CA2399733A1 - Nucleic acid detection methods using universal priming - Google Patents

Nucleic acid detection methods using universal priming Download PDF

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CA2399733A1
CA2399733A1 CA002399733A CA2399733A CA2399733A1 CA 2399733 A1 CA2399733 A1 CA 2399733A1 CA 002399733 A CA002399733 A CA 002399733A CA 2399733 A CA2399733 A CA 2399733A CA 2399733 A1 CA2399733 A1 CA 2399733A1
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target
probe
detection position
sequence
nucleotide
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CA2399733C (en
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Jian-Bing Fan
Mark S. Chee
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Illumina Inc
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    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/682—Signal amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6862—Ligase chain reaction [LCR]
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
    • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
    • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Abstract

The present invention is directed to providing sensitive and accurate assays for genotyping with a minimum or absence of target-specific amplification.</ SDOAB>

Claims (29)

1. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising:
a) providing a first probe comprising:
i) an upstream universal priming site (UUP);
ii) an adapter sequence;
iii) a first target-specific sequence comprising a first base at a readout position; and iv) a downstream universal priming site (DUP);
b) contacting said first probe with said target sequence under conditions whereby only if said first base is perfectly complementary to a nucleotide at said detection position is a first hybridization complex formed;
c) removing non-hybridized first probes;
d) denaturing said hybridization complex;
e) amplifying said first probe to generate a plurality of amplicons;
f) contacting said amplicons with an array of capture probes; and g) determining the nucleotide at said detection position.
2. A method according to claim 1 wherein said amplicons comprise a label.
3. A method according to claim 1 further comprising:
a) providing a second probe comprising:
i) an upstream universal priming site (UUP);
ii) an adapter sequence;
iii) a second target-specific sequence comprising a second base at said readout position; and iv) a downstream universal priming site (DUP);
b) contacting said second probe with said target sequence under conditions whereby only if said second base is perfectly complementary to a nucleotide at said detection position is a second hybridization complex formed;
c) removing non-hybridized second probes;
d) denaturing said second hybridization complex;

e) amplifying said second probe to generate a plurality of amplicons;
f) contacting said amplicons with an array of capture probes; and g) determining the nucleotide at said detection position.
4. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising:
a) providing a plurality of readout probes each comprising:
i) an upstream universal priming site (UUP);
ii) an adapter sequence;
iii) a target-specific sequence comprising a unique base at a readout position; and iv) a downstream universal priming site (DUP);
b) contacting said detection probes with said target sequence under conditions whereby only if said base at said readout position is perfectly complementary to a nucleotide at said detection position is a first hybridization complex formed;
c) removing non-hybridized first probes;
d) denaturing said first hybridization complex;
e) amplifying said detection probes to generate a plurality of amplicons;
f) contacting said amplicons with an array of capture probes; and g) determining the nucleotide at said detection position.
5. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising a first target domain comprising said detection position and a second target domain adjacent to said detection position, wherein said method comprises:
a) hybridizing a first ligation probe to said first target domain, said first ligation probe comprising:
i) an upstream universal priming site (UUP); and ii) a first target-specific sequence; and b) hybridizing a second ligation probe to said second target domain, said second ligation probe comprising:
i) a downstream universal priming site (DUP); and ii) a second target-specific sequence comprising a first base at an interrogation position;
wherein if said first base is perfectly complementary to said nucleotide at said detection position a ligation complex is formed and wherein at least one of said first and second ligation probes comprises an adapter sequence;
c) removing non-hybridized first probes;
d) providing a ligase that ligates said first and second ligation probes to form a ligated probe;
e) amplifying said ligated probe to generate a plurality of amplicons;
f) contacting said amplicons with an array of capture probes; and g) determining the nucleotide at said detection position.
6. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising a first target domain comprising said detection position and a second target domain adjacent to said detection position, wherein said method comprises:
a) hybridizing a first ligation probe to said first target domain, said first ligation probe comprising:
i) an upstream universal priming site (UUP); and ii) a first target-specific sequence; and b) hybridizing a second ligation probe to said second target domain, said second ligation probe comprising:
i) a downstream universal priming site (DUP); and ii) a second target-specific sequence comprising a first base at an interrogation position;
wherein if said first base is perfectly complementary to said nucleotide at said detection position a ligation complex is formed and wherein at least one of said first and second ligation probes comprises an adapter sequence;
c) removing non-hybridized first probes;
d) providing a ligase that ligates said first and second ligation probes to form a ligated probe;
e) hybridizing said ligated probe to a rolling circle (RC) sequence comprising:
i) an upstream priming sequence; and ii) a downstream priming sequence;
f) providing a ligase that ligates said upstream and downstream priming sites to form a circular ligated probe;
g) amplifying said circular ligated probe to generate a plurality of amplicons;
f) contacting said amplicons with an array of capture probes; and g) determining the nucleotide at said detection position.
7. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising a first target domain comprising said detection position and a second target domain adjacent to said detection position, wherein said method comprises:
a) hybridizing a rolling circle (RC) probe to said target sequence, said RC
probe comprising:
i) an upstream universal priming site (UUP); and ii) a first target-specific sequence;
iii) a second target-specific sequence comprising a first base at an interrogation position; and iv) an adapter sequence;
wherein if said first base is perfectly complementary to said nucleotide at said detection position a ligation complex is formed;
c) providing a ligase that ligates said first and second ligation probes to form a ligated probe;
d) amplifying said ligated probe to generate a plurality of amplicons;
e) contacting said amplicons with an array of capture probes; and f) determining the nucleotide at said detection position.
8. A method according to claim 7, further comprising removing non-hybridized RC probe.
9. A method according to claim 1, 4, 5, 6 or 8 wherein said removing comprises:
a) enzymatically adding a binding ligand to said target sequence;
b) binding a hybridization complex comprising said target sequence comprising said binding ligand to a binding partner immobilized on a solid support;
c) washing away unhybridized probes; and d) eluting said probe off said solid support.
10. A method according to claim 1, 4, 5, 6 or 8 wherein said removing is done using a double-stranded specific moiety.
11. A method according to claim 10 wherein said double-stranded specific moiety is an intercalator attached to a support.
12. A method according to claim 9 wherein said support is a bead.
13. A method according to claim 1, 4, 5, 6 or 7 wherein said amplifying is done by:
a) hybridizing a first universal primer to said UUP;
b) providing a polymerase and dNTPs such that said first universal primer is extended;
c) hybridizing a second universal primer to said DUP;
d) providing a polymerase and dNTPs such that said second universal primer is extended; and e) repeating steps a) through d).
14. A method according to claim 1, 4, 5, 6 or 7 wherein said array comprises:
a) a substrate with a patterned surface comprising discrete sites; and b) a population of microspheres comprising at least a first subpopulation comprising a first capture probe and a second subpopulation comprising a second capture probe.
15. A method according to claim 14 wherein said discrete sites comprise wells.
16. A method according to claim 14 or 15 wherein said substrate comprises a fiber optic bundle.
17. A method of determining the identification of a nucleotide at a detection position in a genomic target sequence comprising:
a) attaching a library of genomic target sequences to a solid support;
b) adding at least one probe and an enzyme to form an extended primer;
c) denaturing said extended primer from said target sequence;
d) hybridizing said extended primer to an array comprising capture probes; and e) determining said nucleotide at said detection position.
18. A method according to claim 17, further comprising removing unhybridized probes.
19. A method according to claim 1, 4, 5, 6 or 7, further comprising providing a support on which the target sequence is immobilized.
20. A method according to claim 19, wherein said non-hybridized first probes are removed without removing said target sequence from said support.
21. A method according to claim 1, 4, 5, 6 or 7, further comprising attaching said target sequence to a support.
22. A method according to claim 21, wherein said target sequence is attached to said support by a method selected from the group consisting of labeling said target sequence with a functional attachment moiety, absorption of said target sequence on a charged support, direct chemical attachment of said target sequence to said support and photocrosslinking said target sequence to said support.
23. A method according to claim 1, 4, 5, 6 or 7, wherein said support is selected from the group consisting of paper, plastic and tubes.
24. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising:
a) providing a support on which the target sequence is immobilized;
b) providing a first probe comprising:
i) an upstream universal priming site (UUP);
ii) an adapter sequence;
iii) a first target-specific sequence comprising a first base at a readout position; and iv) a downstream universal priming site (DUP);
c) contacting said first probe with said target sequence under conditions whereby only if said first base is perfectly complementary to a nucleotide at said detection position is a first hybridization complex formed;
d) removing non-hybridized first probes;
e) denaturing said hybridization complex;
f) amplifying said first probe to generate a plurality of amplicons;
g) contacting said amplicons with an array of capture probes; and h) determining the nucleotide at said detection position
25. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising:

a) providing a support on which the target sequence is immobilized;
b) providing a plurality of readout probes each comprising:
i) an upstream universal priming site (UUP);
ii) an adapter sequence;
iii) a target-specific sequence comprising a unique base at a readout position; and iv) a downstream universal priming site (DUP);
c) contacting said detection probes with said target sequence under conditions whereby only if said base at said readout position is perfectly complementary to a nucleotide at said detection position is a first hybridization complex formed;
d) removing non-hybridized first probes;
e) denaturing said first hybridization complex;
f) amplifying said detection probes to generate a plurality of amplicons;
g) contacting said amplicons with an array of capture probes; and h) determining the nucleotide at said detection position.
26. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising a first target domain comprising said detection position and a second target domain adjacent to said detection position, wherein said method comprises:
a) providing a support on which the target sequence is immobilized;
b) hybridizing a first ligation probe to said first target domain, said first ligation probe comprising:
i) an upstream universal priming site (UUP); and ii) a first target-specific sequence; and c) hybridizing a second ligation probe to said second target domain, said second ligation probe comprising:
i) a downstream universal priming site (DUP); and ii) a second target-specific sequence comprising a first base at an interrogation position;
wherein if said first base is perfectly complementary to said nucleotide at said detection position a ligation complex is formed and wherein at least one of said first and second ligation probes comprises an adapter sequence;
d) removing non-hybridized first probes;
e) providing a ligase that ligates said first and second ligation probes to form a ligated probe;

f) amplifying said ligated probe to generate a plurality of amplicons;
g) contacting said amplicons with an array of capture probes; and h) determining the nucleotide at said detection position.
27. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising a first target domain comprising said detection position and a second target domain adjacent to said detection position, wherein said method comprises:
a) providing a support on which the target sequence is immobilized;
b) hybridizing a first ligation probe to said first target domain, said first ligation probe comprising:
i) an upstream universal priming site (UUP); and ii) a first target-specific sequence; and c) hybridizing a second ligation probe to said second target domain, said second ligation probe comprising:
i) a downstream universal priming site (DUP); and ii) a second target-specific sequence comprising a first base at an interrogation position;
wherein if said first base is perfectly complementary to said nucleotide at said detection position a ligation complex is formed and wherein at least one of said first and second ligation probes comprises an adapter sequence;
d) removing non-hybridized first probes;
e) providing a ligase that ligates said first and second ligation probes to form a ligated probe;
f) hybridizing said ligated probe to a rolling circle (RC) sequence comprising:
i) an upstream priming sequence; and ii) a downstream priming sequence;
g) providing a ligase that ligates said upstream and downstream priming sites to form a circular ligated probe;
h) amplifying said circular ligated probe to generate a plurality of amplicons;
i) contacting said amplicons with an array of capture probes; and j) determining the nucleotide at said detection position.
28. A method of determining the identification of a nucleotide at a detection position in a target sequence comprising a first target domain comprising said detection position and a second target domain adjacent to said detection position, wherein said method comprises:

a) providing a support on which the target sequence is immobilized;
b) hybridizing a rolling circle (RC) probe to said target sequence, said RC
probe comprising:
i) an upstream universal priming site (UUP); and ii) a first target-specific sequence;
iii) a second target-specific sequence comprising a first base at an interrogation position; and iv) an adapter sequence;
wherein if said first base is perfectly complementary to said nucleotide at said detection position a ligation complex is formed;
c) providing a ligase that ligates said first and second ligation probes to form a ligated probe;
d) amplifying said ligated probe to generate a plurality of amplicons;
e) contacting said amplicons with an array of capture probes; and f) determining the nucleotide at said detection position.
29. A method according to claim 28, further comprising removing unhybridized RC probe.
CA2399733A 2000-02-07 2001-02-07 Nucleic acid detection methods using universal priming Expired - Lifetime CA2399733C (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US18081000P 2000-02-07 2000-02-07
US60/180,810 2000-02-07
US23473200P 2000-09-22 2000-09-22
US60/234,732 2000-09-22
PCT/US2001/004056 WO2001057269A2 (en) 2000-02-07 2001-02-07 Nucleic acid detection methods using universal priming

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CA2399733C CA2399733C (en) 2011-09-20

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EP (2) EP1990428B1 (en)
JP (1) JP2003521252A (en)
AT (2) ATE411397T1 (en)
AU (1) AU2001238068A1 (en)
CA (1) CA2399733C (en)
DE (2) DE60143723D1 (en)
DK (1) DK1259643T3 (en)
HK (1) HK1047603B (en)
WO (1) WO2001057269A2 (en)

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EP1259643A2 (en) 2002-11-27
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US20040224353A1 (en) 2004-11-11
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US6890741B2 (en) 2005-05-10
US20020132241A1 (en) 2002-09-19
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US20030003490A1 (en) 2003-01-02
ATE492652T1 (en) 2011-01-15
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EP1259643B1 (en) 2008-10-15
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DK1259643T3 (en) 2009-02-23
HK1047603B (en) 2009-03-27

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