Method of detecting nucleotide polymorphism

• US 20030148301A1
• Filed: 10/17/2002
• Published: 08/07/2003
• Est. Priority Date: 12/10/1999
• Status: Abandoned Application

• Current Assignee: Toyoda Gosei Company Limited (Toyota Motor Corporation)
• Original Assignee: Toyoda Gosei Company Limited (Toyota Motor Corporation)
• Inventors: Segawa, Masaya, Takarada, Yutaka, Yoshiga, Satoko, Aono, Toshiya
• Application Number:
  US10/149,262
• Publication Number:
  US 20030148301A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis

Abstract

A method of detecting variation or polymorphism in a nucleic acid sequence, which is useful particularly in diagnosing a hereditary disease, analyzing nucleotide polymorphism, etc., and primers to be used therein. More particularly speaking, this method comprises treating a primer for wild type and one or two primers for variant with DNA polymerase either simultaneously or separately, and detecting the nucleotide polymorphism contained in the nucleic acid sample by judging whether or not the primers are extended, or whether or not the primers are amplified with a reverse primer. In this method, the 3′-end second bases of the primer for wild type and one or two primers for variant correspond to respective nucleotides anticipated in the nucleotide polymorphism site. Further, at least one of the bases from the 3′-end third position to the 5′-end is substituted by a base not complementary to the base in the chain hybridized with the primer in the chromosome or fragment. Furthermore, the not complementary base as described above differs from primer to primer.

Claims

1. A method of detecting a single nucleotide polymorphism contained in a nucleic acid sample, comprising the steps of

(a) applying a wild-type primer and one or two types of variant primer either simultaneously or separately together with DNA polymerase to a chromosome or fragment thereof including a specific single nucleotide polymorphism site contained in a sample, and

(b) detecting the nucleotide polymorphism contained in the nucleic acid sample according to whether or not the primers are elongated,

wherein the second nucleotide from the 3′

end of the primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site.

2. The method of detecting a single nucleotide polymorphism contained in a nucleic acid sample according to claim 1, comprising the steps of:

(a) applying a wild-type primer and 1 or two types of variant primer either simultaneously or separately together with DNA polymerase to a chromosome or fragment thereof including a specific single nucleotide polymorphism site contained in a sample, and

(b) detecting the nucleotide polymorphism contained in the nucleic acid sample according to whether or not the primers are elongated,

wherein the second base from the 3′

end of the primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and

wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain, which hybridizes with the primer in the chromosome or fragment thereof.

3. The detection method according to claim 2, wherein the 3′

end third position base of each primer is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof.

4. The method of detecting a single nucleotide polymorphism contained in a nucleic acid sample according to claim 1, comprising the steps of:

(a) applying a wild-type primer and 1 or two types of variant primer either simultaneously or separately together with DNA polymerase to a chromosome or fragment thereof including a specific single nucleotide polymorphism site contained in a sample, and

(b) detecting the nucleotide polymorphism contained in the nucleic acid sample according to whether or not the primers are elongated,

wherein the second base from the 3′

end of the primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and

wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof, and said non-complementary base differs from primer to primer.

5. The detection method according to claim 4, wherein the 3′

end third position base of each primer is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof, and said non-complementary base differs from primer to primer.

6. The method according to claim 1, wherein the DNA polymerase has double-stranded DNA 3′

exonuclease activity.

7. The method according to claim 1, wherein the DNA polymerase is derived from Pyrococcus sp. KOD1 strain or Hyperthermophilic archaebacterium.

8. The method according to claim 1, including before step (a) a step of amplifying a chromosome or fragment thereof including a specific single nucleotide polymorphism site contained in a sample.

9. The method according to claim 8, wherein the method of amplifying the chromosome or fragment is any one of the group consisting of PCR, NASBA, LCR, SDA, RCR and TMA.

10. The method according to claim 1, wherein hybridization using a detection probes specific to the sequence of the elongation product of at least one of the group consisting of wild type and variant primers is used to detect whether or not each of the primers has been elongated.

11. The method according to claim 10, wherein at least one of the primers or the detection probe is labeled in advance.

12. The method according to claim 10, wherein at least one of the primers or the detection probe is labeled with at least one from the group consisting of enzymes, biotin, fluorescent material, hapten, antigen, antibodies, radioactive material and luminophore.

13. The method according to claim 1, wherein step (a) is performed in a single tube, and hybridization with a detection probe specific to the sequence of the elongation product of at least one of the group consisting of wild-type and variant primers is used to detect whether or not each of the primers has been elongated.

14. A method of detecting a single nucleotide polymorphism contained in a nucleic acid sample, comprising the steps of

(a) applying a wild-type primer and one or two types of variant primer either simultaneously or separately together with DNA polymerase to a chromosome or fragment thereof including a specific single nucleotide polymorphism site contained in a sample, and

(b) detecting the nucleotide polymorphism contained in the nucleic acid sample according to whether or not the chromosome or fragment containing the specific single nucleotide polymorphism site is amplified, and

wherein the second nucleotide from the 3′

end of the primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site.

15. The method of detecting a single nucleotide polymorphism contained in a nucleic acid sample according to claim 14, comprising the steps of

(a) applying a wild-type primer and one or two types of variant primer either simultaneously or separately together with DNA polymerase to a chromosome or fragment thereof including a specific single nucleotide polymorphism site contained in a sample, and

(b) detecting the nucleotide polymorphism contained in the nucleic acid sample according to whether or not the chromosome or fragment containing the specific single nucleotide polymorphism site is amplified,

wherein the second nucleotide from the 3′

end of the primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and

wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain, which hybridizes with the primer in the chromosome or fragment thereof.

16. The detection method according to claim 15, wherein the 3′

end third position base of each primer is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof.

17. The method of detecting a single nucleotide polymorphism contained in a nucleic acid sample according to claim 14, comprising the steps of:

(a) applying a wild-type primer and 1 or two types of variant primer either simultaneously or separately together with DNA polymerase to a chromosome or fragment thereof including a specific single nucleotide polymorphism site contained in a sample, and

(b) detecting the nucleotide polymorphism contained in the nucleic acid sample according to whether or not the chromosome or fragment containing the specific single nucleotide polymorphism site is amplified,

wherein the second base from the 3′

end of the primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and

wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof, and said non-complementary base differs from primer to primer.

18. The detection method according to claim 17, wherein the 3′

end third position base of each primer is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof, and said non-complementary base differs from primer to primer.

19. The method according to claim 14, wherein the DNA polymerase has double-strand DNA 3′

exonuclease activity.

20. The method according to claim 14, wherein the DNA polymerase is derived from Pyrococcus sp. KOD1 strain or Hyperthermophilic archaebacterium.

21. The method according to claim 14, wherein the method of amplifying the chromosome or fragment thereof is any one of the group consisting of PCR, NASBA, LCR, SDA, RCR and TMA.

22. The method according to claim 14, wherein hybridization using a detection probe specific to the sequence of the respective elongation products of the wild-type and/or variant primers is used to detect whether or not a chromosome or fragment containing the specific single nucleotide polymorphism site has been amplified.

23. The method according to claim 22, wherein at least one of the primers or the detection probe is labeled in advance.

24. The method according to claim 22, wherein at least one of the primers or the detection probe is labeled with at least one from the group consisting of enzymes, biotin, fluorescent material, hapten, antigen, antibodies, radioactive material and luminophore.

25. The method according to claim 14, wherein step (a) is performed in a single container, and hybridization with detection probes specific to the sequences of the respective amplification products from the wild-type and/or variant primers is used to detect whether or not the chromosome or fragment containing the specific single nucleotide polymorphism has been amplified.

26. A single nucleotide polymorphism detection reagent kit comprising a wild-type primer, one or two types of variant primer, DNA polymerase and 4 types of deoxynucleoside triphosphate (dNTP), wherein the second base from the 3′

end of each primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site.

27. The kit according to claim 26, being a single nucleotide polymorphism detection reagent kit comprising a wild-type primer, one or two types of variant primer, DNA polymerase and 4 types of deoxynucleoside triphosphate (dNTP), wherein the second base from the 3′

end of each primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof.

28. The kit according to claim 27, wherein the 3′

end third position base of each primer is replaced by a base not complementary to the base of the chain which hybridizes with the primer in the chromosome or fragment thereof.

29. The kit according to claim 26, being a single nucleotide polymorphism detection reagent kit comprising a wild-type primer, one or two types of variant primer, DNA polymerase and 4 types of deoxynucleoside triphosphate (dNTP), wherein the second base from the 3′

end of each primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof, and wherein said non-complementary base differs from primer to primer.

30. The kit according to claim 29, wherein the 3′

end third position base in each primer is replaced by a base not complementary to the base of the chain, which hybridizes with the primer in the chromosome, or fragment thereof, and wherein said non-complementary base differs from primer to primer.

31. A single nucleotide polymorphism detection reagent kit comprising a wild-type primer, one or two types of variant primer, DNA polymerase, 4 types of deoxynucleoside triphosphate (dNTP) and a detection probe, wherein the second base from the 3′

end of each primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site.

32. The kit according to claim 31, being a single nucleotide polymorphism detection reagent kit comprising a wild-type primer, one or two types of variant primer, DNA polymerase, 4 types of deoxynucleoside triphosphate (dNTP) and a detection probe, wherein the second base from the 3′

end of each primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof.

33. The kit according to claim 32, wherein the 3′

end third position base of each primer is replaced by a base not complementary to the base of the chain which hybridizes with the primer in the chromosome or fragment.

34. The kit according to claim 31, being a single nucleotide polymorphism detection reagent kit comprising a wild-type primer, one or two types of variant primer, DNA polymerase, 4 types of deoxynucleoside triphosphate (dNTP) and a detection probe, wherein the second base from the 3′

end of each primer corresponds to the respective nucleotides anticipated in the nucleotide polymorphism site, and wherein at least one of the bases from the 3′

end third position to the 5′

end is replaced by a base not complementary to the base in the chain which hybridizes with the primer in the chromosome or fragment thereof, and wherein said non-complementary base differs from primer to primer.

35. The kit according to claim 34, wherein the 3′

end third position base of each primer is replaced by a base not complementary to the base of the chain, which hybridizes with the primer in the chromosome, or fragment thereof, and wherein said non-complementary base differs from primer to primer.