CA2796223A1 - Detection of nucleic acids by type-specific hybrid capture method - Google Patents

Detection of nucleic acids by type-specific hybrid capture method Download PDF

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Publication number
CA2796223A1
CA2796223A1 CA2796223A CA2796223A CA2796223A1 CA 2796223 A1 CA2796223 A1 CA 2796223A1 CA 2796223 A CA2796223 A CA 2796223A CA 2796223 A CA2796223 A CA 2796223A CA 2796223 A1 CA2796223 A1 CA 2796223A1
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CA
Canada
Prior art keywords
sequence probe
probe
nucleic acid
target nucleic
capture sequence
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Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
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CA2796223A
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French (fr)
Inventor
James Anthony
Attila Lorincz
Inna Williams
John Troy
Yanglin Tang
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Qiagen Gaithersburg LLC
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Qiagen Gaithersburg LLC
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Application filed by Qiagen Gaithersburg LLC filed Critical Qiagen Gaithersburg LLC
Publication of CA2796223A1 publication Critical patent/CA2796223A1/en
Abandoned legal-status Critical Current

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    • 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
    • C12Q1/6832—Enhancement of hybridisation reaction
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/705—Specific hybridization probes for herpetoviridae, e.g. herpes simplex, varicella zoster
    • 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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/708—Specific hybridization probes for papilloma
    • 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

Target-specific hybrid capture (TSHC) provides a nucleic acid detection method that is not only rapid and sensitive, but is also highly specific and capable of discriminating highly homologous nucleic acid target sequences. The method produces DNA/RNA hybrids which can be detected by a variety of methods.

Claims (59)

1. A method of detecting a target nucleic acid comprising:

a) hybridizing a single-stranded or partially single-stranded target nucleic acid to a capture sequence probe and a signal sequence probe, wherein the capture sequence probe and the signal sequence probe hybridize to non-overlapping regions within the target nucleic acid and not to each other, wherein said hybridization forms an RNA/DNA hybrid between said signal sequence probe and the target nucleic acid; and b) detecting the RNA/DNA hybrid by binding an antibody that recognizes the RNA/DNA hybrid to said hybrid, wherein said antibody is detectably labeled.
2. The method of claim 1, further comprising binding the hybrid formed in step a) to a solid phase to form a bound hybrid.
3. The method of claim 1, wherein the signal sequence probe is single-stranded.
4. The method of claim 1, wherein the capture sequence probe is modified with at least one ligand.
5. The method of claim 4, wherein the capture sequence probe is biotinylated.
6. The method of claim 5, wherein the capture sequence probe is linear having a 5' and a 3' end, wherein both the 5' and the 3' ends are biotinylated.
7. The method of claim 1, wherein the capture sequence probe and the signal sequence probe hybridize to regions of the target nucleic acid, wherein the regions are less than 3 kilobases apart.
8. The method of claim 1, wherein the capture sequence probe and the signal sequence probe hybridize to regions of the target nucleic acid, wherein the regions are less than 500 bases apart.
9. The method of claim 1, further comprising the step of forming single-stranded target nucleic acid prior to the hybridization step.
10. The method of claim 1, wherein hybridizations of the capture sequence probe and the signal sequence probe to the target nucleic acid are performed sequentially.
11. The method of claim 1, wherein the hybrid formed in step a) is bound onto a solid phase forming a bound hybrid.
12. The method of claim 11, wherein the bound hybrid is formed at room temperature.
13. The method of claim 11, wherein the solid phase is coated with streptavidin.
14. The method of claim 11, wherein the solid phase is a microplate.
15. The method of claim 1, wherein the antibody is labeled with alkaline-phosphatase.
16. The method of claim 1, further comprising adding a blocker probe to the hybridization step, wherein said Mocker probe hybridizes to excess non-hybridized capture sequence probes.
17. The method of claim 16, wherein the blocker probes are added to the hybridization reaction following the hybridization of the capture sequence probes to the target nucleic acid.
18. The method of claim 16, wherein the blocker probe has a lower melting temperature than that of the capture sequence probe.
19. A method of detecting a target nucleic acid comprising:

a) hybridizing a single stranded or partially single-stranded target nucleic acid to a capture sequence probe and a signal sequence probe, wherein the capture sequence probe and the signal sequence probe hybridize to non-overlapping regions within the target nucleic acid and not to each other, wherein the signal sequence probe comprises a DNA/RNA hybrid region, wherein said hybridization forms a complex; and b) detecting said complex.
20. The method of claim 19 wherein the signal sequence probe comprises of at least 40 base pairs in length.
21. The method of claim 19 wherein the capture sequence probe comprises of at least 6 base pairs in length.
22. The method of claim 21 wherein the capture sequence probe is immobilized on a solid phase.
23. The method of claim 19 wherein said complex is detected by binding an antibody that recognizes the DNA/RNA hybrid region to said region, wherein the antibody is detectably labeled.
24. The method of claim 19 wherein the capture sequence is modified with at least one ligand.
25. The method of claim 24 wherein the ligand is biotin.
26. The method of claim 25, wherein the capture sequence probe is linear having a 5' and 3' end, wherein both the 5' and 3' ends are biotinylated.
27. The method of claim 19, further comprising adding a Mocker probe after the hybridization step, wherein said blocker probe hybridizes to excess non-hybridized capture sequence probe.
28. The method of claim 27, wherein the blocker probes comprise a length of 4-base pairs shorter than the length of the capture sequence probe.
29. A method of detecting a target nucleic acid comprising:

a) hybridizing a single-stranded or partially single-stranded target nucleic acid to a capture sequence probe and a signal sequence probe to form double-stranded hybrids between said probes and the target nucleic acid;

b) binding the hybrid to a solid phase forming a bound hybrid; and c) detecting the bound hybrid, wherein the capture sequence probe and the signal sequence probe hybridize to non-overlapping regions within the target nucleic acid and not to each other.
30. The method of claim 29, wherein hybridization of the capture sequence probe and the signal sequence probe to the target nucleic acid are performed sequentially.
31. The method of claim 29, wherein step a) and step b) are performed simultaneously.
32. The method of claim 29, further comprising adding a blocker probe, wherein said blocker probe hybridizes to excess non-hybridized capture sequence probes.
33. The method of claim 32, wherein the addition of the blocker probe and hybridization step are performed simultaneously.
34. The method of claim 32, wherein the addition of the blocker probe and binding step are performed simultaneously.
35. The method of claim 29, wherein the signal sequence probe is single-stranded.
36. The method of claim 29, wherein the capture sequence probe is modified with at least one ligand.
37. The method of claim 36, wherein the ligand is biotin.
38. The method of claim 37, wherein the capture sequence probe is linear having a 5' and 3' end, wherein both the 5' and the 3' ends are biotinylated.
39. The method of claim 29, wherein the capture sequence probe and the signal sequence probe hybridize to regions of the target nucleic acid, wherein the regions are less than 3 kilobases apart.
40. The method of claim 29, wherein the capture sequence probe and the signal sequence probe hybridize to regions of the target nucleic acid, wherein the regions are less than 500 bases apart.
41. The method of claim 29, wherein the capture sequence probe is a fusion of two or more sequences complementary to different regions of the target nucleic acid or to different target molecules.
42. The method of claim 29, wherein the double-stranded hybrid formed is a DNA/RNA hybrid.
43. The method of claim 29, further comprising the step of forming single-stranded DNA prior to the hybridization step.
44. The method of claim 29, wherein hybridization of the capture sequence probe and the signal sequence probe to the target nucleic acid are performed sequentially.
45. The method of claim 29, wherein step a) and step b) are performed simultaneously.
46. The method of claim 30, wherein the blocker probe has lower melting temperature than that of the capture sequence probe.
47. The method of claim 30, wherein the solid phase is coated with streptavidin.
48. The method of claim 40, wherein the solid phase is a microplate.
49. The method of claim 29, wherein step b) is carried out at about 20 C to 90 C.
50. The method of claim 49, wherein the capture sequence probe comprises at least 6 bases in length.
51. The method of claim 29, wherein step b) is carried out at room temperature.
52. The method of claim 29, wherein the bound hybrid is detected using an antibody that recognizes a hybrid.
53. The method according to claim 29, wherein the signal sequence probe comprises a deleted capture sequence probe region and is complementary to the target nucleic acid.
54. The method according to claim 29, wherein the target nucleic acid is a single nucleotide polymorphism.
55. The method according to claim 54, wherein the specificity of binding hybrid to a solid phase is modulated by temperatures of greater than room temperature.
56. The method according to claim 54, wherein the specificity of binding hybrid to a solid phase is modulated by the addition of blocker probes.
57. The method according to claim 54, wherein the specificity of binding hybrid to a solid phase is modulated by temperatures of greater than room temperature and the addition of blocker probes.
58. The method according to claim 56, wherein the specificity of binding the hybrid to a solid phase is modulated by the addition of blocker probes.
59. The method according to claim 56, wherein the specificity of binding the hybrid to a solid phase is modulated by temperatures of greater than room temperature and the addition of blocker probes.
CA2796223A 2000-06-15 2001-06-15 Detection of nucleic acids by type-specific hybrid capture method Abandoned CA2796223A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US09/594,839 2000-06-15
US09/594,839 US7439016B1 (en) 2000-06-15 2000-06-15 Detection of nucleic acids by type-specific hybrid capture method
CA2413020A CA2413020C (en) 2000-06-15 2001-06-15 Detection of nucleic acids by type-specific hybrid capture method

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CA2413020A Expired - Fee Related CA2413020C (en) 2000-06-15 2001-06-15 Detection of nucleic acids by type-specific hybrid capture method

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US (6) US7439016B1 (en)
EP (3) EP1967594B1 (en)
JP (2) JP5166666B2 (en)
AT (1) ATE548464T1 (en)
AU (2) AU6697401A (en)
BR (1) BR0111992B1 (en)
CA (2) CA2796223A1 (en)
DK (1) DK1967594T3 (en)
ES (1) ES2545183T3 (en)
PT (1) PT1967594E (en)
SI (1) SI1967594T1 (en)
WO (1) WO2001096608A1 (en)

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