Detection of single nucleotide polymorphisms by single molecule analysis

• US 20040101891A1
• Filed: 08/12/2003
• Published: 05/27/2004
• Est. Priority Date: 08/12/2002
• Status: Abandoned Application

• Current Assignee: Gnothis Holding SA
• Original Assignee: Gnothis Holding SA
• Inventors: Rigler, Rudolf, Edman, Lars
• Application Number:
  US10/638,548
• Publication Number:
  US 20040101891A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2525/125 incorporating agents resulting in resistance to degradation
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension

Abstract

The present invention relates to a method for determining a nucleotide polymorphism, particularly a single nucleotide polymorphism (SNP) in a nucleic acid target.

Claims

1. A method for determining a nucleotide polymorphism comprising:

(a) providing a nucleic acid template to be analyzed,

(b) annealing at least one primer to the nucleic acid template, wherein the 3′

-end of the primer is located upstream of a nucleotide polymorphism to be analyzed,

(c) sequence-specific elongating the primer by incorporating at least one labelled nucleotide into the primer,

(d) degrading the nucleic acid template under conditions, wherein the elongated starting primer is substantially stable against degradation, and wherein the elongated primer is liberated from the nucleic acid template and

(e) detecting labels incorporated into the primer which are characteristic for the nucleotide polymorphism to be analyzed.

2. The method of claim 1, wherein the nucleic acid template is a single-stranded DNA or RNA molecule.

3. The method of claim 1 or 2, wherein the nucleic acid template is immobilized on a solid phase.

4. The method of claim 3, wherein the solid phase is a particle.

5. The method of claim 3 or 4, wherein the nucleic acid template is immobilized via its 5′

-end or its 3′

-end to the solid phase.

6. The method of any one of claims 1-5, wherein at least two primers are annealed to the nucleic acid template, wherein each primer is located upstream of a different nucleotide polymorphism to be analyzed.

7. The method of claim 6, wherein a time-resolved detection of individual primers is carried out.

8. The method of any one of claims 1-7, wherein the primer is stabilized against degradation.

9. The method of claim 8, wherein the primer is a nucleic acid analogue comprising modified bonds between nucleotides and/or modified sugar groups.

10. The method of any one of claims 1-9, wherein a single labelled chain termination nucleotide is incorporated into the primer.

11. The method of claim 10, wherein the chain-termination nucleotide is a didesoxynucleoside triphosphate.

12. The method of any one of claims 1-11, wherein the sequence-specific elongation is carried out in the presence of at least two different labelled nucleotides carrying different labelling groups.

13. The method of any one of claims 1-12, wherein the labelling groups are selected from fluorescence groups.

14. The method of any one of claims 1-13, wherein the degradation of the nucleic acid template molecule is direction-specific.

15. The method of any one of claims 1-14, wherein the nucleic acid template molecule is degraded by enzymatic treatment.

16. The method of claim 14 or 15, wherein the degradation is carried out by 5′

→

3′

or 3′

→

5′

exonuclease treatment.

17. The method of claim 16, wherein the exonuclease is selected from the group consisting of T7 DNA polymerase, T7 gene 6 exonuclease, E.coli exonuclease I, E.coli exonuclease II, E.coli exonuclease VII, bacteriophage lambda exonuclease, rec JF and trex 1,2.

18. The method of any one of claims 1-17, wherein at least two primers are liberated from the nucleic acid template sequentially and direction-specifically.

19. The method of any one of claims 1-18, wherein the detection is carried out as a single molecule detection.

20. The method of claim 19, wherein the single molecule detection comprises the steps:

(i) introducing a particle having immobilized thereon a single molecule of the nucleic acid template into a detection apparatus comprising a microchannel,

(ii) trapping the particle at a predetermined position within the detection apparatus, and

(iii) degrading the nucleic acid template within the detection apparatus.