is not hybridized to the target
nucleic acid sequence under the second set of conditions.
[0073] In another aspect, the tagged oligonucleotide and the tag
closing sequence constitute distinct molecules, the tag closing
sequence being a tag closing oligonucleotide. Alternatively, the
tagged oligonucleotide and the tag closing sequence are contained
in the same molecule.
[0074] The tag closing sequence may be joined to the tagged
oligonucleotide by a non-nucleotide linker, for example a
non-nucleotide linker comprising at least one of abasic nucleotides
and polyethylene glycol.
[0075] In another aspect, a 3'-end of the tag closing sequence is
joined to a 5'-end of the tagged oligonucleotide. Alternatively, a
5'-end of the tag closing sequence is joined to a 5'-end of the
tagged oligonucleotide.
[0076] In yet another aspect, the tag closing sequence hybridizes
to the target hybridizing sequence to form an antiparallel duplex
when the target hybridizing sequence is not hybridized to the
target nucleic acid sequence under the second set of
conditions.
[0077] In another aspect, the tag closing sequence is modified to
prevent the initiation of DNA synthesis therefrom, for example by
including a blocking moiety situated at its 3'-terminus.
[0078] In another aspect, the tag closing sequence hybridizes to
the target hybridizing sequence to form a parallel duplex when the
target hybridizing sequence is not hybridized to the target nucleic
acid sequence under the second set of conditions.
[0079] In yet another aspect, the duplex comprises a 3'-terminal
base of the target hybridizing sequence hybridized to a 3'-terminal
base of the tag closing sequence.
[0080] The tag closing sequence, in this aspect, may be modified to
prevent the initiation of DNA synthesis therefrom, for example by
including a blocking moiety situated at its 3'-terminus.
[0081] In another aspect of this embodiment, the first priming
oligonucleotide does stably hybridize to the target nucleic acid
and, thereby, participates in detectable amplification of the
target nucleic acid sequence under the second set of
conditions.
[0082] In another aspect, the kit further comprises a second
priming oligonucleotide which hybridizes to the complement of a
5'-end of the target nucleic acid sequence under the second set of
conditions so that the second priming oligonucleotide can be
extended in a template-dependent manner in the presence of a DNA
polymerase.
[0083] In yet another aspect, a kit of the invention further
comprises a promoter oligonucleotide comprising first and second
regions, the first region comprising a hybridizing sequence which
hybridizes to the complement of a 5'-end of the target nucleic acid
sequence under the second set of conditions, and the second region
comprising a promoter for an RNA polymerase which is situated 5' to
the first region.
[0084] The promoter oligonucleotide, in this aspect, may be
modified to prevent the initiation of DNA synthesis therefrom, for
example by including a blocking moiety situated at its
3'-terminus.
[0085] In yet another aspect, the promoter oligonucleotide can be
extended in a template-dependent manner in the presence of a DNA
polymerase when the hybridizing sequence is hybridized to the
complement of the 5'-end of the target nucleic acid sequence under
the second set of conditions.
[0086] The kits of the invention, in certain aspects, may also
further comprise one or more reagents or components selected from
any one or more of a DNA polymerase (such as a reverse
transcriptase), an RNA polymerase, nucleoside triphosphates, a
solid support for binding a complex comprising the target nucleic
acid and the tagged oligonucleotide. In another aspect, the tagged
oligonucleotide is free in solution.
[0087] In another aspect, the kit does not include a restriction
enzyme capable of cleaving a duplex formed between the tag closing
sequence and the target hybridizing sequence under the second set
of conditions.
[0088] In yet another aspect, the target hybridizing sequence
hybridizes to a 3'-end of multiple target nucleic acid sequences
under the first set of conditions.
[0089] In another embodiment, the tagged oligonucleotide is a
universal bacterial or a universal fungal oligonucleotide. For
example, in one aspect, the target hybridizing sequence hybridizes
to target region at a 3'-end of one or more target nucleic acid
sequences, the target region being present in a plurality of
microorganisms belonging to a class of microorganisms selected from
the group consisting of Eubacteria, Gram-positive bacteria,
Gram-negative bacteria and fungi under the first set of conditions.
In another embodiment, said one or more target nucleic acid
sequences are ribosomal nucleic acid sequences.
[0090] In a more particular aspect, the microorganisms belong to a
class of bacterial microorganisms selected from the group
consisting Staphylococci spp. (e.g., Staphylococcus aureus,
Staphylococcus epidermis and Staphylococcus haemolyticus),
Streptococci spp. (e.g., Streptococcus pneumoniae, Streptococcus
pyogenes, Streptococcus agalactiae, Streptococcus mitis, Viridans
streptococci and beta-hemolytic streptococci), Enterococcus spp.
(e.g., Enterococcus faecium and Enterococcus faecalis), Escherichia
spp. (e.g., Escherichia coli), Klebsiella spp. (e.g., Klebsiella
pneumoniae and Klebsiella oxytoca), Pseudomonas spp. (e.g.,
Pseudomonas aeruginosa), Enterobacter spp. (e.g., Enterobacter
cloacae and Enterobacter aerogenes), Proteus spp. (e.g., Proteus
mirabilis), Bacterioides spp., Clostridium spp., Serratia spp.
(e.g., Serratia marcescens), Acinetobacter spp. (e.g.,
Acinetobacter baumannii) and Stenotrophomonas spp. (e.g.,
Stenotrophomonas maltophilia). At least a portion of these
microorganisms would be appropriate for detection in a sepsis
test.
[0091] In another particular aspect, the microorganisms belong to a
fungal group of microorganisms selected from the group consisting
of Candida spp. (e.g., Candida albicans, Candida tropicalis,
Candida glabrata, Candida parapsilosis, Candida lusitaniae, Candida
krusei, Candida zeylanoides, Candida guilliermondi, Candida
pseudotropicalis and Candida famata), Histoplama capsulatum,
Cryptococcus spp. (e.g., Cryptococcus neoformans, Cryptococcus
albidus and Cryptococcus laurentii) Coccidioides spp. (e.g.,
Coccidioides immitis), Trichosporon spp. (e.g., Trichosporon
cutaneum), Malassezia spp. (e.g., Malassezia furfur), Rhodotorula
spp., Nocardia spp. (e.g., Nocardia asteroides), Fusarium spp. and
Aspergillus spp. (e.g., Aspergillus fumigatus). At least a portion
of these microorganisms would be appropriate for detection in a
sepsis test.
[0092] According to another embodiment of the invention, there is
provided reaction mixture for amplifying a target nucleic acid
sequence, the reaction mixture comprising: a tagged oligonucleotide
comprising first and second regions, the first region comprising a
target hybridizing sequence hybridized to a 3'-end of a target
nucleic acid sequence and the second region comprising a tag
sequence situated 5' to the target hybridizing sequence; a first
oligonucleotide comprising a hybridizing sequence which hybridizes
to a 3'-end of the complement of the target nucleic acid sequence;
and a second oligonucleotide comprising a hybridizing sequence
which hybridizes to the complement of the tag sequence, where
unhybridized tagged oligonucleotide in the reaction mixture has an
inactive form which blocks or prevents the unhybridized tagged
oligonucleotide from hybridizing to the target nucleic acid
sequence.
[0093] In a more particular aspect according to this embodiment,
the inactive form of the tagged oligonucleotide comprises a tag
closing sequence hybridized to the target hybridizing sequence.
[0094] In another aspect, the tagged oligonucleotide and said tag
closing sequence are distinct molecules, the tag closing sequence
being a tag closing oligonucleotide.
[0095] In another aspect, the tagged oligonucleotide and the tag
closing sequence are contained in the same molecule.
[0096] In yet another aspect, the tagged oligonucleotide is not
attached to a solid support.
[0097] Certain other embodiments of the invention relate to the use
of the methods described herein as a means for monitoring
bioprocess samples, streams, and the like. In one embodiment, for
example, there is provided a method for monitoring a bioprocess for
the presence of contaminating nucleic acid comprising the steps of
(a) treating a first bioprocess sample with a tagged
oligonucleotide, wherein said tagged oligonucleotide comprises
first and second regions, the first region comprising a target
hybridizing sequence capable of hybridizing to a target nucleic
acid sequence of an organism of interest and the second region
comprising a tag sequence, situated 5' to said target hybridizing
sequence, which does not stably hybridize to the target nucleic
acid sequence; under conditions wherein the tagged oligonucleotide
stably hybridizes to the target nucleic acid sequence present in
said first sample; (b) removing or inactivating unhybridized tagged
oligonucleotide from the first bioprocess sample; and (c) exposing
a second bioprocess sample, the second bioprocess sample comprising
the first bioprocess sample and further comprising additional
bioprocess samples, to amplification reagents and conditions
sufficient for amplification of the target nucleic acid sequence
using: (i) a first oligonucleotide which hybridizes to a complement
of the tag sequence and (ii) a second oligonucleotide sequence
which hybridizes to a complement of the target nucleic acid
sequence, where detectable amplification resulting from the first
and second oligonucleotides is contributed by the target nucleic
acid sequence of an organism of interest in the first bioprocess
sample and not by the target nucleic acid sequence contributed by
the additional bioprocess samples.
[0098] In another embodiment, the present invention provides a
method for monitoring a bioprocess for the presence of
contaminating nucleic acid comprising the steps of (a) treating a
first bioprocess sample with a first tagged oligonucleotide, where
the first tagged oligonucleotide comprises first and second
regions, the first region comprising a target hybridizing sequence
capable of hybridizing to a target nucleic acid sequence of an
organism of interest and the second region comprising a first tag
sequence, situated 5' to the target hybridizing sequence, which
does not stably hybridize to the target nucleic acid sequence;
under conditions where the first tagged oligonucleotide stably
hybridizes to the target nucleic acid sequence present in said
first sample; (b) treating a second bioprocess sample with a second
tagged oligonucleotide, where the second tagged oligonucleotide
comprises first and second regions, the first region comprising a
target hybridizing sequence capable of hybridizing to the target
nucleic acid sequence of the organism of interest and the second
region comprising a second tag sequence, situated 5' to the target
hybridizing sequence and different from the first tag sequence,
which does not stably hybridize to the target nucleic acid
sequence; under conditions where the second tagged oligonucleotide
stably hybridizes to the target nucleic acid sequence present in
the second sample; and (c) performing a nucleic acid amplification
reaction on a third bioprocess sample, the third bioprocess sample
comprising the first and the second bioprocess samples, using: (i)
a first oligonucleotide which hybridizes to a complement of the
first tag sequence; (ii) a second oligonucleotide sequence which
hybridizes to a complement of the second tag sequence; and (iii) a
third oligonucleotide which hybridizes to a complement of the
target nucleic acid sequence; where the detection of amplification
product resulting from the first and second oligonucleotides is
indicative of the presence of the target nucleic acid sequence of
the organism of interest in the first bioprocess sample, and where
detection of amplification product resulting from the first and
third oligonucleotides is indicative of the presence of the target
nucleic acid sequence of the organism of interest in the second
bioprocess sample.
[0099] In a further embodiment of the invention, a
pre-amplification reaction mixture is provided for the selective
amplification of one or more target nucleic acid sequences, where
the reaction mixture comprises: a tagged oligonucleotide comprising
first and second regions, said first region comprising a target
hybridizing sequence hybridized to a target region contained at a
3'-end of one or more target nucleic acid sequences present in the
reaction mixture and the second region comprises a tag sequence
situated 5' to the target hybridizing sequence; a first
oligonucleotide comprising a hybridizing sequence which hybridizes
to a 3'-end of the complement of one or more of the target nucleic
acid sequences; and a second oligonucleotide comprising a
hybridizing sequence which hybridizes to the complement of the tag
sequence, where the second oligonucleotide preferably does not
stably hybridize to a target nucleic acid containing the target
nucleic acid such that it can be enzymatically extended in the
presence of a nucleic acid polymerase added to the reaction mixture
to produce a primer extension product complementary to one or more
of the target nucleic acid sequences, where the reaction mixture is
substantially free of an active form of the tagged oligonucleotide
which is not hybridized to the target region contained in the one
or more target nucleic acid sequences present in the reaction
mixture, where the active form of the tagged oligonucleotide has an
available target hybridizing sequence for hybridization to the
target region present in a non-target nucleic acid added to the
reaction mixture, and where the reaction mixture does not include a
nucleic acid polymerase capable of extending any of the
oligonucleotides in a template-dependent manner. The "non-target"
nucleic is from a source outside of the reaction mixture and may
contain a sequence identical to that of the target nucleic acid
sequence. The source of the non-target nucleic acid may be
environmental or it may be a component or reagent added to the
reaction mixture, such a nucleic acid polymerase. The tagged
oligonucleotide can be a tagged priming oligonucleotide or a tagged
promoter oligonucleotide having a promoter recognized by an RNA
polymerase situated 5' to the second region.
[0100] In one aspect of this embodiment, the tagged priming
oligonucleotide does not include a promoter for RNA polymerase,
while the first oligonucleotide includes an RNA promoter situated
5' to the hybridizing sequence of the first oligonucleotide. In a
preferred aspect, the first oligonucleotide further includes a
blocking moiety situated at its 3'-terminus In another aspect that
is useful for amplifying an E. coli target sequence, the target
hybridizing sequence of the tagged oligonucleotide consists of SEQ
ID NO:19, its RNA equivalent or a complement thereof, and the first
hybridizing sequence of the first oligonucleotide consists of SEQ
ID NO:20, its RNA equivalent or a complement thereof.
[0101] In another aspect of this embodiment, the tagged
oligonucleotide and the first oligonucleotide may each include a
promoter for an RNA polymerase situated 5' to the tag sequence and
the hybridizing sequence, respectively. In this aspect, the first
oligonucleotide can include a blocking moiety situated at its
3'-terminus.
[0102] In yet another aspect of this embodiment, the tagged
oligonucleotide includes a tag closing sequence joined to its
3'-end, thereby forming a unitary molecule referred to as a "tag
molecule." Depending on the nature of the amplification reaction,
the tag molecule may or may not include a promoter for an RNA
polymerase situated 5' to the tag sequence. In one embodiment, tag
molecules that have not hybridized to the target region of at least
one target nucleic acid sequence remain "free" in the reaction
mixture (i.e., the tag molecules do not form hybrid duplexes other
than through self-hybridization). Self-hybridized tag molecules are
referred to as "hairpin tag molecules," which is an inactive form
of the tag molecule that prevents it from hybridizing to any
complementary nucleic acids that are subsequently added to the
reaction mixture, such as through a contaminated enzyme preparation
or reagent containing non-target nucleic acids. In still another
aspect of this embodiment, substantially all of the tag molecules
in the reaction mixture are in a hybridized state (hybridized
either to the target region of a target nucleic acid sequence or to
themselves in the form of hairpin tag molecules). At least a
portion of the tag molecules which have not hybridized to the
target region of a target nucleic acid sequence (i.e., hairpin tag
molecules) are removed from the reaction mixture by, for example,
subjecting the reaction mixture to a target capture and washing
procedure.
[0103] In a still further aspect of this embodiment, there are
substantially no tagged oligonucleotides that exist in an
unhybridized state when the reaction mixture is exposed to an
enzyme preparation for amplifying the one or more target nucleic
acid sequences. Thus, in this aspect, the reaction mixture is
substantially depleted of unhybridized tagged oligonucleotides
specific for the one or more target nucleic acid sequences provided
by the sample of interest. This may be accomplished with, for
example, a target capture and washing procedure that separates
hybridized tagged oligonucleotides from unhybridized tagged
oligonucleotides, and then selectively removes the unhybridized
tagged oligonucleotides from the reaction mixture.
[0104] In yet another aspect of this embodiment, the tagged
oligonucleotide does not include either a tag closing sequence or a
tag closing oligonucleotide. Accordingly, in this aspect the tagged
oligonucleotide cannot be characterized as being a "tag
molecule."
[0105] In still another aspect of this embodiment, a probe is
included for detecting an amplification product synthesized in an
in vitro reaction that involves enzymatic extension of the tagged
oligonucleotide and the second oligonucleotide. The amplification
product includes copies of one or more of the target nucleic acid
sequences and/or their complements.
[0106] In yet another embodiment, a reaction mixture is provided
for the selective amplification of one or more target nucleic acid
sequences, where the reaction mixture comprises: a tagged
oligonucleotide comprising first and second regions, where the
first region comprises a target hybridizing sequence hybridized to
a 3'-end of a target nucleic acid sequence and the second region
comprises a tag sequence situated 5' to the target hybridizing
sequence; a first oligonucleotide comprising a hybridizing sequence
which hybridizes to a 3'-end of the complement of the target
nucleic acid sequence; and a second oligonucleotide comprising a
hybridizing sequence which hybridizes to the complement of the tag
sequence, where the second oligonucleotide preferably does not
stably hybridize to a target nucleic acid containing the target
nucleic acid such that it can be enzymatically extended in the
presence of a nucleic acid polymerase added to or present in the
reaction mixture to produce a primer extension product
complementary to one or more of the target nucleic acid sequences,
and where substantially all unhybridized tagged oligonucleotide in
the reaction mixture has an inactive form which blocks or prevents
said unhybridized tagged oligonucleotide from hybridizing to the
target nucleic acid sequence.
[0107] The inactive form of the tagged oligonucleotide can comprise
a tag closing sequence hybridized to the target hybridizing
sequence. The tag closing sequence can be a distinct molecule when
not hybridized to the target hybridizing sequence or it can be
contained in a molecule including the tagged oligonucleotide, in
which case the tag closing sequence is preferably joined to the
5'-end of the tagged oligonucleotide by a non-nucleotide linker
(i.e., the constituents of the linker cannot be copied by a nucleic
acid polymerase). The tagged oligonucleotide may or may not be
joined to a solid support and is preferably not directly attached
to solid support (e.g., particles or beads). If joined to a solid
support, either directly or indirectly, the tagged oligonucleotide
may further function as a capture probe for binding and
immobilizing a target nucleic acid sequence.
[0108] The tagged oligonucleotides of the above reaction mixture
embodiments may possess the characterizing features of any of the
various tagged oligonucleotides embodiments described infra. And,
unless specifically excluded, the reaction mixtures may further
include the reagents and components needed to conduct an
amplification reaction.
[0109] These and other features and advantages of the present
invention will become apparent upon reference to the following
detailed description, the attached drawings and the claims. All
references disclosed herein are hereby incorporated by reference in
their entirety as if each was incorporated individually.
BRIEF DESCRIPTION OF THE DRAWINGS
[0110] FIG. 1 illustrates the steps of a transcription-based
amplification reaction initiated with a tagged priming
oligonucleotide that hybridizes to a 3'-end of an RNA target
sequence. A first extension product formed with the tagged priming
oligonucleotide has a 3'-end which is determined by a terminating
oligonucleotide hybridized adjacent to or near the 5'-end of the
RNA target sequence. A blocked promoter oligonucleotide hybridizes
to a 3'-end of the first extension product and is used to generate
RNA transcripts that are cycled into the amplification
reaction.
[0111] FIG. 2 illustrates the use of a hairpin tag molecule in the
amplification reaction of FIG. 1.
[0112] FIGS. 3A and 3B illustrate the steps of a
transcription-mediated amplification reaction initiated with a
tagged promoter oligonucleotide that hybridizes to a 3'-end of an
RNA target sequence.
[0113] FIG. 4 illustrates the use of a hairpin tag molecule in the
amplification reaction of FIGS. 3A and 3B.
[0114] FIG. 5 illustrates the steps of a transcription-based
amplification reaction initiated with a tagged priming
oligonucleotide that hybridizes to a 3'-end of a single-stranded
DNA target sequence. A first extension product formed with the
tagged priming oligonucleotide has a 3'-end which is determined by
a terminating oligonucleotide hybridized adjacent to or near the
5'-end of the DNA target sequence. A displacer oligonucleotide
hybridized 5' to the tagged priming oligonucleotide is extended to
form a second extension product which displaces the first extension
product from the DNA target sequence. A blocked promoter
oligonucleotide hybridizes to a 3'-end of the first extension
product and is used to generate RNA transcripts that are cycled
into the amplification reaction.
[0115] FIG. 6 illustrates the use of a hairpin tag molecule in the
amplification reaction of FIG. 5.
[0116] FIG. 7 illustrates the steps polymerase chain reaction that
is initiated with a tagged priming oligonucleotide that hybridizes
to a DNA target sequence.
[0117] FIG. 8 illustrates the use of a hairpin tag molecule in the
amplification reaction of FIG. 7.
[0118] FIG. 9 illustrates the steps of a reverse transcription
polymerase chain reaction initiated with a tagged priming
oligonucleotide that hybridizes to an RNA target sequence.
[0119] FIG. 10 illustrates the use of a hairpin tag molecule in the
amplification reaction of FIG. 9.
[0120] FIG. 11 illustrates a discrete, 3' blocked tag closing
oligonucleotide hybridized in an antiparallel fashion to the 3'-end
of a tagged priming oligonucleotide, thereby blocking hybridization
of the tagged priming oligonucleotide to a target nucleic acid
sequence.
[0121] FIG. 12 illustrates a discrete, 3' blocked tag closing
oligonucleotide hybridized in an antiparallel fashion to the 3'-end
of a tagged promoter oligonucleotide, thereby blocking
hybridization of the tagged promoter oligonucleotide to a target
nucleic acid sequence.
[0122] FIG. 13 illustrates a hairpin tag molecule that includes a
3' blocked tag closing sequence hybridized in a parallel fashion to
the 3'-end of a tagged priming oligonucleotide, thereby blocking
hybridization of the tagged priming oligonucleotide to a target
nucleic acid sequence. A 5'-end of the tag closing sequence is
joined to the 3'-end of a tag sequence of the tagged priming
oligonucleotide by a non-nucleotide linker.
[0123] FIG. 14 illustrates a hairpin tag molecule that includes a
3' blocked tag closing sequence hybridized in a parallel fashion to
the 3'-end of a tagged promoter oligonucleotide, thereby blocking
hybridization of the tagged promoter oligonucleotide to a target
nucleic acid sequence. A 5'-end of the tag closing sequence is
joined to the 3'-end of a promoter sequence of the tagged promoter
oligonucleotide by a non-nucleotide linker.
[0124] FIG. 15 illustrates a hairpin tag molecule that includes a
3' blocked tag closing sequence hybridized in an antiparallel
fashion to the 3'-end of a tagged priming oligonucleotide, thereby
blocking hybridization of the tagged priming oligonucleotide to a
target nucleic acid sequence. A 5'-end of the tag closing sequence
is joined to the 3'-end of a tag sequence of the tagged priming
oligonucleotide by a non-nucleotide linker.
[0125] FIG. 16 illustrates a hairpin tag molecule that includes a
3' blocked tag closing sequence hybridized in an antiparallel
fashion to the 3'-end of a tagged promoter oligonucleotide, thereby
blocking hybridization of the tagged promoter oligonucleotide to a
target nucleic acid sequence. A 5'-end of the tag closing sequence
is joined to the 3'-end of a promoter sequence of the tagged
promoter oligonucleotide by a non-nucleotide linker.
[0126] FIG. 17 shows the raw curves for HCV amplifications in which
no target was spiked into the amplification reagent. There was no
detectable amplification when the HCV transcript was not spiked
into the target capture or amplification reagents, while the
average TTime for reactions containing 1.times.10.sup.6 copies of
the HCV transcript in the target capture reagent was 6.3
minutes.
[0127] FIG. 18 shows the raw curves for HCV amplifications in which
target was spiked into the amplification reagent. There was no
detectable amplification when the HCV transcript was spiked into
the amplification reagent, while the average TTime for reactions
containing 1.times.10.sup.6 copies of the HCV transcript in the
target capture reagent was 6.3 minutes. The zero samples in target
capture did not amplify, even with 1 million copies HCV 1a spiked
into the amplification reagent.
[0128] FIG. 19 shows the raw curves for HCV amplifications in which
target and tagged nonT7 primer were spiked into the amplification
reagent. The AvgTTime for 1 million copies HCV 1a target present
only in the target capture step with tagged nonT7 primer &
terminating oligonucleotide spiked into the amplification reagent
was 7.2 minutes. The zero samples in target capture with target,
terminating oligonucleotide & tagged nonT7 primer spiked into
the amplification reagent also produced robust amplification with
an AvgTTime=8.6 minutes.
[0129] FIG. 20 is graph showing results from time-dependent
monitoring of nucleic acid amplification reactions that included
either 0 or 10.sup.6 copies of a synthetic E. coli rRNA template.
The thin broken line shows results for the reaction conducted using
0 copies of template, and the heavy solid line shows results for
the reaction conducted using 10.sup.6 copies of template.
[0130] FIG. 21 is graph showing results from time-dependent
monitoring of nucleic acid amplification reactions that included
either 0, 10.sup.3 or 10.sup.5 copies of a synthetic E. coli rRNA
template.
DETAILED DESCRIPTION OF THE INVENTION
[0131] In accordance with the present invention, nucleic acid
amplification methods are provided that desirably reduce or
eliminate false positive amplification signals resulting from
contaminating biological material that may be present in a reagent
or component of an amplification reaction. The provided methods
also allow for less stringent purification and/or sterility efforts
than have been conventionally needed in order to ensure that
enzymes and other reagents or components used in amplification
reactions, and the environment in which amplification reactions are
performed, are free of contamination by microorganisms or
components thereof, such as nucleic acid material, that may yield
false positive results.
[0132] The practice of the present invention will employ, unless
otherwise indicated, conventional techniques of molecular biology,
recombinant DNA, and chemistry, which are within the skill of the
art. Such techniques are explained fully in the literature. See,
e.g., Molecular Cloning A Laboratory Manual, 2nd Ed., Sambrook et
al., ed., Cold Spring Harbor Laboratory Press: (1989); DNA Cloning,
Volumes I and II (D. N. Glover ed., 1985); Oligonucleotide
Synthesis (M. J. Gait ed., 1984); Mullis et al., U.S. Pat. No.
4,683,195; Nucleic Acid Hybridization (B. D. Hames & S. J.
Higgins eds. 1984); B. Perbal, A Practical Guide To Molecular
Cloning (1984); the treatise, Methods In Enzymology (Academic
Press, Inc., N.Y.); and in Ausubel et al., Current Protocols in
Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989).
[0133] Definitions
[0134] The following terms have the following meanings unless
expressly stated to the contrary. It is to be noted that the term
"a" or "an" entity refers to one or more of that entity; for
example, "a nucleic acid," is understood to represent one or more
nucleic acids. As such, the terms "a" (or "an"), "one or more," and
"at least one" can be used interchangeably herein.
[0135] Nucleic Acid
[0136] The term "nucleic acid" is intended to encompass a singular
"nucleic acid" as well as plural "nucleic acids," and refers to any
chain of two or more nucleotides, nucleosides, or nucleobases
(e.g., deoxyribonucleotides or ribonucleotides) covalently bonded
together. Nucleic acids include, but are not limited to, viral
genomes, or portions thereof, either DNA or RNA, bacterial genomes,
or portions thereof, fungal, plant or animal genomes, or portions
thereof, messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA
(tRNA), plasmid DNA, mitochondrial DNA, or synthetic DNA or RNA. A
nucleic acid may be provided in a linear (e.g., mRNA), circular
(e.g., plasmid), or branched form, as well as a double-stranded or
single-stranded form. Nucleic acids may include modified bases to
alter the function or behavior of the nucleic acid, e.g., addition
of a 3'-terminal dideoxynucleotide to block additional nucleotides
from being added to the nucleic acid. As used herein, a "sequence"
of a nucleic acid refers to the sequence of bases which make up a
nucleic acid. The term "polynucleotide" may be used herein to
denote a nucleic acid chain. Throughout this application, nucleic
acids are designated as having a 5'-terminus and a 3'-terminus.
Standard nucleic acids, e.g., DNA and RNA, are typically
synthesized "3'-to-5'," i.e., by the addition of nucleotides to the
5'-terminus of a growing nucleic acid.
[0137] A "nucleotide" is a subunit of a nucleic acid consisting of
a phosphate group, a 5-carbon sugar and a nitrogenous base. The
5-carbon sugar found in RNA is ribose. In DNA, the 5-carbon sugar
is 2'-deoxyribose. The term also includes analogs of such subunits,
such as a methoxy group at the 2' position of the ribose (2'-O-Me).
As used herein, methoxy oligonucleotides containing "T" residues
have a methoxy group at the 2' position of the ribose moiety, and a
uracil at the base position of the nucleotide.
[0138] A "non-nucleotide unit" is a unit that does not
significantly participate in hybridization of a polymer. Such units
must not, for example, participate in any significant hydrogen
bonding with a nucleotide, and would exclude units having as a
component one of the five nucleotide bases or analogs thereof.
[0139] Target Nucleic Acid/Target Sequence
[0140] A "target nucleic acid" is a nucleic acid present in a
nucleic acid sample comprising a "target sequence" to be amplified.
Target nucleic acids may be DNA or RNA as described herein, and may
be either single-stranded or double-stranded. The target nucleic
acid may include other sequences besides the target sequence which
may not be amplified. Typical target nucleic acids include viral
genomes, bacterial genomes, fungal genomes, plant genomes, animal
genomes, rRNA, tRNA, or mRNA from viruses, bacteria or eukaryotic
cells, mitochondrial DNA, or chromosomal DNA.
[0141] Target nucleic acids may be isolated from any number of
sources based on the purpose of the amplification assay being
carried out. Sources of target nucleic acids include, but are not
limited to, clinical specimens (e.g., blood, either whole blood or
platelets, urine, saliva, feces, semen, or spinal fluid),
environmental samples (e.g., water or soil samples), food samples,
beverages, industrial samples (e.g., products and process
materials, including water), seed stocks, cDNA libraries, or total
cellular RNA. By "isolated" it is meant that a sample containing a
target nucleic acid is taken from its natural milieu; however, the
term does not connote any particular degree of purification. If
necessary, target nucleic acids of the present invention are made
available for interaction with the various oligonucleotides of the
present invention. This may include, for example, cell lysis or
cell permeabilization to release the target nucleic acid from
cells, which then may be followed by one or more purification
steps, such as a series of isolation and wash steps. See, e.g.,
Clark et al., "Method for Extracting Nucleic Acids from a Wide
Range of Organisms," U.S. Pat. No. 5,786,208; and Hogan,
"Polynucleotide Matrix-Based Method of Identifying Microorganisms,
U.S. Pat. No. 6,821,770. This may be particularly important where
the sample source or cellular material released into the sample can
interfere with the amplification reaction. Methods to prepare
target nucleic acids from various sources for amplification are
well known to those of ordinary skill in the art. Target nucleic
acids of the present invention may be purified to some degree prior
to the amplification reactions described herein, but in other
cases, the sample is added to the amplification reaction without
any further manipulations.
[0142] The term "target sequence" refers to the particular
nucleotide sequence of the target nucleic acid which is to be
amplified. The "target sequence" includes the complexing sequences
to which oligonucleotides (e.g., tagged oligonucleotides, priming
oligonucleotides and/or promoter oligonucleotides) complex during
the processes of the present invention. Where the target nucleic
acid is originally single-stranded, the term "target sequence" will
also refer to the sequence complementary to the "target sequence"
as present in the target nucleic acid. Where the "target nucleic
acid" is originally double-stranded, the term "target sequence"
refers to both the sense (+) and antisense (-) strands. In choosing
a target sequence, the skilled artisan will understand that a
"unique" sequence should be chosen so as to distinguish between
unrelated or closely related target nucleic acids. As will be
understood by those of ordinary skill in the art, "unique"
sequences are judged from the testing environment. At least the
sequences recognized by the target hybridizing sequence of a tagged
oligonucleotide and the associated detection probe or probes (as
described in more detail elsewhere herein) should be unique in the
environment being tested, but need not be unique within the
universe of all possible sequences. Furthermore, even though the
target sequence should contain a "unique" sequence for recognition
by a tagged oligonucleotide or detection probe, it is not always
the case that the priming oligonucleotide and/or promoter
oligonucleotide are recognizing "unique" sequences. In some
embodiments, it may be desirable to choose a target sequence which
is common to a class of organisms, for example, a sequence which is
common to all E. coli strains that might be in a sample. In other
situations, a very highly specific target sequence, or a target
sequence having at least a highly specific region recognized by the
detection probe, would be chosen so as to distinguish between
closely related organisms, for example, between pathogenic and
non-pathogenic E. coli. A target sequence of the present invention
may be of any practical length. A minimal target sequence includes
a region which hybridizes to the target hybridizing sequence of a
tagged oligonucleotide, the complement of a region which hybridizes
to a priming oligonucleotide or the hybridizing region of a
promoter oligonucleotide, and a region used for detection, e.g., a
region (or complement thereof) which hybridizes to a detection
probe, as described in more detail elsewhere herein. The region
which hybridizes with the detection probe may overlap with or be
contained within the region which hybridizes with the priming
oligonucleotide (or its complement) or the hybridizing region of
the promoter oligonucleotide (or its complement). In addition to
the minimal requirements, the optimal length of a target sequence
depends on a number of considerations, for example, the amount of
secondary structure, or self-hybridizing regions in the sequence.
Determining the optimal length is easily accomplished by those of
ordinary skill in the art using routine optimization methods.
Typically, target sequences of the present invention range from
about 100 nucleotides in length to from about 150 to about 250
nucleotides in length. The optimal or preferred length may vary
under different conditions, which can easily be tested by one of
ordinary skill in the art according to the methods described
herein. The terms "amplicon" refers to a nucleic acid molecule
generated during an amplification procedure that is substantially
complementary or identical to a sequence contained within the
target sequence. The term "amplification product" refers to an
amplicon or some other product indicative of an amplification
reaction.
[0143] Oligonucleotides
[0144] As used herein, the term "oligonucleotide" or "oligo" or
"oligomer" is intended to encompass a singular "oligonucleotide" as
well as plural "oligonucleotides," and refers to any polymer of two
or more of nucleotides, nucleosides, nucleobases or related
compounds used as a reagent in the amplification methods of the
present invention, as well as subsequent detection methods. The
oligonucleotide may be DNA and/or RNA and/or analogs thereof. The
term oligonucleotide does not denote any particular function to the
reagent, rather, it is used generically to cover all such reagents
described herein. An oligonucleotide may serve various different
functions, e.g., it may function as a primer if it is capable of
hybridizing to a complementary strand and can further be extended
in the presence of a nucleic acid polymerase, it may provide a
promoter if it contains a sequence recognized by an RNA polymerase
and allows for transcription, and it may function to prevent
hybridization or impede primer extension if appropriately situated
and/or modified. Specific oligonucleotides of the present invention
are described in more detail below. As used herein, an
oligonucleotide can be virtually any length, limited only by its
specific function in the amplification reaction or in detecting an
amplification product of the amplification reaction.
[0145] Oligonucleotides of a defined sequence and chemical
structure may be produced by techniques known to those of ordinary
skill in the art, such as by chemical or biochemical synthesis, and
by in vitro or in vivo expression from recombinant nucleic acid
molecules, e.g., bacterial or viral vectors. As intended by this
disclosure, an oligonucleotide does not consist solely of wild-type
chromosomal DNA or the in vivo transcription products thereof.
[0146] Oligonucleotides may be modified in any way, as long as a
given modification is compatible with the desired function of a
given oligonucleotide. One of ordinary skill in the art can easily
determine whether a given modification is suitable or desired for
any given oligonucleotide of the present invention. Modifications
include base modifications, sugar modifications or backbone
modifications. Base modifications include, but are not limited to
the use of the following bases in addition to adenine, cytidine,
guanosine, thymine and uracil: C-5 propyne, 2-amino adenine,
5-methyl cytidine, inosine, and dP and dK bases. The sugar groups
of the nucleoside subunits may be ribose, deoxyribose and analogs
thereof, including, for example, ribonucleosides having a
2'-O-methyl (2'-O-ME) substitution to the ribofuranosyl moiety. See
Becker et al., "Method for Amplifying Target Nucleic Acids Using
Modified Primers," U.S. Pat. No. 6,130,038. Other sugar
modifications include, but are not limited to 2'-amino, 2'-fluoro,
(L)-alpha-threofuranosyl, and pentopuranosyl modifications. The
nucleoside subunits may by joined by linkages such as
phosphodiester linkages, modified linkages or by non-nucleotide
moieties which do not prevent hybridization of the oligonucleotide
to its complementary target nucleic acid sequence. Modified
linkages include those linkages in which a standard phosphodiester
linkage is replaced with a different linkage, such as a
phosphorothioate linkage or a methylphosphonate linkage. The
nucleobase subunits may be joined, for example, by replacing the
natural deoxyribose phosphate backbone of DNA with a pseudo peptide
backbone, such as a 2-aminoethylglycine backbone which couples the
nucleobase subunits by means of a carboxymethyl linker to the
central secondary amine (DNA analogs having a pseudo peptide
backbone are commonly referred to as "peptide nucleic acids" or
"PNA" and are disclosed by Nielsen et al., "Peptide Nucleic Acids,"
U.S. Pat. No. 5,539,082.) Other linkage modifications include, but
are not limited to, morpholino bonds.
[0147] Non-limiting examples of oligonucleotides or oligomers
contemplated by the present invention include nucleic acid analogs
containing bicyclic and tricyclic nucleoside and nucleotide analogs
(LNAs). See Imanishi et al., "Bicyclonucleoside and Oligonucleotide
Analogues," U.S. Pat. No. 6,268,490; and Wengel et al.,
"Oligonucleotide Analogues," U.S. Pat. No. 6,670,461.) Any nucleic
acid analog is contemplated by the present invention provided the
modified oligonucleotide can perform its intended function, e.g.,
hybridize to a target nucleic acid under stringent hybridization
conditions or amplification conditions, or interact with a DNA or
RNA polymerase, thereby initiating extension or transcription. In
the case of detection probes, the modified oligonucleotides must
also be capable of preferentially hybridizing to the target nucleic
acid under stringent hybridization conditions.
[0148] While design and sequence of oligonucleotides for the
present invention depend on their function as described below,
several variables must generally be taken into account. Among the
most critical are: length, melting temperature (Tm), specificity,
complementarity with other oligonucleotides in the system, G/C
content, polypyrimidine (T, C) or polypurine (A, G) stretches, and
the 3'-end sequence. Controlling for these and other variables is a
standard and well known aspect of oligonucleotide design, and
various computer programs are readily available to screen large
numbers of potential oligonucleotides for optimal ones.
[0149] The 3'-terminus of an oligonucleotide (or other nucleic
acid) can be blocked in a variety of ways using a blocking moiety,
as described below. A "blocked" oligonucleotide is not efficiently
extended by the addition of nucleotides to its 3'-terminus, by a
DNA- or RNA-dependent DNA polymerase, to produce a complementary
strand of DNA. As such, a "blocked" oligonucleotide cannot be a
"primer."
[0150] As used in this disclosure, the phrase "an oligonucleotide
having a nucleic acid sequence `comprising,` `consisting of,` or
`consisting essentially of` a sequence selected from" a group of
specific sequences means that the oligonucleotide, as a basic and
novel characteristic, is capable of stably hybridizing to a nucleic
acid having the exact complement of one of the listed nucleic acid
sequences of the group under stringent hybridization conditions. An
exact complement includes the corresponding DNA or RNA
sequence.
[0151] The phrase "an oligonucleotide substantially corresponding
to a nucleic acid sequence" means that the referred to
oligonucleotide is sufficiently similar to the reference nucleic
acid sequence such that the oligonucleotide has similar
hybridization properties to the reference nucleic acid sequence in
that it would hybridize with the same target nucleic acid sequence
under stringent hybridization conditions.
[0152] One skilled in the art will understand that "substantially
corresponding" oligonucleotides of the invention can vary from the
referred to sequence and still hybridize to the same target nucleic
acid sequence. This variation from the nucleic acid may be stated
in terms of a percentage of identical bases within the sequence or
the percentage of perfectly complementary bases between the probe
or primer and its target sequence. Thus, an oligonucleotide of the
present invention substantially corresponds to a reference nucleic
acid sequence if these percentages of base identity or
complementarity are from 100% to about 80%. In preferred
embodiments, the percentage is from 100% to about 85%. In more
preferred embodiments, this percentage can be from 100% to about
90%; in other preferred embodiments, this percentage is from 100%
to about 95%. One skilled in the art will understand the various
modifications to the hybridization conditions that might be
required at various percentages of complementarity to allow
hybridization to a specific target sequence without causing an
unacceptable level of non-specific hybridization.
[0153] Tagged Oligonucleotide/Heterologous Tag Sequence
[0154] A "tagged oligonucleotide" as used herein refers to an
oligonucleotide that comprises at least a first region and a second
region, where the first region comprises a "target hybridizing
sequence" which hybridizes to the 3'-end of a target nucleic acid
sequence of interest, and where the second region comprises a "tag
sequence" situated 5' to the target hybridizing sequence and which
does not stably hybridize or bind to a target nucleic acid
containing the target nucleic acid sequence. Hybridization of the
target hybridizing sequence to the target nucleic acid sequence
produces a "tagged target nucleic acid sequence." The features and
design considerations for the target hybridizing sequence component
would be the same as for the priming oligonucleotides discussed
infra.
[0155] The "tag sequence" or "heterologous tag sequence" may be
essentially any heterologous sequence provided that it does not
stably hybridize to the target nucleic acid sequence of interest
and, thereby, participate in detectable amplification. The tag
sequence preferably does not stably hybridize to any sequence
derived from the genome of an organism being tested or, more
particularly, to any target nucleic acid under reaction conditions.
A tag sequence that is present in a tagged oligonucleotide is
preferably designed so as not to substantially impair or interfere
with the ability of the target hybridizing sequence to hybridize to
its target sequence. Moreover, the tag sequence will be of
sufficient length and composition such that once a complement of
the tag sequence has been incorporated into an initial DNA primer
extension product, a tag-specific priming oligonucleotide can then
be used to participate in subsequent rounds of amplification as
described herein. A tag sequence of the present invention is
typically at least 10 nucleotides in length, and may extend up to
15, 20, 25, 30, 35, 40, 50 or more nucleotides in length. Skilled
artisans will recognize that the design of tag sequences and tagged
oligonucleotides for use in the present invention can follow any of
a number of suitable strategies, while still achieving the
objectives and advantages described herein.
[0156] In certain embodiments, the tagged oligonucleotide is a
"tagged priming oligonucleotide" comprising a tag sequence and a
target hybridizing sequence. In other embodiments, the tagged
oligonucleotide is a "tagged promoter oligonucleotide" comprising a
tag sequence, a target hybridizing sequence and a promoter sequence
situated 5' to the tag sequence and effective for initiating
transcription therefrom.
[0157] Inactivating
[0158] The term "inactivating" means that a heterologous tag
sequence is altered so that it does not stably bind to a target
nucleic acid sequence under amplification conditions. In the case
of an unhybridized tagged oligonucleotide, the term "inactivating"
means that the tagged oligonucleotide is altered from an "active"
confirmation which permits the target hybridizing sequence to
hybridize to the target nucleic acid sequence to an "inactive"
confirmation which blocks or otherwise prevents the target
hybridizing sequence from hybridizing to the target nucleic acid
sequence. For example, an inactive confirmation may be formed under
stringency conditions permitting the tag closing sequence to form a
stable hybrid with the target hybridizing sequence (e.g., under
less stringent conditions than the conditions for forming an active
confirmation of the tagged oligonucleotide). Unless further
altered, the tag closing sequence:target hybridizing sequence
hybrid remains closed under amplification conditions.
Alternatively, a duplex formed between the tag closing sequence and
the target hybridizing sequence may be altered by an enzyme, such
as a DNAse, an S1 nuclease, an endonuclease, such as a restriction
enzyme which cleaves a double-stranded restriction site formed
between the tag closing sequence and the target hybridizing
sequence, a ribonuclease activity (e.g., RNAse H activity) for
digesting the RNA component (e.g., target hybridizing sequence) of
a DNA:RNA hybrid, or an exonuclease having a 3'-to-5' or 5'-to-3'
activity for removing nucleotides from the target hybridizing
sequence hybridized to the tag closing sequence. However, to avoid
exposing a sample to a potentially contaminating source of the
target nucleic acid sequence, the use of enzymes to inactivate
tagged oligonucleotides which have not hybridized to the target
nucleic acid sequence is generally not preferred. Other
inactivating means include chemicals for altering the target
hybridizing sequence so that it is incapable of hybridizing to a
target nucleic acid sequence under amplification conditions.
[0159] Moieties can be included in the tag hybridizing sequence to
further stabilize hybrids formed between the target closing
sequence and the target hybridizing sequence of tagged
oligonucleotides, especially where it is anticipated that at least
some of the inactive tagged oligonucleotides will be introduced
into the amplification reaction mixture. Suitable moieties include
modified nucleotides, including LNAs, 2'-O-ME ribonucleotides, 2,6
diamino purine. 5-methyl cytosine, and C-5 propynyl cytosine or
uracil. Those skilled in the art will be able to readily select the
number and positions of such modified nucleotides to limit
breathing at the 5'- and 3'-ends of the tag closing sequence and to
achieve a desired melting temperature of the hybrid without
engaging undue experimentation. Other suitable moieties include
minor groove binders and pendant groups, such as purine, DABCYL,
pyrine and 5'-trimethoxy stilbene CAP.
[0160] Removing
[0161] As used herein, the term "removing" refers to the physical
separation of tagged target nucleic acid sequences from
unhybridized tagged oligonucleotides. Tagged target nucleic acid
sequences can be physically separated from unhybridized tagged
oligonucleotides (or heterologous tag sequences) present in a
nucleic acid sample by a variety of techniques known to those
skilled in the art. By way of example, tagged target nucleic acid
sequences can be bound to a solid support and immobilized in a
nucleic acid sample while unbound material is removed. To remove
unbound material, the solid support can be subjected to one or more
wash/rinse steps. The wash steps are intended to remove remaining
unhybridized tagged oligonucleotides and potentially interfering
cellular or sample material. A rinse step is typically included
where the wash solution contains a component that is inhibitory to
amplification when present at a sufficiently high concentration,
such as a detergent. The solid support preferably binds
specifically to target nucleic acids or tagged target nucleic acid
sequences to prevent unhybridized tagged oligonucleotide (or
unbound heterologous tag sequences) from entering into the
amplification reaction. Exemplary means for capturing, immobilizing
and purifying target nucleic acids are discussed below, an example
of which is disclosed by Weisburg et al., "Two-Step Hybridization
and Capture of a Polynucleotide," U.S. Pat. No. 6,534,273.
[0162] Tag Closing Sequence/Tag Closing Oligonucleotide
[0163] The phrases "tag closing sequence" and "tag closing
oligonucleotide" refer to an oligonucleotide that is complementary
to a portion of the target hybridizing sequence of a tagged
oligonucleotide. The length and sequence of the tag closing
sequence are selected so that the tag closing sequence does not
stably hybridize to the target hybridizing sequence of the tagged
oligonucleotide under a first set of conditions permitting stable
hybridization of the target hybridizing sequence to a target
sequence. The tag closing sequence may include abasic nucleotides
or base mismatches with the target hybridizing sequence. Provided
the tagged oligonucleotide is not hybridized to the target
sequence, the tag closing sequence stably hybridizes to the target
hybridizing sequence under a second set of less stringent
conditions, thus "inactivating" or blocking the tagged
oligonucleotide from hybridizing to the target sequence. The tag
closing sequence may be in the form of a discrete oligonucleotide
or it may be joined to the 5'-end of a tagged oligonucleotide ("tag
molecule"), so that it forms a hairpin structure with the tagged
oligonucleotide under the second set of conditions ("hairpin tag
molecule"). If part of a tag molecule, the tag closing sequence is
preferably joined to the tagged oligonucleotide via a
non-nucleotide linker region (e.g., abasic nucleotides or
polyethylene glycol) of sufficient length for the tag closing
sequence to hybridize to the target hybridizing sequence under the
second set of conditions. The tag closing sequence may be modified
to prevent the initiation of DNA synthesis therefrom, which can
include a blocking moiety situated at its 3'-terminus The tag
closing sequence is at least 3 but no more than about 20 bases in
length. Typical tag closing sequences are from 10 to 16 bases in
length.
[0164] Amplification or Nucleic Acid Amplification
[0165] By "amplification" or "nucleic acid amplification" is meant
production of multiple copies of a target nucleic acid that
contains at least a portion of the intended specific target nucleic
acid sequence. The multiple copies may be referred to as amplicons
or amplification products. In certain embodiments, the amplified
target contains less than the complete target gene sequence
(introns and exons) or an expressed target gene sequence (spliced
transcript of exons and flanking untranslated sequences). For
example, specific amplicons may be produced by amplifying a portion
of the target polynucleotide by using amplification primers that
hybridize to, and initiate polymerization from, internal positions
of the target polynucleotide. Preferably, the amplified portion
contains a detectable target sequence that may be detected using
any of a variety of well-known methods.
[0166] Many well-known methods of nucleic acid amplification
require thermocycling to alternately denature double-stranded
nucleic acids and hybridize primers; however, other well-known
methods of nucleic acid amplification are isothermal. The
polymerase chain reaction (Mullis et al., U.S. Pat. No. 4,683,195;
Mullis, U.S. Pat. No. 4,683,202; and Mullis et al., U.S. Pat. No.
4,800,159), commonly referred to as PCR, uses multiple cycles of
denaturation, annealing of primer pairs to opposite strands, and
primer extension to exponentially increase copy numbers of the
target sequence. In a variation called RT-PCR, reverse
transcriptase (RT) is used to make a complementary DNA (cDNA) from
mRNA, and the cDNA is then amplified by PCR to produce multiple
copies of DNA (Gelfand et al., "Reverse Transcription with
Thermostable DNA Polymerases--High Temperature Reverse
Transcription," U.S. Pat. Nos. 5,322,770 and 5,310,652). Another
method is strand displacement amplification (Walker, G. et al.
(1992), Proc. Natl. Acad. Sci. USA 89, 392-396; Walker et al.,
"Nucleic Acid Target Generation," U.S. Pat. No. 5,270,184; Walker,
"Strand Displacement Amplification," U.S. Pat. No. 5,455,166; and
Walker et al. (1992) Nucleic Acids Research 20, 1691-1696),
commonly referred to as SDA, which uses cycles of annealing pairs
of primer sequences to opposite strands of a target sequence,
primer extension in the presence of a dNTP to produce a duplex
hemiphosphorothioated primer extension product,
endonuclease-mediated nicking of a hemimodified restriction
endonuclease recognition site, and polymerase-mediated primer
extension from the 3' end of the nick to displace an existing
strand and produce a strand for the next round of primer annealing,
nicking and strand displacement, resulting in geometric
amplification of product. Thermophilic SDA (tSDA) uses thermophilic
endonucleases and polymerases at higher temperatures in essentially
the same method (European Pat. No. 0 684 315). Other amplification
methods include: nucleic acid sequence based amplification (Malek
et al., U.S. Pat. No. 5,130,238), commonly referred to as NASBA;
one that uses an RNA replicase to amplify the probe molecule itself
(Lizardi, P. et al. (1988) BioTechnol. 6, 1197-1202), commonly
referred to as Q.beta. replicase; a transcription-based
amplification method (Kwoh, D. et al. (1989) Proc. Natl. Acad. Sci.
USA 86, 1173-1177); self-sustained sequence replication (Guatelli,
J. et al. (1990) Proc. Natl. Acad. Sci. USA 87, 1874-1878; Landgren
(1993) Trends in Genetics 9, 199-202; and Lee, H. et al., NUCLEIC
ACID AMPLIFICATION TECHNOLOGIES (1997)); and,
transcription-mediated amplification (Kacian et al., "Nucleic Acid
Sequence Amplification Methods," U.S. Pat. No. 5,480,784; and
Kacian et al., U.S. Pat. No. 5,399,491), commonly referred to as
TMA. For further discussion of known amplification methods see
Persing, David H., 1993, "In Vitro Nucleic Acid Amplification
Techniques" in Diagnostic Medical Microbiology: Principles and
Applications (Persing et al., Eds.), pp. 51-87 (American Society
for Microbiology, Washington, D.C.). Other illustrative
amplification methods suitable for use in accordance with the
present invention include rolling circle amplification (RCA)
(Lizardi, "Rolling Circle Replication Reporter Systems," U.S. Pat.
No. 5,854,033); Helicase Dependent Amplification (HDA) (Kong et
al., "Helicase Dependent Amplification Nucleic Acids," U.S. Pat.
Appln. Pub. No. US 2004-0058378 A1); and Loop-Mediated Isothermal
Amplification (LAMP) (Notomi et al., "Process for Synthesizing
Nucleic Acid," U.S. Pat. No. 6,410,278).
[0167] Preferred transcription-based amplification systems of the
present invention include TMA, which employs an RNA polymerase to
produce multiple RNA transcripts of a target region (e.g., Kacian
et al., U.S. Pat. Nos. 5,480,784 and 5,399,491; and Becker et al.,
"Single-Primer Nucleic Acid Amplification Methods," U.S. Pat.
Appln. Pub. No. US 2006-0046265 A1). TMA uses a "promoter
oligonucleotide" or "promoter-primer" that hybridizes to a target
nucleic acid in the presence of a reverse transcriptase and an RNA
polymerase to form a double-stranded promoter from which the RNA
polymerase produces RNA transcripts. These transcripts can become
templates for further rounds of TMA in the presence of a second
primer capable of hybridizing to the RNA transcripts. Unlike PCR,
LCR or other methods that require heat denaturation, TMA is an
isothermal method that uses an RNAse H activity to digest the RNA
strand of an RNA:DNA hybrid, thereby making the DNA strand
available for hybridization with a primer or promoter-primer.
Generally, the RNAse H activity associated with the reverse
transcriptase provided for amplification is used.
[0168] In one illustrative TMA method, one amplification primer is
an oligonucleotide promoter-primer that comprises a promoter
sequence which becomes functional when double-stranded, located 5'
of a target-binding sequence, which is capable of hybridizing to a
binding site of a target RNA at a location 3' to the sequence to be
amplified. A promoter-primer may be referred to as a "T7-primer"
when it is specific for T7 RNA polymerase recognition. Under
certain circumstances, the 3' end of a promoter-primer, or a
subpopulation of such promoter-primers, may be modified to block or
reduce primer extension. From an unmodified promoter-primer,
reverse transcriptase creates a cDNA copy of the target RNA, while
RNAse H activity degrades the target RNA. A second amplification
primer then binds to the cDNA. This primer may be referred to as a
"non-T7 primer" to distinguish it from a "T7-primer". From this
second amplification primer, reverse transcriptase creates another
DNA strand, resulting in a double-stranded DNA with a functional
promoter at one end. When double-stranded, the promoter sequence is
capable of binding an RNA polymerase to begin transcription of the
target sequence to which the promoter-primer is hybridized. An RNA
polymerase uses this promoter sequence to produce multiple RNA
transcripts (i.e., amplicons), generally about 100 to 1,000 copies.
Each newly-synthesized amplicon can anneal with the second
amplification primer. Reverse transcriptase can then create a DNA
copy, while the RNAse H activity degrades the RNA of this RNA:DNA
duplex. The promoter-primer can then bind to the newly synthesized
DNA, allowing the reverse transcriptase to create a double-stranded
DNA, from which the RNA polymerase produces multiple amplicons.
Thus, a billion-fold isothermic amplification can be achieved using
two amplification primers.
[0169] In another illustrative TMA method, one or more features as
described in Becker et al., U.S. Pat. Appln. Pub. No. US
2006-0046265 A1 are optionally incorporated. Preferred TMA methods
in this respect include the use of blocking moieties, terminating
moieties, and other modifying moieties that provide improved TMA
process sensitivity and accuracy. Thus, certain preferred
embodiments of the present invention employ tagged
oligonucleotides, as described herein, in conjunction with the
methods as described in Becker et al., U.S. Pat. Appln. Pub. No. US
2006-0046265 A1.
[0170] By "detectable amplification" is meant that a detectable
signal associated with an amplification product in an amplification
reaction mixture rises above a predetermined background or
threshold level (end-point amplification) or rises above a
background or threshold level within a predetermined period of time
(real-time amplification). See, e.g., Light et al., "Method for
Determining the Amount of an Analyte in a Sample," U.S. Pat. Appln.
Pub. No. US 2006-0276972, paragraphs 506-549. The amplification
product contains a sequence having sequence identity with a target
nucleic acid sequence or its complement and can be detected with,
for example, an intercalating dye or a detection probe having
specificity for a region of the target nucleic acid sequence or its
complement.
[0171] "Selective Amplification"
[0172] "Selective amplification" as used herein, refers to the
amplification of a target nucleic acid sequence according to the
present invention where detectable amplification of the target
sequence is limited or substantially limited to amplification of
target sequence contributed by sample of interest that is being
tested and is not contributed by target nucleic acid sequence
contributed by some other sample source, e.g., contamination
present in reagents or components used during amplification
reactions or in the environment or environmental conditions in
which amplification reactions are performed.
[0173] Amplification Conditions
[0174] By "amplification conditions" is meant conditions permitting
nucleic acid amplification according to the present invention.
Amplification conditions may, in some embodiments, be less
stringent than "stringent hybridization conditions" as described
herein. Oligonucleotides used in the amplification reactions of the
present invention hybridize to their intended targets under
amplification conditions, but may or may not hybridize under
stringent hybridization conditions. On the other hand, detection
probes of the present invention hybridize under stringent
hybridization conditions. While the Examples section infra provides
preferred amplification conditions for amplifying target nucleic
acid sequences according to the present invention, other acceptable
conditions to carry out nucleic acid amplifications according to
the present invention could be easily ascertained by someone having
ordinary skill in the art depending on the particular method of
amplification employed.
[0175] Hybridize/Hybridization
[0176] Nucleic acid hybridization is the process by which two
nucleic acid strands having completely or partially complementary
nucleotide sequences come together under predetermined reaction
conditions to form a stable, double-stranded hybrid. Either nucleic
acid strand may be a deoxyribonucleic acid (DNA) or a ribonucleic
acid (RNA) or analogs thereof. Thus, hybridization can involve
RNA:RNA hybrids, DNA:DNA hybrids, RNA:DNA hybrids, or analogs
thereof. The two constituent strands of this double-stranded
structure, sometimes called a hybrid, are held together by hydrogen
bonds. Although these hydrogen bonds most commonly form between
nucleotides containing the bases adenine and thymine or uracil (A
and T or U) or cytosine and guanine (C and G) on single nucleic
acid strands, base pairing can also form between bases which are
not members of these "canonical" pairs. Non-canonical base pairing
is well-known in the art. (See, e.g., ROGER L. P. ADAMS ET AL., THE
BIOCHEMISTRY OF THE NUCLEIC ACIDS (11.sup.th ed. 1992).)
[0177] "Stringent hybridization conditions" or "stringent
conditions" refer to conditions where a specific detection probe is
able to hybridize with target nucleic acids over other nucleic
acids present in the test sample. It will be appreciated that these
conditions may vary depending upon factors including the GC content
and length of the probe, the hybridization temperature, the
composition of the hybridization reagent or solution, and the
degree of hybridization specificity sought. Specific stringent
hybridization conditions are provided in the disclosure below.
[0178] By "nucleic acid hybrid" or "hybrid" or "duplex" is meant a
nucleic acid structure containing a double-stranded,
hydrogen-bonded region where each strand is complementary to the
other, and where the region is sufficiently stable under stringent
hybridization conditions to be detected by means including, but not
limited to, chemiluminescent or fluorescent light detection,
autoradiography, or gel electrophoresis. Such hybrids may comprise
RNA:RNA, RNA:DNA, or DNA:DNA duplex molecules.
[0179] By "complementary" is meant that the nucleotide sequences of
similar regions of two single-stranded nucleic acids, or to
different regions of the same single-stranded nucleic acid have a
nucleotide base composition that allow the single-stranded regions
to hybridize together in a stable, double-stranded hydrogen-bonded
region under stringent hybridization or amplification conditions.
When a contiguous sequence of nucleotides of one single-stranded
region is able to form a series of "canonical" hydrogen-bonded base
pairs with an analogous sequence of nucleotides of the other
single-stranded region, such that A is paired with U or T and C is
paired with G, the nucleotides sequences are "perfectly"
complementary.
[0180] By "preferentially hybridize" is meant that under stringent
hybridization conditions, certain complementary nucleotides or
nucleobase sequences hybridize to form a stable hybrid
preferentially over other, less stable duplexes. By "does not
stably hybridize" is meant that a stable hybrid is not formed in
appreciable and/or detectable amounts under a defined set of
conditions.
[0181] By "stable" or "stably hybridize" is meant that the
temperature of a reaction mixture is at least 2.degree. C. below
the melting temperature of a nucleic acid duplex.
[0182] Promoter Oligonucleotide/Promoter Sequence
[0183] As is well known in the art, a "promoter" is a specific
nucleic acid sequence that is recognized by a DNA-dependent RNA
polymerase ("transcriptase") as a signal to bind to the nucleic
acid and begin the transcription of RNA at a specific site. For
binding, it was generally thought that such transcriptases required
DNA which had been rendered double-stranded in the region
comprising the promoter sequence via an extension reaction,
however, the present inventors have determined that efficient
transcription of RNA can take place even under conditions where a
double-stranded promoter is not formed through an extension
reaction with the template nucleic acid. The template nucleic acid
(the sequence to be transcribed) need not be double-stranded.
Individual DNA-dependent RNA polymerases recognize a variety of
different promoter sequences, which can vary markedly in their
efficiency in promoting transcription. When an RNA polymerase binds
to a promoter sequence to initiate transcription, that promoter
sequence is not part of the sequence transcribed. Thus, the RNA
transcripts produced thereby will not include that sequence.
[0184] According to the present invention, a "promoter
oligonucleotide" refers to an oligonucleotide comprising first and
second regions, and which is preferably modified to prevent the
initiation of DNA synthesis from its 3'-terminus. The "first
region" of a promoter oligonucleotide of the present invention
comprises a base sequence which hybridizes to a DNA template, where
the hybridizing sequence is situated 3', but not necessarily
adjacent to, a promoter region. The hybridizing portion of a
promoter oligonucleotide of the present invention is typically at
least 10 nucleotides in length, and may extend up to 15, 20, 25,
30, 35, 40, 50 or more nucleotides in length. The "second region"
comprises a promoter for an RNA polymerase. A promoter
oligonucleotide of the present invention is engineered so that it
is incapable of being extended by an RNA- or DNA-dependent DNA
polymerase, e.g., reverse transcriptase, preferably comprising a
blocking moiety at its 3'-terminus as described above. Suitable and
preferred promoter oligonucleotides are described herein.
[0185] Universal/Pan Oligonucleotides
[0186] "Universal" oligonucleotides or "pan" oligonucleotides
include oligonucleotides that can be used in an amplification
reaction to identify the presence of nucleic acid sequences of a
class of organisms based upon highly conserved sequences that are
unique to a class of organisms. (As used herein, the term "class"
does not necessarily imply a recognized phylogenetic grouping or
organisms.) For example, the highly conserved 16S ribosomal
RNA-coding sequences contain regions that are found in bacteria, or
groupings of bacteria (e.g., Eubacteria, Gram-positive bacteria or
Gram-negative bacteria), but are not in humans and other higher
organisms, and thus oligonucleotides may be designed and used in a
nucleic acid amplification reaction to detect the presence of
bacterial sequences in a sample of interest. See, e.g., McCabe et
al. (1999) Molecular Genetics and Metabolism 66, 205-211; Schmidt,
T. et al. (1994) Meth. Enzymol. 235, 205-222 (method for
identifying pathogens); Kunishima, S. et al., (2000) Transfusion
40, 1420 (method for detecting bacteria in blood); Greisen, K.
(1994) J. Clin. Microbiol. 32, 335-351 (method for detecting
pathogenic bacteria in cerebral spinal fluid); Jordan, J. (2005) J.
Mol. Diag. 7, 575-581 (method for diagnosing sepsis in neonates);
Rothman, R. et al. (2002) J. Infect. Dis. 186, 1677-1681 (method
for diagnosing acute bacterial endocarditis); and Cox, C. et al.
(2002) Arthritis Res. Ther. 5, R1-R8 (detecting bacteria in
synovial fluid). Similarly, universal oligonucleotides for other
classes of organisms, such as fungal pathogens, have been
described. See, e.g., Maaroati, Y. et al. (2003) J. Clin.
Microbiol. 41, 3293-3298 (method for quantifying Candida albicans
in blood); Carr, M. et al. (2005) J. Clin. Microbiol. 43, 3023-3026
(method for detecting Candida dubliniensis in blood); and White, P.
et al. (2003) J. Med. Microbiol. 52, 229-238 (method for detecting
systemic fungal infections). Essentially any universal
oligonucleotides known or developed for a given class of organism
may be advantageously employed in the methods described herein.
[0187] Priming Oligonucleotide
[0188] A priming oligonucleotide is an oligonucleotide, at least
the 3'-end of which is complementary to a nucleic acid template,
and which complexes (by hydrogen bonding or hybridization) with the
template to give a primer:template complex suitable for initiation
of synthesis by an RNA- or DNA-dependent DNA polymerase. A priming
oligonucleotide is extended by the addition of covalently bonded
nucleotide bases to its 3'-terminus, which bases are complementary
to the template. The result is a primer extension product. A
priming oligonucleotide of the present invention is typically at
least 10 nucleotides in length, and may extend up to 15, 20, 25,
30, 35, 40, 50 or more nucleotides in length. Suitable and
preferred priming oligonucleotides are described herein. Virtually
all DNA polymerases (including reverse transcriptases) that are
known require complexing of an oligonucleotide to a single-stranded
template ("priming") to initiate DNA synthesis, whereas RNA
replication and transcription (copying of RNA from DNA) generally
do not require a primer. By its very nature of being extended by a
DNA polymerase, a priming oligonucleotide does not comprise a
3'-blocking moiety.
[0189] Displacer Oligonucleotide
[0190] A "displacer oligonucleotide" is a priming oligonucleotide
which hybridizes to a template nucleic acid upstream from a
neighboring priming oligonucleotide hybridized to the 3'-end of a
target sequence (referred to herein as the "forward priming
oligonucleotide"). By "upstream" is meant that a 3'-end of the
displacer oligonucleotide complexes with the template nucleic acid
5' to a 3'-end of the forward priming oligonucleotide. When
hybridized to the template nucleic acid, the 3'-terminal base of
the displacer oligonucleotide is preferably adjacent to or spaced
from the 5-terminal base of the forward priming oligonucleotide.
More preferably, the 3'-terminal base of the displacer
oligonucleotide is spaced from 5 to 35 bases from the 5'-terminal
base of the forward priming oligonucleotide. The displacer
oligonucleotide may be provided to a reaction mixture
contemporaneously with the forward priming oligonucleotide or after
the forward priming oligonucleotide has had sufficient time to
hybridize to the template nucleic acid. Extension of the forward
priming oligonucleotide can be initiated prior to or after the
displacer oligonucleotide is provided to a reaction mixture. Under
amplification conditions, the displacer oligonucleotide is extended
in a template-dependent manner, thereby displacing a primer
extension product comprising the forward priming oligonucleotide
which is complexed with the template nucleic acid. Once displaced
from the template nucleic acid, the primer extension product
comprising the forward priming oligonucleotide is available for
complexing with a promoter oligonucleotide. The forward priming
oligonucleotide and the displacer oligonucleotide both
preferentially hybridize to the target nucleic acid. Examples of
displacer oligonucleotides and their uses are disclosed by Becker
et al., "Methods and Kits for Amplifying DNA," U.S. Pat. No.
7,713,697, which enjoys common ownership herewith.
[0191] Blocking Moiety
[0192] As used herein, a "blocking moiety" is a substance used to
"block" the 3'-terminus of an oligonucleotide or other nucleic acid
so that it cannot be efficiently extended by a nucleic acid
polymerase. A blocking moiety may be a small molecule, e.g., a
phosphate or ammonium group, or it may be a modified nucleotide,
e.g., a 3'2' dideoxynucleotide or 3' deoxyadenosine 5'-triphosphate
(cordycepin), or other modified nucleotide. Additional blocking
moieties include, for example, the use of a nucleotide or a short
nucleotide sequence having a 3'-to-5' orientation, so that there is
no free hydroxyl group at the 3'-terminus, the use of a 3' alkyl
group, a 3' non-nucleotide moiety (see, e.g., Arnold et al.,
"Non-Nucleotide Linking Reagents for Nucleotide Probes," U.S. Pat.
No. 6,031,091), phosphorothioate, alkane-diol residues, peptide
nucleic acid (PNA), nucleotide residues lacking a 3' hydroxyl group
at the 3'-terminus, or a nucleic acid binding protein. Preferably,
the 3'-blocking moiety comprises a nucleotide or a nucleotide
sequence having a 3'-to-5' orientation or a 3' non-nucleotide
moiety, and not a 3'2'-dideoxynucleotide or a 3' terminus having a
free hydroxyl group. Additional methods to prepare 3'-blocking
oligonucleotides are well known to those of ordinary skill in the
art.
[0193] Binding Molecule
[0194] As used herein, a "binding molecule" is a substance which
hybridizes to or otherwise binds to an RNA target nucleic acid
adjacent to or near the 5'-end of the desired target sequence, so
as to limit a DNA primer extension product to a desired length,
i.e., a primer extension product having a generally defined 3'-end.
As used herein, the phrase "defined 3'-end" means that the 3'-end
of a primer extension product is not wholly indeterminate, as would
be the case in a primer extension reaction which occurs in the
absence of a binding molecule, but rather that the 3'-end of the
primer extension product is generally known to within a small range
of bases. In certain embodiments, a binding molecule comprises a
base region. The base region may be DNA, RNA, a DNA:RNA chimeric
molecule, or an analog thereof. Binding molecules comprising a base
region may be modified in one or more ways, as described herein.
Exemplary base regions include terminating and digestion
oligonucleotides, as described below. In other embodiments, a
binding molecule may comprise, for example, a protein or drug
capable of binding RNA with sufficient affinity and specificity to
limit a DNA primer extension product to a pre-determined
length.
[0195] Terminating Oligonucleotide
[0196] In the present invention, a "terminating oligonucleotide" is
an oligonucleotide comprising a base sequence that is complementary
to a region of the target nucleic acid in the vicinity of the
5'-end of the target sequence, so as to "terminate" primer
extension of a nascent nucleic acid that includes a priming
oligonucleotide, thereby providing a defined 3'-end for the nascent
nucleic acid strand. A terminating oligonucleotide is designed to
hybridize to the target nucleic acid at a position sufficient to
achieve the desired 3'-end for the nascent nucleic acid strand. The
positioning of the terminating oligonucleotide is flexible
depending upon its design. A terminating oligonucleotide may be
modified or unmodified. In certain embodiments, terminating
oligonucleotides are synthesized with at least one or more 2'-O-ME
ribonucleotides. These modified nucleotides have demonstrated
higher thermal stability of complementary duplexes. The 2'-O-ME
ribonucleotides also function to increase the resistance of
oligonucleotides to exonucleases, thereby increasing the half-life
of the modified oligonucleotides. See, e.g., Majlessi et al. (1988)
Nucleic Acids Res. 26, 2224-9. Other modifications as described
elsewhere herein may be utilized in addition to or in place of
2'-O-ME ribonucleotides. For example, a terminating oligonucleotide
may comprise PNA or an LNA. See, e.g., Petersen et al. (2000) J.
Mol. Recognit. 13, 44-53. A terminating oligonucleotide of the
present invention typically includes a blocking moiety at its
3'-terminus to prevent extension. A terminating oligonucleotide may
also comprise a protein or peptide joined to the oligonucleotide so
as to terminate further extension of a nascent nucleic acid chain
by a polymerase. A terminating oligonucleotide of the present
invention is typically at least 10 bases in length, and may extend
up to 15, 20, 25, 30, 35, 40, 50 or more nucleotides in length.
Suitable and preferred terminating oligonucleotides are described
herein. It should be noted that while a terminating oligonucleotide
typically or necessarily includes a 3'-blocking moiety,
"3'-blocked" oligonucleotides are not necessarily terminating
oligonucleotides. Other oligonucleotides of the present invention,
e.g., promoter oligonucleotides and capping oligonucleotides are
typically or necessarily 3'-blocked as well.
[0197] Insertion Sequence
[0198] As used herein, an "insertion sequence" is a sequence
positioned between the first region (i.e., template binding
portion) and the second region of a promoter oligonucleotide.
Insertion sequences are preferably 5 to 20 nucleotides in length,
more preferably 6 to 18 nucleotides in length, and most preferably
6 to 12 nucleotides in length. The inclusion of insertion sequences
in promoter oligonucleotides increases the rate at which RNA
amplification products are formed. Exemplary insertion sequences
are described herein.
[0199] Target Capture
[0200] Target capture, as used herein, includes any technique
effective to remove all or substantially all unhybridized tagged
oligonucleotide after hybridization of tagged oligonucleotide with
a target nucleic acid sequence but prior to amplification of the
target nucleic acid sequence. Generally, target capture involves
capturing a target polynucleotide onto a solid support, such as
magnetically attractable particles, where the solid support retains
the target polynucleotide during one or more washing steps of the
target polynucleotide purification procedure. In this way, a target
polynucleotide is substantially purified from unhybridized tagged
oligonucleotide prior to a subsequent nucleic acid amplification
step. Numerous target capture methods are known and suitable for
use in conjunction with the methods described herein.
[0201] For example, one illustrative approach described in U.S.
Pat. Appln. Pub. No. US 2006-0068417 A1 uses at least one capture
probe oligonucleotide that contains a target-complementary region
and a member of a specific binding pair that joins a target nucleic
acid to an immobilized probe on a capture support, thus forming a
capture hybrid that is separated from other sample components of a
sample. In another illustrative method, Weisburg et al., in U.S.
Pat. No. 6,110,678, describe a method for capturing a target
polynucleotide in a sample onto a solid support, such as
magnetically attractable particles, with an attached immobilized
probe by using a capture probe and two different hybridization
conditions, which preferably differ in temperature only. The two
hybridization conditions control the order of hybridization, where
the first hybridization conditions allow hybridization of the
capture probe to the target polynucleotide, and the second
hybridization conditions allow hybridization of the capture probe
to the immobilized probe. The method may be used to detect the
presence of a target polynucleotide in a sample by detecting the
captured target polynucleotide or amplified target
polynucleotide.
[0202] Another illustrative target capture technique involves a
hybridization sandwich technique for capturing and for detecting
the presence of a target polynucleotide. See Ranki et al.,
"Detection of Microbial Nucleic Acids By a One-Step Sandwich
Hybridization Test," U.S. Pat. No. 4,486,539. The technique
involves the capture of the target polynucleotide by a probe bound
to a solid support and hybridization of a detection probe to the
captured target polynucleotide. Detection probes not hybridized to
the target polynucleotide are readily washed away from the solid
support. Thus, remaining label is associated with the target
polynucleotide initially present in the sample.
[0203] Another illustrative target capture technique involves a
method that uses a mediator polynucleotide that hybridizes to both
a target polynucleotide and to a polynucleotide fixed on a solid
support. See Stabinsky, "Methods and Kits for Performing Nucleic
Acid Hybridization Assays," U.S. Pat. No. 4,751,177. The mediator
polynucleotide joins the target polynucleotide to the solid support
to produce a bound target. A labeled probe can be hybridized to the
bound target and unbound labeled pro can be washed away from the
solid support.
[0204] Yet another illustrative target capture technique is
disclosed by Englelhardt, "Capture Sandwich Hybridization Method
and Composition," U.S. Pat. No. 5,288,609, which describes a method
for detecting a target polynucleotide. The method utilizes two
single-stranded polynucleotide segments complementary to the same
or opposite strands of the target and results in the formation of a
double hybrid with the target polynucleotide. In one embodiment,
the hybrid is captured onto a support.
[0205] In another illustrative target capture technique, methods
and kits for detecting nucleic acids use oligonucleotide primers
labeled with specific binding partners to immobilize primers and
primer extension products. See Burdick et al., "Diagnostic Kit and
Method Using a Solid Phase Capture Means for Detecting Nucleic
Acids," European Pat. Appln. No. 0 370 694 A2. The label
specifically complexes with its receptor which is bound to a solid
support.
[0206] The above capture techniques are illustrative only, and not
limiting. Indeed, essentially any technique available to the
skilled artisan may be used provided it is effective for removing
all or substantially all unhybridized tagged oligonucleotide after
hybridization of tagged oligonucleotide with a target nucleic acid
sequence but prior to amplification of the target nucleic acid
sequence, as described herein.
[0207] Probe
[0208] By "probe" or "detection probe" is meant a molecule
comprising an oligonucleotide having a base sequence partly or
completely complementary to a region of a target sequence sought to
be detected, so as to hybridize thereto under stringent
hybridization conditions. As would be understood by someone having
ordinary skill in the art, a probe comprises an isolated nucleic
acid molecule, or an analog thereof, in a form not found in nature
without human intervention (e.g., recombined with foreign nucleic
acid, isolated, or purified to some extent).
[0209] The probes of this invention may have additional nucleosides
or nucleobases outside of the targeted region so long as such
nucleosides or nucleobases do not substantially affect
hybridization under stringent hybridization conditions and, in the
case of detection probes, do not prevent preferential hybridization
to the target nucleic acid. A non-complementary sequence may also
be included, such as a target capture sequence (generally a
homopolymer tract, such as a poly-A, poly-T or poly-U tail),
promoter sequence, a binding site for RNA transcription, a
restriction endonuclease recognition site, or may contain sequences
which will confer a desired secondary or tertiary structure, such
as a catalytic active site or a hairpin structure on the probe, on
the target nucleic acid, or both.
[0210] The probes preferably include at least one detectable label.
The label may be any suitable labeling substance, including but not
limited to a radioisotope, an enzyme, an enzyme cofactor, an enzyme
substrate, a dye, a hapten, a chemiluminescent molecule, a
fluorescent molecule, a phosphorescent molecule, an
electrochemiluminescent molecule, a chromophore, a base sequence
region that is unable to stably hybridize to the target nucleic
acid under the stated conditions, and mixtures of these. In one
particularly preferred embodiment, the label is an acridinium
ester. Probes may also include interacting labels which emit
different signals, depending on whether the probes have hybridized
to target sequences. Examples of interacting labels include
enzyme/substrates, enzyme/cofactor, luminescent/quencher,
luminescent/adduct, dye dimers, and Forrester energy transfer
pairs. Certain probes of the present invention do not include a
label. For example, non-labeled "capture" probes may be used to
enrich for target sequences or replicates thereof, which may then
be detected by a second "detection" probe. See, e.g., Weisburg et
al., U.S. Pat. No. 6,534,273. While detection probes are typically
labeled, certain detection technologies do not require that the
probe be labeled. See, e.g., Nygren et al., "Devices and Methods
for Optical Detection of Nucleic Acid Hybridization," U.S. Pat. No.
6,060,237.
[0211] By "stable" or "stable for detection" is meant that the
temperature of a reaction mixture is at least 2.degree. C. below
the melting temperature of a nucleic acid duplex. The temperature
of the reaction mixture is more preferably at least 5.degree. C.
below the melting temperature of the nucleic acid duplex, and even
more preferably at least 10.degree. C. below the melting
temperature of the reaction mixture.
[0212] By "preferentially hybridize" is meant that under stringent
hybridization conditions, probes of the present invention hybridize
to their target sequences, or replicates thereof, to form stable
probe:target hybrids, while at the same time formation of stable
probe:non-target hybrids is minimized. Thus, a probe hybridizes to
a target sequence or replicate thereof to a sufficiently greater
extent than to a non-target sequence, to enable one having ordinary
skill in the art to accurately quantitate the RNA replicates or
complementary DNA (cDNA) of the target sequence formed during the
amplification.
[0213] Probes of a defined sequence may be produced by techniques
known to those of ordinary skill in the art, such as by chemical
synthesis, and by in vitro or in vivo expression from recombinant
nucleic acid molecules. Preferably probes are 10 to 100 nucleotides
in length, more preferably 12 to 50 bases in length, and even more
preferably 18 to 35 bases in length.
[0214] Nucleic Acid "Identity"
[0215] In certain embodiments, a nucleic acid of the present
invention comprises a contiguous base region that is at least 80%,
90%, or 100% identical to a contiguous base region of a reference
nucleic acid. For short nucleic acids, e.g., certain
oligonucleotides of the present invention, the degree of identity
between a base region of a "query" nucleic acid and a base region
of a reference nucleic acid can be determined by manual alignment.
"Identity" is determined by comparing just the sequence of
nitrogenous bases, irrespective of the sugar and backbone regions
of the nucleic acids being compared. Thus, the query:reference base
sequence alignment may be DNA:DNA, RNA:RNA, DNA:RNA, RNA:DNA, or
any combinations or analogs thereof. Equivalent RNA and DNA base
sequences can be compared by converting U's (in RNA) to T's (in
DNA).
[0216] Template
[0217] A "template" is a nucleic acid molecule that is being copied
by a nucleic acid polymerase. A template may be single-stranded,
double-stranded or partially double-stranded, depending on the
polymerase. The synthesized copy is complementary to the template
or to at least one strand of a double-stranded or partially
double-stranded template. Both RNA and DNA are typically
synthesized in the 5'-to-3' direction and the two strands of a
nucleic acid duplex are aligned so that the 5'-termini of the two
strands are at opposite ends of the duplex (and, by necessity, so
then are the 3'-termini). While according to the present invention,
a "target sequence" is always a "template," templates can also
include secondary primer extension products and amplification
products.
[0218] DNA-Dependent DNA Polymerase
[0219] A "DNA-dependent DNA polymerase" is an enzyme that
synthesizes a complementary DNA copy from a DNA template. Examples
are Taq DNA polymerase, a highly thermostable DNA polymerase from
the thermophilic bacterium Thermus aquaticus, for PCR amplification
reactions, DNA polymerase I from E. coli, bacteriophage T7 DNA
polymerase, or DNA polymerases from bacteriophages T4, Phi-29, M2,
or T5. DNA-dependent DNA polymerases of the present invention may
be the naturally occurring enzymes isolated from bacteria or
bacteriophages or expressed recombinantly, or may be modified or
"evolved" forms which have been engineered to possess certain
desirable characteristics, e.g., thermostability, or the ability to
recognize or synthesize a DNA strand from various modified
templates. All known DNA-dependent DNA polymerases require a
complementary primer to initiate synthesis. It is known that under
suitable conditions a DNA-dependent DNA polymerase may synthesize a
complementary DNA copy from an RNA template. RNA-dependent DNA
polymerases (described below) typically also have DNA-dependent DNA
polymerase activity. An example of such a polymerase is the
MasterAmp.TM. Tth DNA Polymerase, which has both DNA-dependent and
RNA-dependent (i.e., reverse transcriptase) DNA polymerase
activities that can be used in both PCR and RT-PCR amplification
reactions (Epicentre Biotechnologies, Madison, Wis.).
[0220] DNA-Dependent RNA Polymerase (Transcriptase)
[0221] A "DNA-dependent RNA polymerase" or "transcriptase" is an
enzyme that synthesizes multiple RNA copies from a double-stranded
or partially-double-stranded DNA molecule having a promoter
sequence that is usually double-stranded. The RNA molecules
("transcripts") are synthesized in the 5'-to-3' direction beginning
at a specific position just downstream of the promoter. Examples of
transcriptases are the DNA-dependent RNA polymerase from E. coli
and bacteriophages T7, T3, and SP6.
[0222] RNA-Dependent DNA Polymerase (Reverse Transcriptase)
[0223] An "RNA-dependent DNA polymerase" or "reverse transcriptase"
("RT") is an enzyme that synthesizes a complementary DNA copy from
an RNA template. All known reverse transcriptases also have the
ability to make a complementary DNA copy from a DNA template; thus,
they are both RNA- and DNA-dependent DNA polymerases. RTs may also
have an RNAse H activity. Preferred is reverse transcriptase
derived from Maloney murine leukemia virus (MMLV-RT). A primer is
required to initiate synthesis with both RNA and DNA templates.
[0224] Selective RNAses
[0225] As used herein, a "selective RNAse" is an enzyme that
degrades the RNA portion of an RNA:DNA duplex but not
single-stranded RNA, double-stranded RNA or DNA. An exemplary
selective RNAse is RNAse H. Enzymes other than RNAse H which
possess the same or similar activity are also contemplated in the
present invention. Selective RNAses may be endonucleases or
exonucleases. Most reverse transcriptase enzymes contain an RNAse H
activity in addition to their polymerase activities. However, other
sources of the RNAse H are available without an associated
polymerase activity. The degradation may result in separation of
RNA from a RNA:DNA complex. Alternatively, a selective RNAse may
simply cut the RNA at various locations such that portions of the
RNA melt off or permit enzymes to unwind portions of the RNA. Other
enzymes which selectively degrade RNA target sequences or RNA
products of the present invention will be readily apparent to those
of ordinary skill in the art.
[0226] Sense/Antisense Strand(s)
[0227] Discussions of nucleic acid synthesis are greatly simplified
and clarified by adopting terms to name the two complementary
strands of a nucleic acid duplex. Traditionally, the strand
encoding the sequences used to produce proteins or structural RNAs
are designated as the "sense (+)" strand and its complement the
"antisense (-)" strand. It is now known that in many cases, both
strands are functional, and the assignment of the designation
"sense" to one and "antisense" to the other must then be arbitrary.
Nevertheless, the terms are very useful for designating the
sequence orientation of nucleic acids and will be employed herein
for that purpose.
[0228] Specificity of the System
[0229] The term "specificity," in the context of an amplification
system, is used herein to refer to the characteristic of an
amplification system which describes its ability to distinguish
between target and non-target sequences dependent on sequence and
assay conditions. In terms of a nucleic acid amplification,
specificity generally refers to the ratio of the number of specific
amplicons produced to the number of side-products (i.e., the
signal-to-noise ratio), described in more detail below.
[0230] Sensitivity
[0231] The term "sensitivity" is used herein to refer to the
precision with which a nucleic acid amplification reaction can be
detected or quantitated. The sensitivity of an amplification
reaction is generally a measure of the smallest copy number of the
target nucleic acid that can be reliably detected in the
amplification system, and will depend, for example, on the
detection assay being employed, and the specificity of the
amplification reaction, i.e., the ratio of specific amplicons to
side-products.
[0232] Bioprocess
[0233] A "bioprocess," as used herein, refers generally to any
process in which living cells, or components thereof, are present,
either intended or unintended. For example, essentially any
manufacturing or other process that employs one or more samples or
sample streams, at least one of which comprises living cells, or
components thereof, or may comprise such cells or components as a
result of unintended contamination, is considered a bioprocess. In
many such processes it is desirable to have the ability to detect,
identify and/or control the presence and/or sources of living cells
or components thereof within a process. Using the methods of the
present invention, for example, the presence and/or sources of
contaminating microorganisms or other biological material or
components thereof in one or more bioprocess samples or streams may
be monitored. In addition, the purification/sterilization
requirements within certain samples/streams of a bioprocess may be
advantageously reduced using the methods of the invention as set
forth herein.
[0234] As discussed above, the present invention is directed
generally to nucleic acid amplification methods that desirably
reduce or eliminate false positive amplification signals resulting
from contaminating biological material, such as nucleic acid
material, that may be present in one or more reagents, samples or
components that are used in an amplification reaction, or that may
be present in the environment in which amplification reactions are
performed. The invention further offers the advantage of requiring
less stringent purification and/or sterility efforts conventionally
needed in order to ensure that enzymes and other reagents used in
amplification reactions, and the environment in which amplification
reactions are performed, are free of bacterial and other nucleic
acid contamination that may yield false positive results.
Accordingly, the methods of the invention are particularly useful
in detecting, monitoring and/or quantitating microorganisms (or
contaminating nucleic acids from other sources) in clinical
samples, bioprocess samples or sample streams, foodstuffs, water,
industrial and environmental samples, seed stocks, and other types
of material where the presence of microorganisms or other forms of
contamination may need to be detected and/or monitored.
[0235] The present invention can be adapted for use in essentially
any amplification procedure requiring a template-binding priming
oligonucleotide capable of extension in the presence of nucleic
acid polymerase. Incorporation of the tagged oligonucleotides (or
heterologous tag sequences) into such primer-dependent
amplification procedures can be accomplished without substantially
modifying the reagents and reaction conditions of such procedures.
Any needed modifications should be minor and would be well within
the knowledge and capabilities of a skilled molecular biologist.
Descriptions of various illustrative amplification procedures
adopting tagged oligonucleotides follows.
[0236] FIG. 1 illustrates an adaptation of an isothermal,
transcription-based amplification reaction known as reverse
transcription-mediated amplification (rTMA), various aspects of
which are disclosed in Becker et al., U.S. Pat. No. 7,374,885. The
reaction of this illustrative embodiment is initiated by treating
an RNA target sequence in a nucleic acid sample with both a tagged
priming oligonucleotide and a terminating oligonucleotide. The
tagged priming oligonucleotide includes a target hybridizing
sequence that hybridizes to a 3'-end of the target sequence and a
tag sequence situated 5' to the target hybridizing sequence. The
terminating oligonucleotide hybridizes to a target nucleic acid
containing the target sequence in the vicinity of the 5'-end of the
target sequence. The terminating oligonucleotide is used to end
primer extension of a nascent nucleic acid that includes the tagged
priming oligonucleotide. Thus, the target nucleic acid forms a
stable complex with the tagged priming oligonucleotide at the
3'-end of the target sequence and the terminating oligonucleotide
located adjacent to or near the 5'-end of the target sequence prior
to initiating a primer extension reaction. See FIG. 1, Step 1.
Unhybridized tagged priming oligonucleotide is made unavailable for
hybridization to the target sequence prior to initiating a primer
extension reaction with the tagged priming oligonucleotide,
preferably by inactivating and/or removing the unhybridized tagged
priming oligonucleotide from the nucleic acid sample.
[0237] An extension reaction is then initiated from the 3'-end of
the tagged priming oligonucleotide with a DNA polymerase, e.g.,
reverse transcriptase, to produce a first DNA primer extension
product that includes the tag sequence and a region complementary
to the target sequence. See FIG. 1, Steps 2 and 3. The first DNA
primer extension product is then separated from the target sequence
using an enzyme that selectively degrades the target sequence
(e.g., RNAse H activity). See FIG. 1, Step 4.
[0238] Next, the first DNA primer extension product is treated with
a promoter oligonucleotide having a hybridizing sequence and a
promoter for an RNA polymerase situated 5' to the hybridizing
sequence. The hybridizing sequence hybridizes to a region of the
first DNA primer extension product that is complementary to the
3'-end of the target sequence, thereby forming a promoter
oligonucleotide:first DNA primer extension product hybrid. In the
illustrated reaction, the promoter oligonucleotide is modified to
prevent the initiation of DNA synthesis, preferably by situating a
blocking moiety at the 3'-end of the promoter oligonucleotide
(e.g., nucleotide sequence having a 3'-to-5' orientation). See FIG.
1, Step 5. The 3'-end of the first DNA primer extension product is
preferably extended to add a sequence complementary to the
promoter, resulting in the formation of a double-stranded promoter
sequence. See FIG. 1, Steps 6 and 7. Multiple copies of a first RNA
product complementary to at least a portion of the first DNA primer
extension product, not including the promoter portion, are then
transcribed using an RNA polymerase which recognizes the
double-stranded promoter and initiates transcription therefrom. See
FIG. 1, Steps 8 and 9. As a result, the base sequence of the first
RNA product is substantially identical to the base sequence of the
target sequence and the complement of the tag sequence.
[0239] The first RNA products are treated with a priming
oligonucleotide which hybridizes to the complement of the tag
sequence to form a priming oligonucleotide:first RNA product
hybrid, and the 3'-end of the priming oligonucleotide is extended
with the DNA polymerase to produce a second DNA primer extension
product complementary to the first RNA product. See FIG. 1, Steps
10-12. The second DNA primer extension product is then separated
from the first RNA product using an enzyme that selectively
degrades the first RNA product (e.g., RNAse H activity). See FIG.
1, Step 13.
[0240] The second DNA primer extension product is treated with the
promoter oligonucleotide, which hybridizes to the 3'-end of the
second DNA primer extension product to form a promoter
oligonucleotide:second DNA primer extension product hybrid. See
FIG. 1, Step 14. The promoter oligonucleotide:second DNA primer
extension product hybrid then re-enters the amplification cycle at
Step 6 of FIG. 1, where transcription is initiated from the
double-stranded promoter and the cycle continues.
[0241] FIG. 3 illustrates an adaptation of an isothermal,
transcription-based amplification reaction referred to as
transcription-mediated amplification (TMA), various aspects of
which are disclosed in Kacian et al., U.S. Pat. Nos. 5,399,491 and
5,824,518. The reaction of this illustrative embodiment is
initiated by treating an RNA target sequence in a nucleic acid
sample with a tagged promoter oligonucleotide. The tagged promoter
oligonucleotide includes a tag sequence, a target hybridizing
sequence and a promoter sequence for an RNA polymerase, where the
target hybridizing sequence hybridizes to a 3'-end of the target
sequence. Thus, the target sequence forms a stable complex with the
tagged promoter oligonucleotide at the 3'-end of the target
sequence prior to initiating a primer extension reaction. See FIG.
3, Step 1. The promoter sequence is situated 5' to the tag
sequence, and the tag sequence is situated 5' to the target
hybridizing sequence. Unhybridized tagged promoter oligonucleotide
is made unavailable for hybridization to the target sequence prior
to initiating a primer extension reaction with the tagged priming
oligonucleotide, preferably by inactivating and/or removing the
unhybridized tagged priming oligonucleotide from the nucleic acid
sample.
[0242] An extension reaction is then initiated from the 3'-end of
the tagged promoter oligonucleotide with a DNA polymerase, e.g.,
reverse transcriptase, to produce a first DNA primer extension
product that includes the tag and promoter sequence and a region
complementary to the target sequence. See FIG. 1, Steps 2 and 3.
The first DNA primer extension product is then separated from the
target sequence to which it is hybridized using an enzyme that
selectively degrades that portion of the target sequence which is
hybridized to the first DNA primer extension product (e.g., RNAse H
activity). See FIG. 3, Step 4.
[0243] Next, the first DNA primer extension product is treated with
a priming oligonucleotide which hybridizes to a region of the first
DNA primer extension product that is complementary to a 5'-end of
the target sequence, thereby forming a priming
oligonucleotide:first DNA primer extension product hybrid. See FIG.
3, Step 5. The 3'-end of the priming oligonucleotide is extended by
a DNA polymerase to produce a second DNA primer extension product
complementary to at least a portion of the first DNA primer
extension product, and containing a double-stranded promoter
sequence. See FIG. 3, Steps 6 and 7. This second DNA primer
extension product is used as a template to transcribe multiple
copies of a first RNA product complementary to the second DNA
primer extension product, not including the promoter portion, using
an RNA polymerase which recognizes the double-stranded promoter and
initiates transcription therefrom. See FIG. 3, Step 8 and 9. The
base sequence of the first RNA product is substantially identical
to the base sequence of the tag sequence and the complement of the
target sequence.
[0244] The first RNA product is treated with the priming
oligonucleotide, the 3'-end of which is extended by the DNA
polymerase to produce a third DNA primer extension product
complementary to the first RNA product. See FIG. 3, Steps 10-12.
The third DNA primer extension product is then separated from the
first RNA product using an enzyme which selectively degrades the
first RNA product (e.g., RNAse H activity). See FIG. 3, Step 13.
The third DNA primer extension product is treated with a promoter
oligonucleotide having a hybridizing sequence which hybridizes to a
complement of the tag sequence at the 3'-end of the third DNA
primer extension product, and further comprises a promoter for an
RNA polymerase which is situated 5' to the hybridizing sequence.
See FIG. 3, Step 14. The 3'-end of the third DNA primer extension
product is extended to add sequence complementary to the promoter
sequence. See FIG. 3, Step 15. The 3'-end of the promoter
oligonucleotide is extended with the DNA polymerase to produce a
fourth DNA primer extension product complementary to the third DNA
primer extension product. See FIG. 3, Step 16. Multiple copies of a
second RNA product complementary to the third DNA primer extension
product, not including the promoter portion, are transcribed from
the double-stranded promoter and re-enter the amplification cycle
at Step 9 of FIG. 3. The base sequence of the second RNA product is
substantially identical to the base sequence of the tag sequence
and the complement of the target sequence.
[0245] FIG. 5 illustrates an adaptation of an rTMA amplification
reaction for amplifying a DNA target sequence, various aspects of
which are disclosed in Becker et al., U.S. Pat. No. 7,713,697. The
reaction of this illustrative embodiment is initiated by treating a
DNA target sequence in a nucleic acid sample with a tagged priming
oligonucleotide and a terminating oligonucleotide. The tagged
priming oligonucleotide includes a target hybridizing sequence
hybridized to a 3'-end of the target sequence and a tag sequence
situated 5' to the target hybridizing sequence. The target
hybridizing sequence preferably hybridizes to a single-stranded
form of the target sequence, although it may hybridize to a
double-stranded form of the target sequence through strand
invasion, which can be facilitated by, for example, DNA breathing
(e.g., AT rich regions), low salt conditions, and/or the use of
DMSO and/or osmolytes, such as betaine. The target sequence is
preferably rendered single-stranded by heating the nucleic acid
sample. The terminating oligonucleotide hybridizes to a region of a
target nucleic acid containing the target sequence in the vicinity
of the 5'-end of the target sequence. The terminating
oligonucleotide is used to end primer extension of a nascent
nucleic acid that includes the tagged priming oligonucleotide.
Thus, the target nucleic acid forms a stable complex with the
tagged priming oligonucleotide at the 3'-end of the target sequence
and the terminating oligonucleotide located adjacent to or near the
5'-end of the target sequence. See FIG. 5, Steps 1-3. Unhybridized
tagged priming oligonucleotide is made unavailable for
hybridization to the target sequence prior to initiating a primer
extension reaction with the tagged priming oligonucleotide,
preferably by inactivating and/or removing the unhybridized tagged
priming oligonucleotide from the nucleic acid sample.
[0246] An extension reaction is then initiated from the 3'-end of
the tagged priming oligonucleotide with a DNA polymerase, e.g.,
reverse transcriptase, to produce a first DNA primer extension
product that includes the tag sequence and a region complementary
to the target sequence. See FIG. 5, Steps 4 and 5.
[0247] The nucleic acid sample is further treated with a displacer
oligonucleotide which hybridizes to the target nucleic acid
upstream from the tagged oligonucleotide such that a primer
extension reaction can be initiated therefrom, so that the first
DNA primer extension product is displaced when a 3'-end of the
displacer oligonucleotide is extended by the DNA polymerase. See
FIG. 5, Steps 6-8. The order of the illustrated steps is not meant
to imply that the nucleic acid sample of this embodiment must be
treated with the tagged priming oligonucleotide before it is
treated with the displacer oligonucleotide to be operational. In
certain embodiments, it is preferable to have these two
oligonucleotides hybridize to the target nucleic acid substantially
simultaneously.
[0248] Next, the first DNA primer extension product is treated with
a promoter oligonucleotide having a hybridizing sequence and a
promoter for an RNA polymerase situated 5' to the hybridizing
sequence. The hybridizing sequence hybridizes to a region of the
first DNA primer extension product that is complementary to the
3'-end of the target sequence, thereby forming a promoter
oligonucleotide:first DNA primer extension product hybrid. In the
illustrated reaction, the promoter oligonucleotide is modified to
prevent the initiation of DNA synthesis by situating a blocking
moiety at the 3'-end of the promoter oligonucleotide (e.g.,
nucleotide sequence having a 3'-to-5' orientation). See FIG. 5,
Step 9. The 3'-end of the first DNA primer extension product is
extended to add sequences complementary to the promoter, resulting
in the formation of a double-stranded promoter sequence. See FIG.
5, Steps 10 and 11. Multiple copies of a first RNA product
complementary to at least a portion of the first DNA primer
extension product, not including the promoter, are transcribed
using an RNA polymerase which recognizes the double-stranded
promoter and initiates transcription therefrom. See FIG. 5, Step 12
and 13. As a result, the base sequence of the first RNA product is
substantially identical to the base sequence of the target sequence
and the complement of the tag sequence.
[0249] The first RNA products are contacted with a priming
oligonucleotide which hybridizes to the complement of the tag
sequence to form a priming oligonucleotide:first RNA product
hybrid, and the 3'-end of the priming oligonucleotide is extended
with the DNA polymerase to produce a second DNA primer extension
product complementary to the first RNA product. See FIG. 5, Step
14-16. The second DNA primer extension product is separated from
the first RNA product using and enzyme that selectively degrades
the first RNA product (e.g., RNAse H activity). See FIG. 5, Step
17.
[0250] The second DNA primer extension product is treated with the
promoter oligonucleotide to form a promoter oligonucleotide: second
DNA primer extension product hybrid. See FIG. 5, Step 18. The
promoter oligonucleotide:second primer extension product hybrid
then re-enters the amplification cycle at Step 10 of FIG. 5, where
transcription is initiated from the double-stranded promoter and
the cycle continues.
[0251] FIG. 7 illustrates an adaptation of a polymerase chain
reaction (PCR), various aspects of which are disclosed in, for
example, Mullis et al., U.S. Pat. Nos. 4,683,195 and 4,800,159;
Mullis, U.S. Pat. No. 4,682,202; and Gelfand et al., U.S. Pat. No.
5,804,375. The reaction of this illustrative embodiment is
initiated by treating a denatured DNA target sequence in a nucleic
acid sample with a tagged priming oligonucleotide. The tagged
priming oligonucleotide includes a target hybridizing sequence that
hybridizes to a 3'-end of the target sequence and a tag sequence
situated 5' to the target hybridizing sequence. Thus, the target
sequence forms a stable complex with the tagged priming
oligonucleotide at the 3'-end of the target sequence prior to
initiating a primer extension reaction. See FIG. 7, Steps 1-3.
Unhybridized tagged priming oligonucleotide is made unavailable for
hybridization to the target sequence prior to initiating a primer
extension reaction with the tagged priming oligonucleotide,
preferably by inactivating and/or removing the unhybridized tagged
priming oligonucleotide from the nucleic acid sample.
[0252] An extension reaction is then initiated from the 3'-end of
the tagged priming oligonucleotide with a DNA polymerase, e.g., Taq
DNA polymerase, to produce a first DNA primer extension product
that includes the tag sequence and a region complementary to the
target sequence. See FIG. 7, Steps 4 and 5. Next, the
double-stranded product resulting from the first primer extension
reaction is denatured and the first DNA primer extension product is
contacted with a first priming oligonucleotide which hybridizes to
a region of the first DNA primer extension product that is
complementary to the 5'-end of the target sequence. See FIG. 7,
Steps 6 and 7.
[0253] In a second primer extension reaction, the 3'-end of the
first priming oligonucleotide is extended with the DNA polymerase
to produce a second DNA primer extension product that is
complementary to a portion of the first primer extension product
and includes the target sequence and the complement of the tag
sequence. See FIG. 7, Steps 8 and 9. The double-stranded product
resulting from the second primer extension reaction is denatured
and the second DNA primer extension product is contacted with a
second priming oligonucleotide that hybridizes to the complement of
the tag sequence. See FIG. 7, Steps 10 and 11.
[0254] The 3'-end of the second priming oligonucleotide is then
extended in a third primer extension reaction with the DNA
polymerase to produce a third DNA primer extension product that is
complementary to the second DNA primer extension product. FIG. 7,
Steps 12 and 13. The double-stranded product resulting from the
third primer extension reaction is denatured and the second and
third DNA primer extension products are available for participation
in the repeated cycles of a polymerase chain reaction using as
primers the first and second priming oligonucleotides. See FIG. 7,
Steps 14-16.
[0255] FIG. 9 illustrates an adaptation of a reverse transcription
polymerase chain reaction (RT-PCR), various aspects of which are
disclosed in, for example, Gelfand et al., U.S. Pat. Nos. 5,322,770
and 5,310,652. The reaction of this illustrative embodiment is
initiated by treating an RNA target sequence in a nucleic acid
sample with a tagged priming oligonucleotide. The tagged priming
oligonucleotide includes a target hybridizing sequence and a tag
sequence situated 5' to the target hybridizing sequence. Thus, the
target sequence forms a stable complex with the tagged priming
oligonucleotide at the 3'-end of the target sequence prior to
initiating a primer extension reaction. See FIG. 9, Step 1.
Unhybridized tagged priming oligonucleotide is made unavailable for
hybridization to the target sequence prior to initiating a primer
extension reaction with the tagged priming oligonucleotide,
preferably by inactivating and/or removing the unhybridized tagged
priming oligonucleotide from the nucleic acid sample.
[0256] An extension reaction is then initiated from the 3'-end of
the tagged priming oligonucleotide with a DNA polymerase, e.g.,
MasterAmp.TM. Tth DNA Polymerase, to produce a first DNA primer
extension product that includes the tag sequence and a region
complementary to the target sequence. See FIG. 9, Steps 2 and 3.
The first DNA primer extension product is then separated from the
target nucleic acid sequence to which it is hybridized using an
enzyme that selectively degrades that portion of a target nucleic
acid containing the target sequence that is complementary to the
first DNA primer extension product (e.g., RNAse H activity). See
FIG. 9, Step 4.
[0257] Next, the first DNA primer extension product is treated with
a first priming oligonucleotide which hybridizes to a region of the
first DNA primer extension product that is complementary to the
5'-end of the target sequence to form a first DNA primer extension
product:first priming oligonucleotide hybrid. See FIG. 9, Step 5. A
second primer extension reaction extends the 3'-end of the first
priming oligonucleotide with the DNA polymerase to produce a DNA
second primer extension product complementary to at least a portion
of the first primer extension product and includes the target
sequence and the complement of the tag sequence. See FIG. 9, Steps
6 and 7. The first and second DNA primer extension products are
then separated from each other by denaturation. See FIG. 9, Step 8.
The first and second extension products are then available to
participate in the repeated cycles of a polymerase chain reaction
using as primers the first priming oligonucleotide and a second
priming oligonucleotide which hybridizes to the complement of the
tag sequence. See FIG. 9, Steps 9 and 10; FIG. 7, Steps 13-16.
[0258] In other illustrative embodiments of the present invention,
a heterologous tag sequence which has not formed part of a tagged
target nucleic acid sequence is inactivated prior to exposing the
tagged target nucleic acid sequence to reagents and conditions
sufficient for detectable amplification of a target nucleic acid
sequence. In a preferred aspect, the inactivated heterologous tag
sequence is in the form of a tagged oligonucleotide which has not
hybridized to the target nucleic acid sequence. Tagged
oligonucleotides are described above and include first and second
regions, where the first region comprises a target hybridizing
sequence which hybridizes to a 3'-end of a target nucleic acid
sequence under a first set of conditions, and the second region
comprises a tag sequence which is located 5' to the first region of
the tagged oligonucleotide. The target hybridizing sequence has a
free 3' hydroxyl group that can be enzymatically extended in the
presence of a DNA polymerase in a template-dependent manner. The
tagged oligonucleotide has an "active" confirmation which permits
the target hybridizing sequence to hybridize to the target nucleic
acid sequence and an "inactive" confirmation which blocks the
target hybridizing sequence from hybridizing to the target nucleic
acid sequence. The inactive confirmation is generally formed under
less stringent conditions than the conditions for forming the
active confirmation of the tagged oligonucleotide.
[0259] The inactive confirmation of the tagged oligonucleotide can
be formed by hybridizing a tag closing sequence to the target
hybridizing sequence of the tagged oligonucleotide. The tag closing
sequence can constitute a discrete molecule or it can be tethered
to the tagged oligonucleotide by a linker which joins the 3'-end or
5'-end of the tag closing sequence to the 5'-end of a region of the
tagged oligonucleotide containing a tag sequence ("tagged priming
oligonucleotide") or a promoter sequence located 5' to a tag
sequence ("tagged promoter oligonucleotide"), thereby forming a
self-hybridized, hairpin tag molecule comprising the tagged
oligonucleotide. The linker does not include nucleotide bases that
can be copied by a polymerase and is preferably a non-nucleotide
linker comprised of non-nucleotide constituents. Suitable
non-nucleotide linkers for joining the tag closing sequence to the
tagged oligonucleotide include abasic nucleotides and polyethylene
glycol. Other suitable linkers include nucleotide analogs, such as
LNAs and 2'-O-Me. The association kinetics are best when the tag
closing sequence and the target hybridizing sequence of the tagged
oligonucleotide are contained in the same molecule.
[0260] Under selective conditions, the tag closing sequence can
hybridize to the target hybridizing sequence of the tagged
oligonucleotide in an antiparallel orientation, as shown in FIGS.
2, 4, 6, 8, 10, 11, 12, 15 and 16, or in a parallel orientation, as
shown in FIGS. 13 and 14. If the tag closing sequence is a discrete
molecule, as illustrated in FIGS. 11 and 12, or joined to the
tagged oligonucleotide by a non-nucleotide linker attached to its
5'-end, as illustrated in FIGS. 2, 4, 6, 8, 10, 15 and 16, then the
tag closing sequence is preferably modified to prevent primer
extension by a DNA polymerase, such as by positioning a blocking
moiety at its 3'-terminus. Suitable blocking moieties are described
herein. When hybridized in an antiparallel orientation, as
illustrated in FIGS. 13 and 14, the 3'-terminal base of the tag
closing sequence is preferably hybridized to the 3'-terminal base
of the target hybridizing sequence of the tagged oligonucleotide.
More preferably, the tag closing sequence is modified to prevent
primer extension by a DNA polymerase.
[0261] The length and base content of the tag closing sequence are
selected so that hybridization of the tagged oligonucleotide to the
target nucleic acid sequence is favored under a first set of
conditions and, when the tagged oligonucleotide is not hybridized
to the target nucleic acid sequence, so that the tag closing
sequence can form a stable hybrid with the target hybridizing
sequence under a second, less stringent set of conditions. The tag
closing sequence should be selected so that it is not readily
displaced from the target hybridizing sequence under the
amplification conditions to which it may be subjected. Typically,
the tag closing sequence will hybridize to from 5 to 20 contiguous
or non-contiguous bases of the target hybridizing sequence.
Suitable tag closing sequences preferably range from 5 to 15 bases
in length. To bias the target hybridizing sequence toward the
target nucleic acid under the first set of conditions, the tag
closing sequence may include, for example, one or more abasic
nucleotides, base mismatches or members of wobble base pairs. Tag
closing sequences are preferably selected to specifically hybridize
to the target hybridizing sequence more strongly than any
non-specific interactions with other nucleic acids present in an
amplification reaction.
[0262] Following inactivation, inactive tagged oligonucleotides are
preferably removed from a sample to limit unintended interactions
with target nucleic acid sequences entering the sample from a
potentially contaminating source. Removal can be accomplished by
immobilizing target nucleic acids in a sample on a solid support
and then removing other components of the sample, including
inactivated tagged oligonucleotides. To ensure that inactive tagged
oligonucleotides are removed, the number of non-specific
interactions between the solid support and nucleic acids present in
the sample should be limited. Any known solid support may be used
for sample processing, such as matrices and particles that are free
in solution. Particularly preferred supports are magnetic spheres
that are monodisperse (i.e., uniform in size.+-.5%), thereby
providing consistent results, which is particularly advantageous
for use in an automated procedure.
[0263] Particularly preferred amplification techniques for
incorporating the tagged oligonucleotides of the present invention
include isothermal amplification reactions, such as TMA and
variations of TMA, like real-time TMA, which incorporates one or
more feature of the methods described by Becker et al., U.S. Pat.
No. 7,374,885, and Becker et al., U.S. Pat. No. 7,713,697. For
example, certain preferred real-time TMA methods include the use of
blocking moieties, terminating moieties, and/or other modifying
moieties that provide improved TMA process sensitivity and
accuracy.
[0264] Promoter oligonucleotides may be modified to prevent the
synthesis of DNA therefrom. For example, a promoter oligonucleotide
may comprise a blocking moiety attached at its 3'-terminus to
prevent primer extension in the presence of a polymerase. In one
example, at least about 80% of the oligonucleotides present in the
amplification reaction which comprise a promoter further comprise a
3'-blocking moiety. In another embodiment, at least about 85%, 90%,
95%, 96%, 97%, 98%, 99% or 100% of the oligonucleotides provided to
the amplification reaction which comprise a promoter are further
modified to comprise a 3'-blocking moiety. In another embodiment,
any oligonucleotide used in an amplification reaction of the
present invention which comprises a promoter sequence further
comprises a 3'-terminus blocking moiety.
[0265] Certain embodiments of the present invention relate to
amplification of a target nucleic acid comprising an RNA target
sequence. In some cases, the target nucleic acid has indeterminate
3'- and 5'-ends relative to the desired RNA target sequence. The
target nucleic acid is treated with a priming oligonucleotide which
has a base region sufficiently complementary to a 3'-end of the RNA
target sequence to hybridize therewith and, as discussed above,
further comprises a heterologous tag sequence in the first primer
extension reaction. Priming oligonucleotides are designed to
hybridize to a suitable region of any desired target sequence,
according to primer design methods well known to those of ordinary
skill in the art. While the presence of the tag sequence in a
priming oligonucleotide may alter the binding characteristics of a
target hybridizing region to a target nucleic acid sequence, the
artisan skilled in the molecular arts can readily design priming
oligonucleotides which contain both target hybridizing regions and
tag sequences that can be used in accordance with the methods
described herein. Suitable priming oligonucleotides are described
in more detail herein. Additionally, the 5'-end of a priming
oligonucleotide (preferably not a tagged priming oligonucleotide)
may include one or modifications which improve the binding
properties (e.g., hybridization or base stacking) of the priming
oligonucleotide to a DNA extension product or to an RNA
amplification product, as discussed more fully infra, provided the
modifications do not substantially interfere with the priming
function of the priming oligonucleotide or cleavage of an RNA
amplification product to which the priming oligonucleotide is
hybridized. The 3'-end of the priming oligonucleotide is extended
by an appropriate DNA polymerase, e.g., an RNA-dependent DNA
polymerase ("reverse transcriptase") in an extension reaction using
the RNA target sequence or amplification product as a template to
give a DNA primer extension product which is complementary to the
RNA template or amplification product.
[0266] DNA primer extension products are separated (at least
partially) from an RNA template using an enzyme which degrades the
RNA template or amplification product. Suitable enzymes, i.e.,
"selective RNAses," are those which act on the RNA strand of an
RNA:DNA complex, and include enzymes which comprise an RNAse H
activity. Some reverse transcriptases include an RNAse H activity,
including those derived from Moloney murine leukemia virus and
avian myeloblastosis virus. According to preferred amplification
embodiments, the selective RNAse may be provided as an RNAse H
activity of a reverse transcriptase, or may be provided as a
separate enzyme, e.g., as an E. coli RNAse H or a T. thermophilus
RNAse H. Other enzymes which selectively degrade RNA present in an
RNA:DNA duplex may also be used.
[0267] When the target sequence is DNA, a DNA primer extension
product can be separated from the template by treating the target
nucleic acid with a displacer oligonucleotide. The displacer
oligonucleotide has a priming function and is designed to hybridize
to the target nucleic acid upstream from the priming
oligonucleotide (referred to as the "forward priming
oligonucleotide" in this embodiment). By "upstream" is meant that a
3'-end of the displacer oligonucleotide hybridizes to the target
nucleic acid upstream from a 3'-end of the forward priming
oligonucleotide. Thus, the displacer oligonucleotide and the
forward priming oligonucleotide may hybridize to overlapping or
distinct regions of the target nucleic acid. In preferred
embodiments, the 3'-terminus of the displacer oligonucleotide is
adjacent to or spaced up to 5 to 35 bases from the 5'-terminus of
the forward priming oligonucleotide relative to the target nucleic
acid (i.e., the target nucleic acid has up to 5 to 35, contiguous
unbound nucleotides situated between the 3'-terminal base of the
displacer oligonucleotide and the 5'-terminal base of the priming
oligonucleotide when both oligonucleotides are hybridized to the
target nucleic acid). The displacer oligonucleotide is generally
from 10 to 50 nucleotides in length and may include one or more
modifications at the 5'-end which improve the binding properties
(e.g., hybridization or base stacking) of the displacer
oligonucleotide to the target nucleic acid, provided that the
modifications do not substantially interfere with the priming
function of the displacer oligonucleotide. The displacer
oligonucleotide and the forward priming oligonucleotide are
designed to hybridize to the target nucleic acid under the same
conditions. The target nucleic acid is preferably treated with the
displacer oligonucleotide after the forward priming oligonucleotide
has had sufficient time to hybridize to the target nucleic acid.
Alternatively, the target nucleic acid is treated with both the
displacer oligonucleotide and the forward priming oligonucleotide
before exposing the mixture to a polymerase suitable for extending
the 3'-ends of the displacer oligonucleotide and the forward
priming oligonucleotide. In the presence of the DNA polymerase, the
3'-end of the displacer oligonucleotide is extended in a
template-dependent manner to form a second DNA primer extension
product which displaces the first DNA primer extension product from
the target nucleic acid, thereby making it available for
hybridization to a promoter oligonucleotide. In an alternative
approach, conditions could be established whereby the promoter
oligonucleotide gains access the first DNA primer extension product
through stand invasion facilitated by, for example, DNA breathing
(e.g., AT rich regions), low salt conditions, and/or the use of
DMSO and/or osmolytes, such as betaine. The promoter
oligonucleotide of this embodiment is the same as that described
above and, likewise, is modified to prevent the promoter
oligonucleotide from functioning as a priming oligonucleotide for a
DNA polymerase (e.g., the promoter oligonucleotide includes a
blocking moiety at its 3'-terminus).
[0268] In certain embodiments, the methods of the present invention
further comprise treating the target nucleic acid as described
above to limit the length of the DNA primer extension product to a
certain desired length. Such length limitation is typically carried
out through use of a "binding molecule" which hybridizes to or
otherwise binds to the RNA target nucleic acid adjacent to or near
the 5'-end of the desired target sequence. In certain embodiments,
a binding molecule comprises a base region. The base region may be
DNA, RNA, a DNA:RNA chimeric molecule, or an analog thereof.
Binding molecules comprising a base region may be modified in one
or more ways, as described elsewhere herein. Suitable binding
molecules include, but are not limited to, a binding molecule
comprising a terminating oligonucleotide or a terminating protein
that binds RNA and prevents primer extension past its binding
region, or a binding molecule comprising a modifying molecule, for
example, a modifying oligonucleotide such as a "digestion"
oligonucleotide that directs hydrolysis of that portion of the RNA
target hybridized to the digestion oligonucleotide, or a
sequence-specific nuclease that cuts the RNA target.
[0269] Illustrative terminating oligonucleotides of the present
invention have a 5'-base region sufficiently complementary to the
target nucleic acid at a region adjacent to, near to, or
overlapping with the 5'-end of the target sequence, to hybridize
therewith. In certain embodiments, a terminating oligonucleotide is
synthesized to include one or more modified nucleotides. For
example, certain terminating oligonucleotides of the present
invention comprise one or more 2'-O-ME ribonucleotides, or are
synthesized entirely of 2'-O-ME ribonucleotides. See, e.g.,
Majlessi et al. (1998) Nucleic Acids Res., 26, 2224-2229. A
terminating oligonucleotide of the present invention typically also
comprises a blocking moiety at its 3'-end to prevent the
terminating oligonucleotide from functioning as a primer for a DNA
polymerase. In some embodiments, the 5'-end of a terminating
oligonucleotide of the present invention overlaps with and is
complementary to at least about 2 nucleotides of the 5'-end of the
target sequence. Typically, the 5'-end of a terminating
oligonucleotide of the present invention overlaps with and is
complementary to at least 3, 4, 5, 6, 7, or 8 nucleotides of the
5'-end of the target sequence, but no more than about 10
nucleotides of the 5'-end of the target sequence. (As used herein,
the term "end" refers to a 5'- or 3'-region of an oligonucleotide,
nucleic acid or nucleic acid region which includes, respectively,
the 5'- or 3'-terminal base of the oligonucleotide, nucleic acid or
nucleic acid region.) Suitable terminating oligonucleotides are
described in more detail herein.
[0270] A single-stranded DNA primer extension product, or "first"
DNA primer extension product, which has either a defined 3'-end or
an indeterminate 3'-end, is treated with a promoter oligonucleotide
which comprises a first region sufficiently complementary to a
3'-region of the DNA primer extension product to hybridize
therewith, a second region comprising a promoter for an RNA
polymerase, e.g., T7 polymerase, which is situated 5' to the first
region, e.g., immediately 5' to or spaced from the first region,
and modified to prevent the promoter oligonucleotide from
functioning as a primer for a DNA polymerase (e.g., the promoter
oligonucleotide includes a blocking moiety attached at its
3'-terminus). Upon identifying a desired hybridizing "first
region," suitable promoter oligonucleotides can be constructed by
one of ordinary skill in the art using only routine procedures.
Those of ordinary skill in the art will readily understand that a
promoter region has certain nucleotides which are required for
recognition by a given RNA polymerase. In addition, certain
nucleotide variations in a promoter sequence might improve the
functioning of the promoter with a given enzyme, including the use
of insertion sequences.
[0271] Insertion sequences may be positioned between the first and
second regions of promoter oligonucleotides and function to
increase amplification rates. (The tag sequence of a tagged
promoter oligonucleotide may provide this beneficial effect.) The
improved amplification rates may be attributable to several
factors. First, because an insertion sequence increases the
distance between the 3'-end and the promoter sequence of a promoter
oligonucleotide, it is less likely that a polymerase, e.g., reverse
transcriptase, bound at the 3'-end of the promoter oligonucleotide
will interfere with binding of the RNA polymerase to the promoter
sequence, thereby increasing the rate at which transcription can be
initiated. Second, the insertion sequence selected may itself
improve the transcription rate by functioning as a better template
for transcription than the target sequence. Third, since the RNA
polymerase will initiate transcription at the insertion sequence,
the primer extension product synthesized by the priming
oligonucleotide, using the RNA transcription product as a template,
will contain the complement of the insertion sequence toward the
3'-end of the primer extension product. By providing a larger
target binding region, i.e., one which includes the complement of
the insertion sequence, the promoter oligonucleotide may bind to
the primer extension product faster, thereby leading to the
production of additional RNA transcription products sooner.
Insertion sequences are preferably 5 to 20 nucleotides in length
and should be designed to minimize intramolecular folding and
intermolecular binding with other oligonucleotides present in the
amplification reaction mixture. Programs which aid in minimizing
secondary structure are well known in the art and include Michael
Zucker's mfold software for predicting RNA and DNA secondary
structure using nearest neighbor thermodynamic rules. The latest
version of Michael Zucker's mfold software can be accessed on the
Web at www.bioinfo.rpi.edu/applications/mfold using a hypertext
transfer protocol (http) in the URL. Useful insertion sequences may
be identified using in vitro selection methods well known in the
art without engaging in anything more than routine
experimentation.
[0272] Assaying promoter oligonucleotides with variations in the
promoter sequences is easily carried out by the skilled artisan
using routine methods. Furthermore, if it is desired to utilize a
different RNA polymerase, the promoter sequence in the promoter
oligonucleotide is easily substituted by a different promoter.
Substituting different promoter sequences is well within the
understanding and capabilities of those of ordinary skill in the
art. For real-time TMA, promoter oligonucleotides provided to the
amplification reaction mixture are modified to prevent efficient
initiation of DNA synthesis from their 3'-termini, and preferably
comprise a blocking moiety attached at their 3'-termini.
Furthermore, terminating oligonucleotides and capping
oligonucleotides, and even probes used in certain embodiments of
the present invention also optionally comprise a blocking moiety
attached at their 3'-termini.
[0273] Where a terminating oligonucleotide is used, the first
region of the promoter oligonucleotide is designed to hybridize
with a desired 3'-end of the DNA primer extension product with
substantial, but not necessarily exact, precision. Subsequently,
the second region of the promoter oligonucleotide may act as a
template, allowing the first DNA primer extension product to be
further extended to add a base region complementary to the second
region of the promoter oligonucleotide, i.e., the region comprising
the promoter sequence, rendering the promoter double-stranded. An
RNA polymerase which recognizes the promoter binds to the promoter
sequence, and initiates transcription of multiple RNA copies
complementary to the DNA primer extension product, which copies are
substantially identical to the target sequence. By "substantially
identical" it is meant that the multiple RNA copies may have
additional nucleotides either 5' or 3' relative to the target
sequence, or may have fewer nucleotides either 5' or 3' relative to
the target sequence, depending on, e.g., the boundaries of "the
target sequence," the transcription initiation point, or whether
the priming oligonucleotide comprises additional nucleotides 5' of
the primer region (e.g., a linked "cap" as described herein). Where
a target sequence is DNA, the sequence of the RNA copies is
described herein as being "substantially identical" to the target
sequence. It is to be understood, however, that an RNA sequence
which has uridine residues in place of the thymidine residues of
the DNA target sequence still has a "substantially identical"
sequence. The RNA transcripts so produced may automatically recycle
in the above system without further manipulation. Thus, this
reaction is autocatalytic. In those embodiments where a binding
molecule or other means for terminating a primer extension reaction
is not used, the first region of the promoter oligonucleotide is
designed to hybridize with a selected region of the first DNA
primer extension product which is expected to be 5' to the
3'-terminus of the first DNA primer extension product, but since
the 3'-terminus of the first DNA primer extension product is
indeterminate, the region where the promoter oligonucleotide
hybridizes probably will not be at the actual 3'-end of the first
DNA primer extension product. According to this embodiment, it is
generally the case that at least the 3'-terminal base of the first
DNA primer extension product does not hybridize to the promoter
oligonucleotide. Thus, according to this embodiment the first DNA
primer extension product will likely not be further extended to
form a double-stranded promoter.
[0274] The formation of a double-stranded promoter sequence through
extension of a template nucleic acid is not necessary to permit
initiation of transcription of RNA complementary to the first DNA
primer extension product. The resulting "first" RNA products are
substantially identical to the target sequence, having a 5'-end
defined by the transcription initiation point, and a 3'-end defined
by the 5'-end of the first DNA primer extension product. A
sufficient number of first RNA products are produced to
automatically recycle in the system without further manipulation.
The priming oligonucleotide hybridizes to the 3'-end of the first
RNA products, and is extended by a DNA polymerase to form a second
DNA primer extension product. Unlike the first DNA primer extension
product formed without the use of a terminating oligonucleotide or
other binding molecule, the second DNA primer extension product has
a defined 3'-end which is complementary to the 5'-ends of the first
RNA products. The second DNA primer extension product is separated
(at least partially) from the RNA template using an enzyme which
selectively degrades the RNA template. The single-stranded second
DNA primer extension product is then treated with a promoter
oligonucleotide as described above, and the second region of the
promoter oligonucleotide acts as a template, allowing the second
DNA primer extension product to be further extended to add a base
region complementary to the second region of the promoter
oligonucleotide, i.e., the region comprising the promoter sequence,
rendering the promoter double-stranded. An RNA polymerase which
recognizes the promoter binds to the promoter sequence, and
initiates transcription of multiple "second" RNA products
complementary to the second DNA primer extension product, and
substantially identical to the target sequence. The second RNA
transcripts so produced automatically recycle in the above system
without further manipulation. Thus, this reaction is
autocatalytic.
[0275] In any of the embodiments described above, once a desired
region for the target sequence is identified, that region can be
analyzed to determine where selective RNAse degradation will
optimally cause cuts or removal of sections of RNA from the RNA:DNA
duplex. Analyses can be conducted to determine the effect of the
RNAse degradation of the target sequence by RNAse H activity
present in AMV reverse transcriptase or MMLV reverse transcriptase,
by an exogenously added selective enzyme with an RNAse activity,
e.g., E. coli RNAse H, or selective enzymes with an RNAse activity
from other sources, and by combinations thereof. Following such
analyses, the priming oligonucleotide can be selected for so that
it will hybridize to a section of RNA which is substantially
nondegraded by the selective RNAse present in the reaction mixture,
because substantial degradation at the binding site for the priming
oligonucleotide could inhibit initiation of DNA synthesis and
prevent optimal extension of the primer. In other words, a priming
oligonucleotide is typically selected to hybridize with a region of
the RNA target nucleic acid or the complement of the DNA target
nucleic acid, located so that when the RNA is subjected to
selective RNAse degradation, there is no substantial degradation
which would prevent formation of the primer extension product.
[0276] Conversely, the site for hybridization of the promoter
oligonucleotide may be chosen so that sufficient degradation of the
RNA strand occurs to permit efficient hybridization of the promoter
oligonucleotide to the DNA strand. Typically, only portions of RNA
are removed from the RNA:DNA duplex through selective RNAse
degradation and, thus, some parts of the RNA strand will remain in
the duplex. Selective RNAse degradation on the RNA strand of an
RNA:DNA hybrid results in the dissociation of small pieces of RNA
from the hybrid. Positions at which RNA is selectively degraded may
be determined through standard hybridization analyses. Thus, a
promoter oligonucleotide may be selected which will more
efficiently bind to the DNA after selective RNAse degradation,
i.e., will bind at areas where RNA fragments are selectively
removed.
[0277] Promoters or promoter sequences suitable for incorporation
in promoter oligonucleotides used in the methods of the present
invention are nucleic acid sequences (either naturally occurring,
produced synthetically or a product of a restriction digest) that
are specifically recognized by an RNA polymerase that recognizes
and binds to that sequence and initiates the process of
transcription, whereby RNA transcripts are produced. Typical, known
and useful promoters include those which are recognized by certain
bacteriophage polymerases, such as those from bacteriophage T3, T7,
and SP6, and a promoter from E. coli. The sequence may optionally
include nucleotide bases extending beyond the actual recognition
site for the RNA polymerase which may impart added stability or
susceptibility to degradation processes or increased transcription
efficiency. Promoter sequences for which there is a known and
available polymerase that is capable of recognizing the initiation
sequence are particularly suitable to be employed.
[0278] Suitable DNA polymerases for use in accordance with the
methods of the invention include reverse transcriptases.
Particularly suitable DNA polymerases include AMV reverse
transcriptase and MMLV reverse transcriptase. Some of the reverse
transcriptases suitable for use in the methods of the present
invention, such as AMV and MMLV reverse transcriptases, have an
RNAse H activity. Indeed, according to certain embodiments of the
present invention, the only selective RNAse activity in the
amplification reaction is provided by the reverse transcriptase--no
additional selective RNAse is added. However, in some situations it
may also be useful to add an exogenous selective RNAse, such as E.
coli RNAse H. Although the addition of an exogenous selective RNAse
is not required, under certain conditions, the RNAse H activity
present in, e.g., AMV reverse transcriptase may be inhibited or
inactivated by other components present in the reaction mixture. In
such situations, addition of an exogenous selective RNAse may be
desirable. For example, where relatively large amounts of
heterologous DNA are present in the reaction mixture, the native
RNAse H activity of the AMV reverse transcriptase may be somewhat
inhibited and thus the number of copies of the target sequence
produced accordingly reduced. In situations where the target
nucleic acid comprises only a small portion of the nucleic acid
present (e.g., where the sample contains significant amounts of
heterologous DNA and/or RNA), it is particularly useful to add an
exogenous selective RNAse. See, e.g., Kacian et al, U.S. Pat. No.
5,399,491.
[0279] RNA amplification products produced by the methods described
above may serve as templates to produce additional amplification
products related to the target sequence through the above-described
mechanisms. The system is autocatalytic and amplification by the
methods of the present invention occurs without the need for
repeatedly modifying or changing reaction conditions such as
temperature, pH, ionic strength and the like. These methods do not
require an expensive thermal cycling apparatus, nor do they require
several additions of enzymes or other reagents during the course of
an amplification reaction.
[0280] As noted above, the methods of the present invention are
useful in assays for detecting and/or quantitating specific nucleic
acid target sequences in clinical, water, environmental,
industrial, beverage, food, seed stocks and other samples or to
produce large numbers of RNA amplification products from a specific
target sequence for a variety of uses. For example, the present
invention is useful to screen clinical samples (e.g., blood, urine,
feces, saliva, semen, or spinal fluid), food, water, laboratory
and/or industrial samples for the presence of specific nucleic
acids, specific organisms (e.g., using species-specific
oligonucleotides) and/or specific classes of organisms in
applications such as in sterility testing (e.g., using universal
oligonucleotides). The present invention can be used to detect the
presence of, for example, viruses, bacteria, fungi, or
parasites.
[0281] The amplification product can be detected by any
conventional means. For example, amplification product can be
detected by hybridization with a detectably labeled probe and
measurement of the resulting hybrids. Design criteria in selecting
probes for detecting particular target sequences are well known in
the art and are described in, for example, Hogan et al., "Methods
for Making Oligonucleotide Probes for the Detection and/or
Quantitation of Non-Viral Organisms," U.S. Pat. No. 6,150,517.
Hogan teaches that probes should be designed to maximize homology
for the target sequence(s) and minimize homology for possible
non-target sequences. To minimize stability with non-target
sequences, Hogan instructs that guanine and cytosine rich regions
should be avoided, that the probe should span as many destabilizing
mismatches as possible, and that the length of perfect
complementarity to a non-target sequence should be minimized.
Contrariwise, stability of the probe with the target sequence(s)
should be maximized, adenine and thymine rich regions should be
avoided, probe:target hybrids are preferably terminated with
guanine and cytosine base pairs, extensive self-complementarity is
generally to be avoided, and the melting temperature of
probe:target hybrids should be about 2-10.degree. C. higher than
the assay temperature.
[0282] In a particular embodiment, the amplification product can be
assayed by the Hybridization Protection Assay ("HPA"), which
involves hybridizing a chemiluminescent oligonucleotide probe to
the target sequence, e.g., an acridinium ester-labeled ("AE")
probe, selectively hydrolyzing the chemiluminescent label present
on unhybridized probe, and measuring the chemiluminescence produced
from the remaining probe in a luminometer. See, e.g., Arnold et
al., "Homogenous Protection Assay," U.S. Pat. No. 5,283,174 and
NORMAN C. NELSON ET AL., NONISOTOPIC PROBING, BLOTTING, AND
SEQUENCING, ch. 17 (Larry J. Kricka ed., 2d ed. 1995).
[0283] In further embodiments, the present invention provides
quantitative evaluation of the amplification process in real-time
by methods described herein. Evaluation of an amplification process
in "real-time" involves determining the amount of amplicon in the
reaction mixture either continuously or periodically during the
amplification reaction, and the determined values are used to
calculate the amount of target sequence initially present in the
sample. There are a variety of methods for determining the amount
of initial target sequence present in a sample based on real-time
amplification. These include those disclosed by Wittwer et al.,
"Method for Quantification of an Analyte," U.S. Pat. No. 6,303,305,
and Yokoyama et al., "Method for Assaying Nucleic Acid," U.S. Pat.
No. 6,541,205. Another method for determining the quantity of
target sequence initially present in a sample, but which is not
based on a real-time amplification, is disclosed by Ryder et al.,
"Method for Determining Pre-Amplification Levels of a Nucleic Acid
Target Sequence from Post-Amplification Levels of Product," U.S.
Pat. No. 5,710,029. Amplification products may be detected in
real-time through the use of various self-hybridizing probes, most
of which have a stem-loop structure. Such self-hybridizing probes
are labeled so that they emit differently detectable signals,
depending on whether the probes are in a self-hybridized state or
an altered state through hybridization to a target sequence. By way
of example, "molecular torches" are a type of self-hybridizing
probe which includes distinct regions of self-complementarity
(referred to as "the target binding domain" and "the target closing
domain") which are connected by a joining region (e.g.,
non-nucleotide linker) and which hybridize to each other under
predetermined hybridization assay conditions. In a preferred
embodiment, molecular torches contain single-stranded base regions
in the target binding domain that are from 1 to about 20 bases in
length and are accessible for hybridization to a target sequence
present in an amplification product under strand displacement
conditions. Under strand displacement conditions, hybridization of
the two complementary regions (which may be fully or partially
complementary) of the molecular torch is favored, except in the
presence of the target sequence, which will bind to the
single-stranded region present in the target binding domain and
displace all or a portion of the target closing domain. The target
binding domain and the target closing domain of a molecular torch
include a detectable label or a pair of interacting labels (e.g.,
luminescent/quencher) positioned so that a different signal is
produced when the molecular torch is self-hybridized than when the
molecular torch is hybridized to the target sequence, thereby
permitting detection of probe:target duplexes in a test sample in
the presence of unhybridized molecular torches. Molecular torches
and a variety of types of interacting label pairs are disclosed by
Becker et al., "Molecular Torches," U.S. Pat. No. 6,534,274.
[0284] Another example of a detection probe having
self-complementarity is a "molecular beacon." Molecular beacons
include nucleic acid molecules having a target complement sequence,
an affinity pair (or nucleic acid arms) holding the probe in a
closed conformation in the absence of a target sequence present in
an amplification product, and a label pair that interacts when the
probe is in a closed conformation. Hybridization of the target
sequence and the target complement sequence separates the members
of the affinity pair, thereby shifting the probe to an open
conformation. The shift to the open conformation is detectable due
to reduced interaction of the label pair, which may be, for
example, a fluorophore and a quencher (e.g., DABCYL and EDANS).
Molecular beacons are disclosed by Tyagi et al., "Detectably
Labeled Dual Confirmation Oligonucleotide Probes, Assays and Kits,"
U.S. Pat. No. 5,925,517, and Tyagi et al., "Nucleic Acid Detection
Probes Having Non-FRET Fluorescence Quenching and Kits and Assays
Including Such Probes," U.S. Pat. No. 6,150,097.
[0285] Other self-hybridizing probes for use in the present
invention are well known to those of ordinary skill in the art. By
way of example, probe binding pairs having interacting labels, such
as those disclosed by Morrison, "Competitive Homogenous Assay,"
U.S. Pat. No. 5,928,862 and Gelfand et al., U.S. Pat. No. 5,804,375
for PCR reactions, might be adapted for use in the present
invention. Additional detection systems include "molecular
switches," as disclosed by Arnold et al., "Oligonucleotides
Comprising a Molecular Switch," U.S. Pat. Appln. Pub. No. US
2005-0042638 A1. And other probes, such as those comprising
intercalating dyes and/or fluorochromes, might be useful for
detection of amplification products in the present invention. See,
e.g., Ishiguro et al., "Method of Detecting Specific Nucleic Acid
Sequences," U.S. Pat. No. 5,814,447.
[0286] In those methods of the present invention where the initial
target sequence and the RNA transcription product share the same
sense, it may be desirable to initiate amplification before adding
probe for real-time detection. Adding probe prior to initiating an
amplification reaction may slow the rate of amplification since
probe which binds to the initial target sequence has to be
displaced or otherwise remove during the primer extension step to
complete a primer extension product having the complement of the
target sequence. The initiation of amplification is judged by the
addition of amplification enzymes (e.g., a reverse transcriptase
and an RNA polymerase).
[0287] In addition to the methods described herein, the present
invention is drawn to kits comprising one or more of the reagents
required for carrying out the methods of the present invention.
Kits comprising various components used in carrying out the present
invention may be configured for use in any procedure requiring
amplification of nucleic acid target molecules, and such kits can
be customized for various different end-users. Suitable kits may be
prepared, for example, for microbiological analysis, blood
screening, disease diagnosis, water testing, product release or
sterility testing, environmental or industrial analysis, food or
beverage testing, or for general laboratory use. Kits of the
present invention provide one or more of the components necessary
to carry out nucleic acid amplifications according to the
invention. Kits may include reagents suitable for amplifying
nucleic acids from one particular target or may include reagents
suitable for amplifying multiple targets. Kits of the present
invention may further provide reagents for real-time detection of
one or more nucleic acid targets in a single sample, for example,
one or more self-hybridizing probes as described above. Kits may
comprise a carrier that may be compartmentalized to receive in
close confinement one or more containers such as vials, test tubes,
wells, and the like. Preferably at least one of such containers
contains one or more components or a mixture of components needed
to perform the amplification methods of the present invention.
[0288] A kit according to one embodiment of the present invention
can include, for example, in one or more containers, a tagged
oligonucleotide, alone or in combination with a tag closing
oligonucleotide or joined to a tag closing sequence, a binding
molecule or other means for terminating a primer extension
reaction, and, optionally, an extender oligonucleotide and/or a
capping oligonucleotide. If real-time detection is used, the one or
more containers may include one or more reagents for real-time
detection of at least one nucleic acid target sequence in a single
sample, for example, one or more self-hybridizing probes as
described above. Another container may contain an enzyme reagent,
such as a heat stable DNA polymerase for performing a PCR or RT-PCR
reaction, or a mixture of a reverse transcriptase (either with or
without RNAse H activity), an RNA polymerase, and optionally an
additional selective RNAse enzyme for a transcription-based
amplification reaction. These enzymes may be provided in
concentrated form or at working concentration, usually in a form
which promotes enzyme stability. The enzyme reagent may also be
provided in a lyophilized form. See Shen et al., "Stabilized Enzyme
Compositions for Nucleic Acid Amplification," U.S. Pat. No.
5,834,254. Another one or more containers may contain an
amplification reagent in concentrated form, e.g., 10.times.,
50.times., or 100.times., or at working concentration. An
amplification reagent will contain one or more of the components
necessary to run the amplification reaction, e.g., a buffer,
MgCl.sub.2, KCl, dNTPs, rNTPs, EDTA, stabilizing agents, etc.
Certain of the components, e.g., MgCl.sub.2 and rNTPs, may be
provided separately from the remaining components, allowing the end
user to titrate these reagents to achieve more optimized
amplification reactions. Another one or more containers may include
reagents for detection of amplification products, including one or
more labeled oligonucleotide probes. Probes may be labeled in a
number of alternative ways, e.g., with radioactive isotopes,
fluorescent labels, chemiluminescent labels, nuclear tags,
bioluminescent labels, intercalating dyes, or enzyme labels. In
some embodiments, a kit of the present invention will also include
one or more containers containing one or more positive and negative
control target nucleic acids which can be utilized in amplification
experiments in order to validate the test amplifications carried
out by the end user. In some instances, one or more of the reagents
listed above may be combined with an internal control. Of course,
it is also possible to combine one or more of these reagents in a
single tube or other containers. Supports suitable for use with the
invention, e.g., test tubes, multi-tube units, multi-well plates,
etc., may also be supplied with kits of the invention. Finally a
kit of the present invention may include one or more instruction
manuals.
[0289] Kits of the invention may contain virtually any combination
of the components set out above or described elsewhere herein. As
one skilled in the art would recognize, the components supplied
with kits of the invention will vary with the intended use for the
kits, and the intended end user. Thus, kits may be specifically
designed to perform various functions set out in this application
and the components of such kits will vary accordingly.
[0290] The present invention is further drawn to various
oligonucleotides including, for example, the target specific
oligonucleotides exemplified below. It is to be understood that
oligonucleotides of the present invention may be DNA, RNA, DNA:RNA
chimerics and analogs thereof, and, in any case, the present
invention includes RNA equivalents of DNA oligonucleotides and DNA
equivalents of RNA oligonucleotides.
[0291] Detection probes of the present invention may include, for
example, an acridinium ester label, or labeled, self-hybridizing
regions flanking the sequence which hybridizes to the target
sequence. In various embodiments, these labeled oligonucleotide
probes optionally or preferably are synthesized to include at least
one modified nucleotide, e.g., a 2'-O-ME ribonucleotide; or these
labeled oligonucleotide probes optionally or preferably are
synthesized entirely of modified nucleotides, e.g., 2'-O-ME
ribonucleotides.
[0292] It will be understood by one of ordinary skill in the
relevant arts that other suitable modifications and adaptations to
the methods, compositions, reaction mixtures and kits described
herein are readily apparent from the description of the invention
contained herein in view of information known to the ordinarily
skilled artisan, and may be made without departing from the scope
of the invention or any embodiment thereof. Having now described
the present invention in detail, the same will be more clearly
understood by reference to the following examples, which are
included herewith for purposes of illustration only and are not
intended to be limiting of the invention.
EXAMPLES
[0293] Examples are provided below illustrating certain aspects and
embodiments of the invention. The examples below are believed to
accurately reflect the details of experiments actually performed,
however, it is possible that some minor discrepancies may exist
between the work actually performed and the experimental details
set forth below which do not affect the conclusions of these
experiments or the ability of skilled artisans to practice them.
Skilled artisans will appreciate that these examples are not
intended to limit the invention to the specific embodiments
described therein. Additionally, those skilled in the art, using
the techniques, materials and methods described herein, could
easily devise and optimize alternative amplification systems for
carrying out these and related methods while still being within the
spirit and scope of the present invention.
[0294] Unless otherwise indicated, oligonucleotides and modified
oligonucleotides in the following examples were synthesized using
standard phosphoramidite chemistry, various methods of which are
well known in the art. See e.g., Carruthers et al. (1987) Meth.
Enzymol. 154, 287. Unless otherwise stated herein, modified
nucleotides were 2'-O-ME ribonucleotides, which were used in the
synthesis as their phosphoramidite analogs.
Example 1
Selective Amplification of HCV using Tagged Oligonucleotides in a
Real-Time TMA Reaction
[0295] The following series of experiments were conducted to
evaluate whether the use of a tagged oligonucleotide to modify a
target nucleic acid sequence in a nucleic acid sample of interest
prior to a transcription-mediated amplification reaction would
permit the selective amplification of target nucleic acid sequence
contributed by the nucleic acid sample of interest, while not
amplifying target nucleic acid sequence contributed by sources
other than the nucleic acid sample of interest.
[0296] Reagents and protocol conditions used in the performed
experiments, as well as a discussion of the results and conclusions
of the experiments, are set forth below.
[0297] I. Oligonucleotides
[0298] Unless otherwise indicated, oligonucleotides were
synthesized using an Expedite.TM. 8909 DNA Synthesizer (PerSeptive
Biosystems, Framingham, Mass.) using standard phosphoramidite
chemistry. See, e.g., Carruthers et al. (1987) Meth. Enzymol. 154,
287. Sequences are from 5'-to-3'. The blocking moiety, if present,
is at the 3'-end.
[0299] 1. Tagged Priming Oligonucleotide:
TABLE-US-00001 (SEQ ID NO: 1)
GTTTGTATGTCTGTTGCTATTATGTCTACAGGCATTGAGCGGGTTGATCC AAGAAAGGAC; 12
pmol/rxn
[0300] 2. Priming Oligonucleotide:
TABLE-US-00002 (SEQ ID NO: 2) GTTTGTATGTCTGTTGCTATTAT; 12
pmol/rxn
[0301] 3. Promoter Oligonucleotide:
TABLE-US-00003 (SEQ ID NO: 3)
ATTTAATACGACTCACTATAGGGAGACCACAACGGTTTCTAGCCATGGCG TTAGTATGAG; 12
pmol/rxn
[0302] Blocking Moiety: A 3'-to-3' linkage prepared using
3'-dimethyltrityl-N-benzoyl-2'-deoxycytidine, 5'-succinoyl-long
chain alkylamino-CPG (Glen Research Corporation, Sterling, Va.;
Cat. No. 20-0102-01)
[0303] 4. Terminating Oligonucleotide:
TABLE-US-00004 (SEQ ID NO: 4)
AmUmGmGmCmUmAmGmAmCmGmCmUmUmUmCmUmGmCmGmUmGmAmAmGm Am; 0.8
pmol/rxn
[0304] Blocking Moiety: Same as promoter oligonucleotide
[0305] 5. Extender Oligonucleotide:
TABLE-US-00005 (SEQ ID NO: 5) TGTCGTGCAGCCTCCAGGACCCCCCCTCCCG
GGAGAGCCATA; 12 pmol/rxn
[0306] Blocking Moiety: Same as promoter oligonucleotide
[0307] 6. First Capture Probe:
TABLE-US-00006 (SEQ ID NO: 6)
GmGmGmCmAmCmUmCmGmCmAmAmGmCmAmmCmCmCmUmTTTAAAAAAAA AAAAAAA
AAAAAAAAAAAAAAA; 3 pmol/rxn
[0308] 7. Second Capture Probe:
TABLE-US-00007 (SEQ ID NO: 7)
CmAmUmGmGmUmGmCmAmCmGmGmUmCmUmAmCmGmTTTAAAAAAAAAAA AAAAAAA
AAAAAAAAAAAA; 3 pmol/rxn
[0309] 8. Detection Probe:
TABLE-US-00008 (SEQ ID NO: 8)
CmGmUmUmCmCmGmCmAmGmAmCmCmAmCmUmAmUm(Linker)GmAmAm CmGm; 4
pmol/rxn
[0310] Probe Type: Molecular torch
[0311] Linker: 9-O-Dimethoxytrityl-triethylene glycol,
1-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite (Glen Research
Corporation, Sterling, Va.; Cat. No. 10-1909-90)
[0312] 5' Label: 6-Carboxyfluorescein (FAM) (BioGenex, San Ramon,
Calif.; Cat. No. BGX-3008-01)
[0313] 3' Label: 4-(4'-dimethylaminophenylazo)benzoic acid (DABCYL)
(Prime Synthesis, Inc., Aston, Pa.)
[0314] II. Reagents and Other Protocol Information
[0315] 1. Amplification Reagent. The "Amplification Reagent" or
"AMP Reagent" comprised 11.6 mM Trizma.RTM. base buffer, 15 mM
Trizma.RTM. hydrochloride buffer, 25 mM MgCl.sub.2, 23.3 mM
KCl.sub.2, 3.33% (v/v) glycerol, 0.05 mM zinc acetate, 0.76 mM
dATP, 0.76 mM dCTP, 0.76 mM dGTP, 0.76 mM d PIP, 0.02% (v/v)
ProClin 300 Preservative (Supelco, Bellefonte, Pa.; Cat. No.
48126), 6.0 mM ATP, 6.0 mM CTP, 6.0 mM GTP, and 6.0 mM UTP, pH 7.81
to 8.0 at 22.degree. C.
[0316] 2. Enzyme Reagent. The "Enzyme Reagent" comprised 70 mM
N-acetyl-L-cysteine, 10% (v/v) TRITON.RTM. X-102 detergent, 16 mM
HEPES, 3 mM EDTA, 0.05% (w/v) sodium azide, 20 mM Trizma.RTM. base
buffer, 50 mM KCl.sub.2, 20% (v/v) glycerol, 165.6 mM trehalose, pH
7, and containing 224 RTU/.mu.L Moloney murine leukemia virus
("MMLV") reverse transcriptase and 140 U/.mu.L T7 RNA polymerase,
where one unit (i.e., RTU or U) of activity is defined as the
synthesis and release of 5.75 fmol cDNA in 15 minutes at 37.degree.
C. for MMLV reverse transcriptase, and the production of 5.0 fmol
RNA transcript in 20 minutes at 37.degree. C. for T7 RNA
polymerase.
[0317] 3. Wash Solution. The "Wash Solution" comprised 10 mM HEPES,
6.5 mM NaOH, 1 mM EDTA, 0.3% (v/v) ethyl alcohol, 0.02% (w/v)
methyl paraben, 0.01% (w/v) propyl paraben, 150 mM NaCl, and 0.1%
(w/v) sodium dodecyl sulfate, pH 7.5.
[0318] 4. Transport Medium. The "Transport Medium" comprised 150 mM
HEPES, 8% (w/v) lithium lauryl sulfate, and 100 mM ammonium
sulfate, pH 7.5.
[0319] 5. Target Capture Reagent. The "Target Capture Reagent" or
"TCR" comprised the components listed below. Additional information
about the formulation of this mixture is described below under
Target Capture Reagent Procedure (IIIA). The concentrations listed
represent the final concentrations of the components after having
been combined with the magnetic particle solution. The magnetic
particles were Sera-Mag.TM. MG-CM Carboxylate Modified (Seradyn,
Inc., Indianapolis, Ind.; Cat. No. 24152105-050250), 1 micron,
super-paramagnetic particles covalently bound 5'-amino modified
oligo(dT).sub.14. The HEPES, lithium hydroxide, lithium chloride,
EDTA, lithium lauryl sulfate and ammonium sulfate components were
introduced with the TCR diluent and Transport Medium. [0320] First
Capture Probe; 15.0 nM [0321] Second Capture Probe; 15.0 nM [0322]
Tagged Priming Oligonucleotide; 60.0 nM [0323] Terminating
Oligonucleotide; 4.0 nM [0324] HEPES, Free Acid, Dihydrate; 118.7
mM [0325] Lithium Hydroxide, Monohydrate; 98.9 mM [0326] Lithium
Chloride, High Purity; 470.6 mM [0327] EDTA, Free Acid; 25.0 mM
[0328] Lithium Lauryl Sulfate; 110.2 mM [0329] Ammonium Sulfate;
37.5 mM [0330] Seradyn Poly dT14 Magnetic Particles; 0.075
ug/uL
[0331] 6. Transcript Buffer. The "Transcript Buffer" comprised 0.2%
lithium lauryl sulfate.
[0332] 7. Transcript Used. HCV Transcript
[0333] 8. Product Numbers of Certain Materials or Equipment
Used.
[0334] KingFisher.TM. Plate (Thermo Labsystems, Franklin, Mass.;
Cat. No. 97002540)
[0335] MJ Research microtiter plate (Bio-Rad Laboratories, Inc.,
Hercules, Calif.; Cat. No. HSP-9665)
[0336] Solo HT Incubator (Thermo Labsystems, Franklin, Mass.; Cat.
No. 5161580)
[0337] KingFisher.TM. Comb (Thermo Labsystems, Franklin, Mass.;
Cat. No. 97002510)
[0338] Eppendorf.RTM. Thermomixer R (Eppendorf North America;
Westbury, N.Y.; Cat. No. 022670107 or 022670158)
[0339] DNA Engine Opticon.RTM. 2 Real-Time PCR Detection System
(Bio-Rad Laboratories, Inc., Hercules, Calif.; Cat. No. CFB-3220)
9. Additional Protocol Information.
[0340] For the described experiments, 3.3 .mu.L of
target-containing transcript buffer was added to each 2.0 ml
microtube in step B6 below. The tagged priming oligonucleotide and
the terminating oligonucleotide were in water before being added to
the 2.0 mL microtubes. Samples were vortexed for about 5 seconds.
Incubating for 10 minutes at 60.degree. C. was found to be
generally sufficient to capture the transcript. The plates were
kept at room temperature for 5 minutes following the 10 minute
incubation to allow the plates to cool before the target capture
steps. This is also where the plates were transferred from the Solo
HT Incubator to the KingFisher System. The speed of the thermomixer
was 1400 rpm.
[0341] III. Target Capture Protocol
[0342] A. Target Capture Reagent (TCR) Procedure.
[0343] Magnetic beads were slowly mixed at room temperature (RT)
for 45 minutes and 150 .mu.L magnetic beads were added to 5 mL TCR
diluent (15 ug beads/rxn when 50 .mu.L used per sample). The
solution was slowly mixed at room temperature for 35 minutes, at
which time capture probe was added to 5 mL of the TCR diluent (to a
final concentration of 0.12 pmol/.mu.L (6-pmol/50 .mu.L rxn).
[0344] B. Sample Preparation.
[0345] AMP Reagent was prepared containing the promoter
oligonucleotide, extender oligonucleotide and priming
oligonucleotide (volume=1,600 .mu.L). The solution was vortexed and
placed at 2-8.degree. C. until needed. Detection probe was prepared
in Enzyme Reagent and placed at 2-8.degree. C. until needed. Target
dilutions were prepared in 0.2% LLS. 50 .mu.L TCR was transferred
into 200 .mu.L microplate wells. Each target copy level, tagged
priming oligonucleotide and terminating oligonucleotide were added
to 1.2 mL 50% Transport Medium, 50% H.sub.2O in 2.0 mL microtubes.
Target samples were vortexted and 150 .mu.L transferred into 200
.mu.L microplate (Plate 1) well containing 50 .mu.L TCR (each well
contained zero or 1 million copies HCV transcript plus appropriate
amounts of tagged priming and terminating oligonucleotides).
[0346] C. Target Capture Protocol.
[0347] The 200 .mu.L microplate (Plate 1) was incubated at
60.degree. C. for 10 minutes using Labsystems Solo HT Incubator
(Plate 1), and the microplate was then placed at RT for 5 minutes
(Plate 1). 200 .mu.L microplates (Plates 2 & 3) were prepared
with 200 uL Wash Reagent. Amplification plate (Plate 4-MJ research
96 well microtiter plate) was prepared with 30 .mu.L AMP Reagent
per well. The 96 well comb was placed into Plate 1. All four plates
were loaded into the KingFisher 96 unit and the target capture
protocol was initiated, as follows.
[0348] Plate 1 was mixed for 5 minutes at very slow speed and beads
were collected for 12 counts and then released into Plate 2 for 10
seconds using slow speed. Plate 1 was then mixed for 1 second using
very slow speed, beads collected for 12 counts, and the beads were
released into Plate 2 for 10 seconds using slow speed.
[0349] Plate 2 was mixed for 30 seconds at medium speed and beads
were collected for 12 counts and then released into Plate 3 for 10
seconds using very slow speed. Plate 2 was then mixed for 1 second
at very slow speed and beads were collected for 12 counts and
released into Plate 3 for 10 seconds using very slow speed.
[0350] Plate 3 was mixed for 30 seconds at medium speed, beads were
collected for 12 counts, and the beads were released into Plate 4
for 10 seconds using medium speed. Plate 3 was then mixed for 1
second at very slow speed, beads collected for 12 counts and
released into plate 4 for 10 seconds using medium speed.
[0351] The 96 well microtiter plate (Plate 4) was removed and
transferred to the bench, covered with a sealing card, and placed
in the DNA Engine Opticon.RTM. 2 Real-Time PCR Detection System
(Bio-Rad Laboratories; Hercules, Calif.) ("real-time
instrument").
[0352] D. Real Time TMA.
[0353] Real-time TMA was performed as follows. The plate was
incubated for 5 minutes at 42.degree. C. and then removed and
placed on a 42.degree. C. thermomixer. Each reaction well received
a 10 .mu.L aliquot of the Enzyme Reagent. The microtiter plate was
covered with an adhesive tape seal, shaken gently for 30 seconds on
the thermomixer, and then placed into the real-time instrument at
42.degree. C., where real-time assay monitoring was commenced.
TTime values, which served as indicators of the amount of amplicon
synthesized, were determined from the monitored fluorescence
signals. See Light et al., U.S. Pat. Appln. Pub. No. US
2006-0276972, paragraphs 506-549.
[0354] IV. Results and Conclusion
[0355] Experiments were performed according to the procedures
described above for detecting an HCV transcript (8 replicates). The
TCR in each test contained the same tagged priming oligonucleotide.
A target capture step was performed for binding HCV transcript and
removing unhybridized tagged priming oligonucleotide and
terminating oligonucleotide. After the target capture step, an AMP
Reagent was contacted with the beads of the TCR, with the AMP
Reagent containing a priming oligonucleotide specific for the
complement of the tag sequence. No tagged priming oligonucleotide
was included in this step.
[0356] Eight replicates were run for each condition. The detection
probe was added via the Enzyme Reagent at 4 pmol per reaction. The
HCV AMP Reagent contained 12 pmol promoter oligonucleotide, 12 pmol
extender oligonucleotide and 12 pmol priming oligonucleotide per
reaction.
[0357] The first set of experiments compared the results of
reactions in which no copies of the HCV transcript were spiked into
the TCR or AMP Reagent with the results of reactions in which
1.times.10.sup.6 copies of the HCV transcript were spiked into the
TCR. FIG. 17 shows the raw curves for HCV amplifications in which
no target was spiked into the AMP Reagent. There was no detectable
amplification when the HCV transcript was not spiked into the TCR
or AMP Reagent, while the average TTime for reactions containing
1.times.10.sup.6 copies of the HCV transcript in the TCR was 6.3
minutes. The "TTime" values relate to time of emergence (time at
which signal rises above background), and a summary of these values
for the experiments performed is set forth in Table 1 below.
[0358] A second set of experiments compared the results of
reactions in which 1.times.10.sup.6 copies of the HCV transcript
were spiked into the AMP Reagent only with reactions in which
1.times.10.sup.6 copies of the HCV transcript were spiked into the
TCR only. FIG. 18 shows the raw curves for HCV amplifications in
which target was spiked into the AMP Reagent. There was no
detectable amplification when the HCV transcript was spiked into
the AMP Reagent, while the average TTime for reactions containing
1.times.10.sup.6 copies of the HCV transcript in the TCR was 6.3
minutes (Table 1). The zero target in TC samples did not amplify,
even with 1 million copies HCV transcript spiked into the AMP
Reagent.
[0359] A third set of experiments compared the results of reactions
in which 1.times.10.sup.6 copies of the HCV transcript and the
tagged priming oligonucleotide were provided in the AMP Reagent (no
copies of the HCV transcript in TCR) with the results of reactions
in which 1.times.10.sup.6 copies of the HCV transcript were
provided in the TCR and the tagged priming oligonucleotide was
provided in the AMP Reagent. FIG. 19 shows that the AvgTTime for 1
million copies HCV transcript present only in the target capture
step with tagged priming and terminating oligonucleotides spiked
into the AMP Reagent was 7.2 minutes. The zero samples with target,
terminating oligonucleotide and tagged priming oligonucleotide
spiked into the AMP Reagent also produced robust amplification with
an AvgTTime=8.6 minutes (Table 1).
TABLE-US-00009 TABLE 1 TTime Summary (AvgTTimes & SDTTimes)
Target Target Avg. T SDT Sample ID Name Amt Total RN1 TN1 Time Time
1 million target HCV 1E6 8 7 8 6.3 0.11 in TC-x6.0 1 million target
HCV 1E6 8 8 8 7.2 0.20 in TC, tagged non-T7 primer &
terminating oligonucleotide in amp-x6.0 1 million target HCV 1E6 8
8 7 6.3 0.05 in TC-x6.0 Zero target in HCV 0.00 8 8 0 N/A N/A TC, 1
million target in amp-x0.0 Zero target in HCV 0.00 8 8 8 8.6 0.21
TC, 1 million target, tagged non-T7 primer & terminating
oligonucleotide in amp-x0.0 Zero target in HCV 0.00 8 8 0 N/A N/A
TC-x0.0
[0360] The results of these experiments demonstrate that only when
the tagged priming oligonucleotide was present in the AMP Reagent
along with the priming oligonucleotide did zero TCR samples amplify
when 1 million copies of HCV transcript were spiked into the AMP
Reagent. Thus, HCV transcript entering the system through the AMP
Reagent is not amplified unless the tagged priming oligonucleotide
is also provided with the AMP Reagent.
[0361] The preceding Example demonstrated how a tagged priming
oligonucleotide that hybridized to an HCV template could be used
for selectively detecting HCV nucleic acids in a sample of interest
without interference from contaminating nucleic acid introduced
subsequent to a target capture step. The following Example
illustrates how a similar approach was used for detecting bacterial
nucleic acids in a sample of interest despite the presence of
contaminating templates in reagents used for performing the
amplification reaction. Advantageously, non-complexed tagged
priming oligonucleotide was substantially absent from the reaction
mixture at the time a complex comprising the tagged priming
oligonucleotide and the template contacted the DNA polymerase used
in the amplification reaction.
[0362] Example 2 below describes two procedures for amplifying E.
coli rRNA nucleic acids, where the procedures differed by the use
of both a tagged priming oligonucleotide and target capture. The
first procedure employed an E. coli specific non-tagged priming
oligonucleotide in combination with a terminating oligonucleotide,
a promoter oligonucleotide and a detection probe. The second
procedure employed a tagged priming oligonucleotide having a
target-complementary sequence identical to that contained in the E.
coli specific non-tagged priming oligonucleotide of the first
procedure, a tag-specific priming oligonucleotide, as well as a
terminating oligonucleotide, a promoter oligonucleotide and a
detection probe. The tag-specific priming oligonucleotide, which
had a nucleotide sequence corresponding to a segment of HIV-1,
hybridized to the complement of the tag sequence contained in the
tagged priming oligonucleotide, but did not hybridize to the E.
coli rRNA template nucleic acid or the complement thereof. In the
case of the second procedure, the terminating oligonucleotide, the
promoter oligonucleotide and the detection probe were identical to
those used in the first procedure. As demonstrated below,
amplification reactions that omitted the tagged priming
oligonucleotide failed to discriminate between samples containing 0
and 10.sup.6 copies of a synthetic E. coli rRNA target. Conversely,
the approach that included use of a tagged priming oligonucleotide
and target capture clearly distinguished samples containing 0 and
10.sup.3 copies of the synthetic E. coli rRNA target.
Example 2
Use of a Tagged Priming Oligonucleotide Allows Discrimination
Between Sample-Derived Templates and Exogenous Templates
[0363] A. Amplification using a Non-Tagged Priming Oligonucleotide
without Target Capture
[0364] In a first procedure, amplification reactions employing a
synthetic E. coli rRNA template were performed using a non-tagged
priming oligonucleotide that hybridized to the template, a promoter
oligonucleotide, a terminating oligonucleotide and a molecular
torch detection probe. Reactions were primed using the synthetic
template added directly into the reaction mixtures (i.e., without
undergoing target capture purification) at 0 or 10.sup.6
copies/reaction. A molecular torch detection probe was used to
monitor amplicon production as a function of time. In the
nucleotide sequences presented below, 2'-O-methyl ribose (2'-O-Me)
modifications of the polynucleotide backbone are indicated by lower
case "m." Blocking moieties at the 3' termini of the promoter
oligonucleotide and terminating oligonucleotide comprised a
3'-to-3' linkage that was prepared using
3'-dimethyltrityl-N-benzoyl-2'-deoxycytidine, 5'-succinoyl-long
chain alkylamino-CPG (Glen Research Corporation, Sterling, Va.;
Cat. No. 20-0102-01). Oligonucleotides, reagents and essential
methods used in the procedure were as follows.
[0365] I. Oligonucleotides:
[0366] 1. Non-Tagged Priming Oligonucleotide:
TABLE-US-00010 (SEQ ID NO: 9) CmUmGmCmTGGCACGGAGTTAGCCGGTGCTTC
[0367] 2. Promoter Oligonucleotide:
TABLE-US-00011 (SEQ ID NO: 10)
ATTTAATACGACTCACTATAGGGAGAGAAGGCCTTCGGGTTGTAAAG- block
[0368] 3. Terminating Oligonucleotide:
TABLE-US-00012 (SEQ ID NO: 11)
GmCmCmUmUmCmUmUmCmAmUmAmCmAmCmGmCmGm-block
[0369] 4. Detection Probe:
TABLE-US-00013 (SEQ ID NO: 12)
.sup.1CmUmGmCmGmGmGmUmAmAmCmGmUmCmAmAmUmGmAmGmCmAmAmAm.sup.2
CGCAG.sup.3 .sup.1fluorescein .sup.2C9 linker .sup.3DABCYL
[0370] 5. Synthetic E. Coli rRNA Template:
TABLE-US-00014 (SEQ ID NO: 13)
AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCT
AACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGA
CGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGG
GATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAA
AGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATT
AGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGT
CTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCT
ACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGC
AGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCA
GCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCC
GCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGA
GGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGG
TTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATC
TGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGT
AGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGC
CCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACA
GGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGG
TTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGC
CTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCC
CGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACC
TTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCT
TCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGT
GAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTG
CCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGA
GGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTA
CACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCA
AGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCG
ACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGT
GAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTG
GGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACT
TTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAA
CCTGCGGTTGGATCACCTCCTTA
[0371] II. Reagents and Other Protocol Information:
[0372] Amplification and enzyme reagents were essentially as
described under Example 1. Procedures using the non-tagged priming
oligonucleotide that hybridized to the E. coli template did not
employ target capture oligonucleotides or reagents, did not employ
transport medium or wash solution, and did not employ an extender
oligonucleotide.
[0373] A. Real-Time Amplification Protocol.
[0374] Sample solutions were prepared using primerless
amplification reagent, non-tagged priming oligonucleotide, promoter
oligonucleotide, terminating oligonucleotide, detection probe and
synthetic template nucleic acid. Each well of a 96-well microtiter
plate received a 30 .mu.L aliquot of the prepared sample solution.
The microtiter plate was covered with an adhesive tape seal,
incubated first for 10 minutes at 60.degree. C. in the DNA ENGINE
OPTICON.RTM. 2 (Bio-Rad Laboratories; Hercules, Calif.)
temperature-controlled real-time instrument, and then
temperature-adjusted to 42.degree. C. for 5 minutes. Thereafter,
the plate was removed from the real-time instrument and placed onto
a 42.degree. C. thermomixer. Each reaction well received a 10 .mu.L
aliquot of the enzyme reagent. The microtiter plate was covered
with an adhesive tape seal, shaken gently for 30 seconds on the
thermomixer, and then placed into the real-time instrument at
42.degree. C. where real-time assay monitoring was commenced. TTime
values, which served as indicators of the amount of amplicon
synthesized, were determined from the monitored fluorescence
signals.
[0375] III. Results and Conclusion
[0376] As indicated in FIG. 20, substantially identical results
were observed in reactions that included either 0 or 10.sup.6
copies of the template nucleic acid, and so the assay showed no
discrimination between these two conditions. More specifically,
fluorescent signals indicating formation of E. coli nucleic acid
amplification products emerged from background levels at
substantially similar times (i.e., TTime=31.74 minutes at the 0
copy level, and 31.19 minutes at the 10.sup.6 copy level) in both
reactions. Thus, a real-time amplification profile characteristic
of high levels of the nucleic acid template was obtained even in
the absence of added E. coli rRNA template. This was consistent
with the presence of contaminating bacterial nucleic acid templates
in one or more of the reagents used for carrying out the
amplification reactions following the target capture procedure.
[0377] B. Amplification using a Tagged Priming Oligonucleotide and
Target Capture
[0378] In a second procedure, a tagged priming oligonucleotide and
target capture step were employed for performing amplification
reactions using test samples containing either 0, 10.sup.3 or
10.sup.5 copies of the synthetic E. coli transcript.
Oligonucleotides used in the procedure are indicated below. The
molecular torch detection probe was added as a component of the
enzyme reagent. Following target capture, tagged priming
oligonucleotide that was not hybridized to template nucleic acid
was removed from the system by standard target capture and wash
steps. The complex that included the rRNA template and the tagged
priming oligonucleotide remained captured on super-paramagnetic
particles. Amplification reactions were carried out using reagents
essentially as described above, except for substitution of a
non-specific target capture probe for the sequence-specific capture
probes employed in Example 1. Amplification reactions were carried
out in replicates of six and monitored using a molecular torch
detection probe essentially as described in Example 1, except that
an extender oligonucleotide was omitted. As above, 2'-O-methyl
ribose (2'-O-Me) modifications of the polynucleotide backbone in
the sequences presented below are indicated by lower case "m."
Blocking moieties at the 3' termini of the promoter oligonucleotide
and terminating oligonucleotide comprised a 3'-to-3' linkage that
was prepared using 3'-dimethyltrityl-N-benzoyl-2'-deoxycytidine,
5'-succinoyl-long chain alkylamino-CPG (Glen Research Corporation,
Sterling, Va.; Cat. No. 20-0102-01). Oligonucleotides, reagents and
essential methods used in the procedure were as follows.
[0379] I. Oligonucleotides:
[0380] 1. Tagged Priming Oligonucleotide:
TABLE-US-00015 (SEQ ID NO: 14)
GTTTGTATGTCTGTTGCTATTATGTCTACCTGCTGGCACGGAGTTAGCCG GTGCTTC
[0381] 2. Tag-Specific Priming Oligonucleotide:
TABLE-US-00016 (SEQ ID NO: 15) GTTTGTATGTCTGTTGCTATTAT
[0382] 3. Promoter Oligonucleotide:
TABLE-US-00017 (SEQ ID NO: 10)
ATTTAATACGACTCACTATAGGGAGAGAAGGCCTTCGGGTTGTAA AG-block
[0383] 4. Terminating Oligonucleotide:
TABLE-US-00018 (SEQ ID NO: 11)
GmCmCmUmUmCmUmUmCmAmUmAmCmAmCmGmCmGm-block
[0384] 5. Non-Specific Capture Probe:
TABLE-US-00019 (SEQ ID NO: 16)
KmKmKmKmKmKmKmKmKmKmKmKmKmKmKmKmKmKmTTTAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAA
[0385] 6. Detection Probe:
TABLE-US-00020 (SEQ ID NO: 12)
.sup.1CmUmGmCmGmGmGmUmAmAmCmGmUmCmAmAmUmGmAmGmCmAmAmAm.sup.2
CGCAG.sup.3 .sup.1fluorescein .sup.2C9 linker .sup.3DABCYL
[0386] 7. Synthetic E. Coli rRNA Template
[0387] (See above)
[0388] II. Reagents and Other Protocol Information
[0389] Reagents and experimental protocols were essentially as
described under Example 1, with the substitution of a non-specific
target capture oligonucleotide for the first and second capture
oligonucleotides, the substitution of the above-presented E.
coli-specific oligonucleotides for HCV-specific oligonucleotides,
and the omission of an extender oligonucleotide.
[0390] III. Non-Specific Target Capture Protocol
[0391] A. Target Capture Reagent (TCR) Preparation.
[0392] A stock suspension of magnetic beads was mixed at room
temperature for 30 minutes. An aliquot of about 150 .mu.L of the
magnetic bead suspension was added to 5 mL of TCR diluent (15 .mu.g
beads/reaction when using 50 .mu.L/sample), and then slowly mixed
at room temperature for 30 minutes. Next, the non-specific capture
oligonucleotide was added to 5 mL of the TCR mixture to yield a
final concentration of 0.12 pmol/.mu.L. The prepared TCR was mixed
gently at room temperature until needed.
[0393] B. Sample Preparation.
[0394] Amplification solution was prepared using primerless
amplification reagent, promoter oligonucleotide and tag-specific
priming oligonucleotide. The prepared amplification solution was
mixed by vortexing and then maintained at 2-8.degree. C. until
needed. Enzyme reagent containing the molecular torch detection
probe was next prepared and maintained at 2-8.degree. C. until
needed. Dilutions of the template rRNA were prepared in 0.2% LLS
(lithium lauryl sulfate). Aliquots (50 .mu.L) of the magnetic bead
target capture solution were transferred into the wells of a
microtiter plate for a KINGFISHER 96 (Thermo Fisher Scientific,
Inc.; Waltham, Mass.) magnetic particle processor. Samples of
diluted template, tagged priming oligonucleotide and terminating
oligonucleotide were then added to 1.5 mL of 50% transport medium
diluted with water. The target-containing sample mixture was
vortexed, and 150 .mu.L aliquots transferred into the microtiter
plate (Plate 1) wells containing 50 .mu.L target capture solution
(each well contained 0, 10.sup.3 or 10.sup.5 copies of the E. coli
transcript and the appropriate amount of tagged priming
oligonucleotide and terminating oligonucleotide).
[0395] C. Target Capture Protocol.
[0396] First there was prepared a microtiter plate containing 200
.mu.L of wash reagent (Plate 2). Another microtiter plate (Plate 3)
for conducting amplification reactions was prepared, with each well
to be used for a reaction containing 30 .mu.L of amplification
reagent. All three plates (Plates 1-3) were loaded into the
magnetic particle processor unit. Magnetic beads harboring nucleic
acid complexes were isolated from Plate 1, washed in Plate 2, and
then transferred into Plate 3 using standard procedures familiar to
those having an ordinary level of skill in the art. Plate 3 was
removed from the magnetic particle processor unit, covered with an
adhesive tape seal, and then placed into the temperature-controlled
real-time instrument.
[0397] D. Real-Time Amplification Protocol.
[0398] Plate 3 was incubated at 42.degree. C. for 5 minutes in the
real-time instrument. The microtiter plate was removed from the
real-time instrument and placed onto a 42.degree. C. thermomixer.
Each reaction well received a 10 .mu.L aliquot of enzyme reagent
containing detection probe, and was then covered with an adhesive
tape seal. The plate was shaken gently for 60 seconds on the
thermomixer, and then placed back into the real-time instrument at
42.degree. C. where real time assay monitoring was commenced. TTime
values, which served as indicators of the amount of amplicon
synthesized, were determined from the monitored fluorescence
signals.
[0399] IV. Results and Conclusion
[0400] FIG. 21 graphically illustrates the benefits of the
disclosed approach to nucleic acid amplification. Procedures that
employed a tagged priming oligonucleotide complementary to a target
of interest, a target capture step, and a tag-specific priming
oligonucleotide that was not complementary to the target of
interest (i.e., the E. coli rRNA) yielded dramatically reduced
background amplification levels, and so easily permitted
discrimination between 0 and 10.sup.3 copies of the bacterial
template nucleic acid. More specifically, the average TTime values
determined for reactions carried out using 10.sup.5 copies,
10.sup.3 copies, and 0 copies of the E. coli template were 24.7
minutes, 30.6 minutes and 37.5 minutes, respectively. Taken
together with the results presented in FIG. 4, these findings were
consistent with the presence of bacteria-derived nucleic acids in
common reagents used for conducting in vitro nucleic acid
amplification reactions. Despite this fact, the procedure employing
a tagged priming oligonucleotide was useful for detecting E. coli
nucleic acids contained in a test sample without interference from
exogenous template nucleic acids contributed by the amplification
reagents. For example, a qualitative assay for detecting E. coli
nucleic acids at a level of 10.sup.3 copies or greater in a test
sample could depend on achieving a threshold fluorescence signal or
TTime value after a predetermined reaction time (e.g., 35
minutes).
[0401] The following Example presents comparative results showing
how two different detection probes influenced the profiles of
real-time amplification run curves. The results further showed how
the tagged priming oligonucleotide approach could be used for
discriminating 0 and 10.sup.3 copies of the synthetic E. coli
template nucleic acid--a level approximating the number of copies
of 16S rRNA present in a single bacterium.
[0402] Example 3 describes detection of E. coli rRNA templates in
real-time amplification reactions using three different detection
probes.
Example 3
Alternative Torch Designs can Improve Assay Results
[0403] Amplification reactions were conducted and monitored in a
real-time format using one of three different detection probes. The
synthetic template nucleic acid, non-specific capture
oligonucleotide, tagged priming oligonucleotide, termination
oligonucleotide, promoter oligonucleotide and tag-specific priming
oligonucleotide used for performing the reactions were identical to
those used in the second procedure of the preceding Example. The E.
coli target hybridizing portion of the tagged priming
oligonucleotide corresponded to nucleotide positions 24-57 of SEQ
ID NO:14 (i.e., the target hybridizing sequence corresponding to
SEQ ID NO:19). The E. coli target hybridizing portion of the
promoter oligonucleotide corresponded to nucleotide positions 27-47
of SEQ ID NO:10 (i.e., the target hybridizing sequence
corresponding to SEQ ID NO:20). Four replicates were run for each
condition. As before, detection probe was added with the enzyme
reagent. Reagents and protocols for non-specific target capture,
sample preparation, and real-time amplification also were
essentially as described in the second procedure of the preceding
Example. Notably, reactions were conducted using 0, 10.sup.3 or
10.sup.5 copies of the synthetic E. coli template. As above,
2'-O-methyl ribose (OMe) modifications of the polynucleotide
backbone in the sequences presented below are indicated by lower
case "m." Blocking moieties at the 3' termini of the promoter
oligonucleotide and terminating oligonucleotide comprised a
3'-to-3' linkage that was prepared using
3'-dimethyltrityl-N-benzoyl-2'-deoxycytidine, 5'-succinoyl-long
chain alkylamino-CPG (Glen Research Corporation, Sterling, Va.;
Cat. No. 20-0102-01). Oligonucleotides, reagents and essential
methods used in the procedure were as follows.
[0404] I. Oligonucleotides:
[0405] 1. Tagged Priming Oligonucleotide:
TABLE-US-00021 (SEQ ID NO: 14)
GTTTGTATGTCTGTTGCTATTATGTCTACCTGCTGGCACGGAGTTAGCCG GTGCTTC
[0406] 2. Tag-Specific Priming Oligonucleotide:
TABLE-US-00022 (SEQ ID NO: 15) GTTTGTATGTCTGTTGCTATTAT
[0407] 3. Promoter Oligonucleotide:
TABLE-US-00023 (SEQ ID NO: 10)
ATTTAATACGACTCACTATAGGGAGAGAAGGCCTTCGGGTTGTAA AG-block
[0408] 4. Terminating Oligonucleotide:
TABLE-US-00024 (SEQ ID NO: 11)
GmCmCmUmUmCmUmUmCmAmUmAmCmAmCmGmCmGm-block
[0409] 5. Non-Specific Capture Probe:
TABLE-US-00025 (SEQ ID NO: 16)
KmKmKmKmKmKmKmKmKmKmKmKmKmKmKmKmKmKmTTTAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAA
[0410] 6. Detection Probe:
TABLE-US-00026 (SEQ ID NO: 17)
.sup.1CmGmAmGmCmAmAmAmGmGmUmAmUmUmAmAmCm.sup.2GmCmUmCmGm.sup.3 (SEQ
ID NO: 18)
.sup.1CmGmAmGmCmAmAmAmGmGmUmAmUmUmAmAmCmUmUmUmAmCmUmCm.sup.2
GmCmUmCmGm.sup.3 .sup.1fluorescein .sup.2C9 linker .sup.3DABCYL
[0411] 7. Synthetic E. Coli rRNA Template
[0412] (See above)
[0413] II. Reagents and Other Protocol Information
[0414] Reagents and experimental protocols were essentially as
described under Example 2, with a slight change to the conditions
used for target capture.
[0415] III. Non-Specific Target Capture Protocol:
[0416] A. Target Capture Reagent (TCR) Preparation.
[0417] A stock suspension of magnetic beads was mixed at room
temperature for 25 minutes. A 150 .mu.L aliquot of the magnetic
bead suspension was added to 5 mL of TCR diluent (15 .mu.g
beads/reaction when using 50.micro.L/sample), and then slowly mixed
at room temperature for 25 minutes. Next, the non-specific capture
oligonucleotide was added to 5 mL of the TCR mixture to yield a
final concentration of 0.12 pmol/.mu.L. The prepared TCR was mixed
gently at room temperature until needed.
[0418] B. Sample Preparation.
[0419] Amplification solutions were prepared using primerless AMP
Reagent, promoter oligonucleotide and tag-specific priming
oligonucleotide. The prepared amplification solutions were mixed by
vortexing and then maintained at 2-8.degree. C. until needed.
Enzyme Reagents containing the molecular torch detection probes
were next prepared and maintained at 2-8.degree. C. until needed.
Dilutions of the template rRNA were prepared in 0.2% LLS, as
described above. Aliquots (50 .mu.L) of the magnetic bead target
capture solution were transferred into the wells of a microtiter
plate for a KINGFISHER 96 (Thermo Fisher Scientific, Inc.; Waltham,
Mass.) magnetic particle processor. Samples of diluted template,
tagged priming oligonucleotide and terminating oligonucleotide were
then added to 1.5 mL of 50% Transport Medium diluted with water.
The target-containing sample mixture was vortexed, and 150 .mu.L
aliquots transferred into the microtiter plate (Plate 1) wells
containing 50 .mu.L target capture solution (each well contained 0,
10.sup.3 or 10.sup.5 copies of the E. coli transcript and the
appropriate amount of tagged priming oligonucleotide and
terminating oligonucleotide).
[0420] C. Target Capture Protocol.
[0421] The microtiter plate (Plate 1) was incubated at 60.degree.
C. for 15 minutes using a SOLO HT incubator (Thermo Labsystems;
Franklin, Mass.). The microtiter plate was then placed on the bench
at room temperature and allowed to equilibrate for 5 minutes (Plate
1). Next, there was prepared a second microtiter plate containing
200 .mu.L of Wash Reagent (Plate 2). A third microtiter plate
(Plate 3) for conducting amplification reactions was prepared, with
each well to be used for a reaction containing 30 .mu.L of
amplification reagent. All three plates were loaded into the
magnetic particle processor unit. Magnetic beads harboring nucleic
acid complexes were isolated from Plate 1, washed in Plate 2, and
then transferred into Plate 3 using standard procedures familiar to
those having an ordinary level of skill in the art. Plate 3 was
removed from the magnetic particle processor unit, covered with an
adhesive tape seal, and then placed into the temperature-controlled
real-time instrument.
[0422] D. Real-Time Amplification Protocol.
[0423] Plate 3 was incubated in the real-time instrument at
42.degree. C. for 5 minutes. The microtiter plate was removed from
the real-time instrument and placed onto the 42.degree. C.
thermomixer. Each reaction well received a 10 .mu.L aliquot of
Enzyme Reagent containing detection probe, and was then covered
with an adhesive tape seal. The plate was shaken gently for 60
seconds on the thermomixer, and then placed back into the real-time
instrument at 42.degree. C. where real-time assay monitoring was
commenced. TTime values, which served as indicators of the amount
of amplicon synthesized, were determined from the monitored
fluorescence signals.
[0424] IV. Results and Conclusion
[0425] The results presented in Table 2 summarize the average TTime
values (column 3), and the standard deviations of the average TTime
values (column 4) for reactions conducted using the different
detection probes. The tabular summary confirmed that all of the
tested detection probes yielded very good results in the real-time
assays. Each probe advantageously gave a very low signal at the 0
copy level of input target. More specifically, amplicon detected in
reactions carried out using 0 copies of input synthetic template
was essentially undetectable when the reactions included the
detection probes of SEQ ID NO:17 and SEQ ID NO:18. Thus, reactions
that included one of the detection probes identified by SEQ ID
NO:17 and SEQ ID NO:18 gave outstanding results that easily
permitted detection of template nucleic acids corresponding roughly
to the amount contained in a single bacterium.
TABLE-US-00027 TABLE 2 Use of Alternative Detection Probes for
Improved Assay Discrimination Template Amount AvgTTime SDTTime
(copies) Detection Probe (minutes) (minutes) 0 SEQ ID NO: 17 N/A
N/A .sup. 10.sup.3 38.2 2.81 .sup. 10.sup.5 26.4 0.32 0 SEQ ID NO:
18 N/A N/A .sup. 10.sup.3 35.9 2.33 .sup. 10.sup.5 28.8 0.45
[0426] Taken in view of the results presented Examples 2 and 3,
each of SEQ ID Nos:12, and 17-18 represent preferred molecular
torches for detecting E. coli using the methods described herein.
Highly preferred probes useful for detecting E. coli nucleic acids
will have target-complementary sequences corresponding to
nucleotide positions 2-24 contained within the probe of SEQ ID
NO:12 (i.e., the target hybridizing sequence corresponding to SEQ
ID NO:21), or nucleotide positions 2-17 contained within the probe
of SEQ ID NO:17 (i.e., the target hybridizing sequence
corresponding to SEQ ID NO:22), or nucleotide positions 2-24
contained within the probe of SEQ ID NO:18 (i.e., the target
hybridizing sequence corresponding to SEQ ID NO:23). Generally
speaking, probes useful for detecting E. coli nucleic acids will
have target hybridizing sequences of at least 16 contiguous
nucleotides contained within the sequence of
TGCGGGTAACGTCAATGAGCAAAGGTATTAACTTTACTC (SEQ ID NO:24). Overall
preferred lengths of desirable probes will be up to 39 nucleotides,
more preferably up to 29 nucleotides, more preferably up to 23
nucleotides, or still more preferably up to 16 nucleotides. Of
course, useful probes may include RNA and DNA equivalent bases, and
include the complements of the foregoing described probes.
[0427] While the present invention has been described and shown in
considerable detail with reference to certain preferred
embodiments, those skilled in the art will readily appreciate other
embodiments of the present invention. Accordingly, the present
invention is deemed to include all modifications and variations
encompassed within the spirit and scope of the following appended
claims.
Sequence CWU 1
1
24160DNAArtificialHCV-specific tagged priming oligonucleotide
1gtttgtatgt ctgttgctat tatgtctaca ggcattgagc gggttgatcc aagaaaggac
60223DNAArtificialTag-specific priming oligonucleotide 2gtttgtatgt
ctgttgctat tat 23360DNAArtificialHCV-specific promoter
oligonucleotide 3atttaatacg actcactata gggagaccac aacggtttct
agccatggcg ttagtatgag 60426RNAHepatitis C
virusmisc_feature(1)..(26)2' methoxy analogs 4auggcuagac gcuuucugcg
ugaaga 26542DNAArtificialExtender oligonucleotide 5tgtcgtgcag
cctccaggac cccccctccc gggagagcca ta 42652DNAArtificialHCV-specific
capture probe 6gggcacucgc aagcacccut ttaaaaaaaa aaaaaaaaaa
aaaaaaaaaa aa 52751DNAArtificialHCV-specific capture probe
7cauggugcac ggucuacgtt taaaaaaaaa aaaaaaaaaa aaaaaaaaaa a
51823RNAArtificialHCV-specific molecular torch hybridization
probemisc_feature(1)..(23)2' methoxy
analogsmisc_feature(18)..(19)non-nucleotide linker 8cguuccgcag
accacuauga acg 23928DNAEscherichia colimisc_feature(1)..(4)2'
methoxy analogs 9cugctggcac ggagttagcc ggtgcttc
281047DNAArtificialE. coli-specific promoter oligonucleotide
10atttaatacg actcactata gggagagaag gccttcgggt tgtaaag
471118RNAEscherichia colimisc_feature(1)..(18)2' methoxy analogs
11gccuucuuca uacacgcg 181229DNAArtificialE. coli-specific molecular
torch hybridization probemisc_feature(1)..(24)2' methoxy
analogsmisc_feature(24)..(25)non-nucleotide
linkermisc_feature(25)..(29)DNA 12cugcggguaa cgucaaugag caaacgcag
29131542DNAArtificialSynthetic E. coli rRNA template 13aaattgaaga
gtttgatcat ggctcagatt gaacgctggc ggcaggccta acacatgcaa 60gtcgaacggt
aacaggaaga agcttgcttc tttgctgacg agtggcggac gggtgagtaa
120tgtctgggaa actgcctgat ggagggggat aactactgga aacggtagct
aataccgcat 180aacgtcgcaa gaccaaagag ggggaccttc gggcctcttg
ccatcggatg tgcccagatg 240ggattagcta gtaggtgggg taacggctca
cctaggcgac gatccctagc tggtctgaga 300ggatgaccag ccacactgga
actgagacac ggtccagact cctacgggag gcagcagtgg 360ggaatattgc
acaatgggcg caagcctgat gcagccatgc cgcgtgtatg aagaaggcct
420tcgggttgta aagtactttc agcggggagg aagggagtaa agttaatacc
tttgctcatt 480gacgttaccc gcagaagaag caccggctaa ctccgtgcca
gcagccgcgg taatacggag 540ggtgcaagcg ttaatcggaa ttactgggcg
taaagcgcac gcaggcggtt tgttaagtca 600gatgtgaaat ccccgggctc
aacctgggaa ctgcatctga tactggcaag cttgagtctc 660gtagaggggg
gtagaattcc aggtgtagcg gtgaaatgcg tagagatctg gaggaatacc
720ggtggcgaag gcggccccct ggacgaagac tgacgctcag gtgcgaaagc
gtggggagca 780aacaggatta gataccctgg tagtccacgc cgtaaacgat
gtcgacttgg aggttgtgcc 840cttgaggcgt ggcttccgga gctaacgcgt
taagtcgacc gcctggggag tacggccgca 900aggttaaaac tcaaatgaat
tgacgggggc ccgcacaagc ggtggagcat gtggtttaat 960tcgatgcaac
gcgaagaacc ttacctggtc ttgacatcca cggaagtttt cagagatgag
1020aatgtgcctt cgggaaccgt gagacaggtg ctgcatggct gtcgtcagct
cgtgttgtga 1080aatgttgggt taagtcccgc aacgagcgca acccttatcc
tttgttgcca gcggtccggc 1140cgggaactca aaggagactg ccagtgataa
actggaggaa ggtggggatg acgtcaagtc 1200atcatggccc ttacgaccag
ggctacacac gtgctacaat ggcgcataca aagagaagcg 1260acctcgcgag
agcaagcgga cctcataaag tgcgtcgtag tccggattgg agtctgcaac
1320tcgactccat gaagtcggaa tcgctagtaa tcgtggatca gaatgccacg
gtgaatacgt 1380tcccgggcct tgtacacacc gcccgtcaca ccatgggagt
gggttgcaaa agaagtaggt 1440agcttaacct tcgggagggc gcttaccact
ttgtgattca tgactggggt gaagtcgtaa 1500caaggtaacc gtaggggaac
ctgcggttgg atcacctcct ta 15421457DNAArtificialE. coli-specific
tagged priming oligonucleotide 14gtttgtatgt ctgttgctat tatgtctacc
tgctggcacg gagttagccg gtgcttc 571523DNAArtificialTag-specific
priming oligonucleotide 15gtttgtatgt ctgttgctat tat
231651DNAArtificialnon-specific capture
probemisc_feature(1)..(18)2' methoxy
analogsmisc_feature(19)..(51)DNA 16kkkkkkkkkk kkkkkkkktt taaaaaaaaa
aaaaaaaaaa aaaaaaaaaa a 511722RNAArtificialE. coli-specific
molecular torch hybridization probemisc_feature(1)..(22)2' methoxy
analogsmisc_feature(17)..(18)non-nucleotide linker 17cgagcaaagg
uauuaacgcu cg 221829RNAArtificialE. coli-specific molecular torch
hybridization probemisc_feature(1)..(29)2' methoxy
analogsmisc_feature(24)..(25)non-nucleotide linker 18cgagcaaagg
uauuaacuuu acucgcucg 291934DNAEscherichia coli 19gtctacctgc
tggcacggag ttagccggtg cttc 342021DNAEscherichia coli 20gaaggccttc
gggttgtaaa g 212123RNAEscherichia coli 21ugcggguaac gucaaugagc aaa
232216RNAEscherichia coli 22gagcaaaggu auuaac 162323RNAEscherichia
coli 23gagcaaaggu auuaacuuua cuc 232439DNAEscherichia coli
24tgcgggtaac gtcaatgagc aaaggtatta actttactc 39
* * * * *
References