Polymorphism Detection Method

• US 20080193936A1
• Filed: 03/22/2006
• Published: 08/14/2008
• Est. Priority Date: 03/22/2005
• Status: Abandoned Application

• Current Assignee: Enigma Diagnostics Limited
• Original Assignee: Enigma Diagnostics Limited
• Inventors: Squirrell, David James
• Application Number:
  US11/909,218
• Publication Number:
  US 20080193936A1
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]

Abstract

A method for detecting the presence or absence of a polymorphism at a particular position within a nucleic acid sequence in a sample, said method comprising i) annealing a pair of probes to said nucleic acid sequence, said probes being designed such that they anneal adjacent each other, and only completely anneal to one form of the sequence, in a reaction mixture which is substantially free of ATP; ii) ligating together any completely annealed pairs of probes in the presence of NAD and a nucleic acid ligase which uses NAD as a substrate/ iii) phosphorylating any AMP released by a ligation event to ATP, and iv) detecting ATP, in particular using a bioluminescent reaction, in the resultant reaction mixture. Kits for conducting this method are also described and claimed.

Claims

1. A method for detecting the presence of a polymorphism at a particular position within a target nucleic acid sequence in a sample, said method comprising

i) annealing a pair of probes to said nucleic acid sequence, said probes being designed such that they anneal adjacent each other, and only completely anneal to one form of the sequence, in a reaction mixture which is substantially free of ATP;

ii) ligating together each completely annealed pair of probes in the presence of NAD and a nucleic acid ligase which uses NAD as a substrate, whereby AMP is released;

iii) phosphorylating the released AMP to ATP; and

iv) detecting ATP in the resultant reaction mixture.

2. The method of claim 1, wherein ATP is detected using a bioluminescent system.

3. The method of claim 2, wherein the bioluminescent system is a luciferase/luciferin system.

4. The method of claim 1, wherein as a pre-treatment step, the sample containing the nucleic acid sequence is treated to remove ATP such that the sample is substantially free of ATP.

5. The method of claim 4, wherein the sample is a biological sample.

6. The method of claim 1, wherein the nucleic acid ligase is a thermostable ligase, and the method is part of a ligase chain reaction.

7. The method of claim 1, wherein the target nucleic acid is double stranded and two pairs of probes are used, each pair corresponding to each one strand of the target nucleic acid.

8. The method of claim 7, wherein the probes of each pair anneal directly adjacent each other on the target nucleic acid strand.

9. The method of claim 1, wherein the probes bind such that they are separated by a small gap, which does not contain any adenine bases therebetween, and the reaction mixture further contains a DNA polymerase and nucleotides suitable for extending the upstream probe across said gap, provided the 3′

end of the upstream probe matches the corresponding base on the target nucleic acid.

18. The method of claim 7, wherein each pair of probes binds such that they are separated by a small gap, which does not contain any adenine bases therebetween, and the reaction mixture further contains a DNA polymerase and nucleotides suitable for extending each upstream probe across said gaps, provided the 3′

end of each upstream probe matches the corresponding base on the target nucleic acid strand.

10. A kit for detecting a polymorphism within a target nucleic acid sequence, said kit comprising a nucleic acid ligase which uses NAD as a substrate, a phosphorylating agent, and one or more reagents able to produce a bioluminescent signal.

11. The kit of claim 10, wherein the phosphorylating agent is selected from the group consisting of a combination of phosphoenolpyruvate synthase, phosphate and phosphoenolpyruvate;

a combination of a nucleoside triphosphate-adenylate kinase, NTP and adenylate kinase; and

pyruvate phosphate dikinase.

12. The kit of claim 10, wherein the one or more reagents able to produce a bioluminescent signal is selected from the group consisting of luciferase, luciferin, and a combination thereof.

13. The kit of claim 10, further comprising a pair of probes suitable for annealing to the target nucleic acid.

14. The kit of claim 13, wherein the target nucleic acid is double stranded and the kit further comprises two pairs of probes, each pair being capable of annealing to corresponding regions on one strand of the target nucleic acid.

15. The kit of claim 10, further comprising magnesium salts.

16. The kit of claim 10, further comprising at least one agent selected from the group consisting of NAD, a buffer, and potassium salts.

17. The kit of claim 10, further comprising a deaminase enzyme.