Method of determining zygosity by ligation and cleavage

• US 5,856,093 A
• Filed: 06/07/1995
• Issued: 01/05/1999
• Est. Priority Date: 04/04/1994
• Status: Expired due to Term

• Current Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Brenner, Sydney
• Primary Examiner(s): Zitomer, Stephanie W.
• Assistant Examiner(s): TRAN, PAUL
• Application Number:
  US08/478,239
• Time in Patent Office: 1,308 Days
• Field of Search: 435/6, 435/18, 435/91.1, 435/91.52, 435/91.53, 536/24.3, 935/77, 935/78
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: Y02P 20/582 Recycling of unreacted starting or intermediate materials

Abstract

The invention provides a method of nucleic acid sequence analysis based on repeated cycles of ligation to and cleavage of probes at the terminus of a target polynucleotide. At each such cycle one or more terminal nucleotides are identified and one or more nucleotides are removed from the end of the target polynucleotide, such that further cycles of ligation and cleavage can take place. At each cycle the target sequence is shortened by one or more nucleotides until the nucleotide sequence of the target polynucleotide is determined. The method obviates electrophoretic separation of similarly sized DNA fragments and eliminates the difficulties associated with the detection and analysis of spatially overlapping bands of DNA fragments in a gel, or like medium. The invention further obviates the need to generate DNA fragments from long single stranded templates with a DNA polymerase.

Claims

1. A method of determining the zygosity of an individual at a predetermined genetic locus having a plurality of allelic forms of DNA, the method comprising the steps of:

(a) providing a sample of the DNA from the predetermined genetic locus such that the sample of DNA comprises polynucleotides, each polynucleotide of the sample having a protruding strand and a recessed strand;

(b) ligating a probe having a protruding strand and a nuclease recognition site to an end of each polynucleotide to form one or more ligated complexes, the one or more ligated complexes being formed only from those probes whose protruding strands form perfectly matched duplexes with the protruding strands of the polynucleotides of the sample, and the nuclease recognition site being of a nuclease whose cleavage site is separate from its recognition site;

(c) identifying the kind and relative abundance of nucleotides in the protruding strand of the polynucleotide, by the identity of the probe ligated thereto or by extending a strand of the polynucleotide or probe;

(d) cleaving the ligated complexes with said nuclease that recognizes said nuclease recognition site and cuts the ligated complexes to give an augmented probe and a new protruding strand on the polynucleotide; and

(e) repeating steps (b) through (d) until the nucleotide sequences of the polynucleotides of the genetic locus are determined, thereby determining the zygosity of the individual.

2. The method of claim 1 wherein each of said polynucleotides is attached to a separate solid phase support or a separate region of the same solid phase support.

3. The method of claim 2 wherein said nuclease is a type IIs restriction endonuclease and wherein said step of identifying includes identifying a nucleotide in each of said protruding strands of said polynucleotides by extending a strand of each of said polynucleotides with a nucleic acid polymerase in the presence of chain-terminating nucleoside triphosphates.

4. The method of claim 3 further including the step of removing unligated probe from said polynucleotide after said step of ligating.

5. The method of claim 4 wherein said chain-terminating nucleoside triphosphates are labeled dideoxynucleoside triphosphates and wherein said step of identifying includes identifying said nucleotide by the label on the labeled dideoxynucleoside triphosphates incorporated into said recessed strand of said polynucleotide.

6. The method of claim 5 further including the steps of excising said labeled dideoxynucleotides and extending said recessed strands with a nucleic acid polymerase.

7. The method of claim 6 wherein said step of excising is carried out with T4 DNA polymerase in the presence of deoxyribonucleoside triphosphates.

8. The method of claim 2 wherein said nuclease is a type IIs restriction endonuclease and wherein said step of identifying includes identifying a nucleotide in each of said protruding strands of said polynucleotides by the identity of the probe ligated thereto.

9. The method of claim 8 wherein the step of providing further includes blocking the recognition sites of said nuclease on said polynucleotides.

10. The method of claim 5 wherein said blocking said recognition sites includes treating said polynucleotides with a methylase.

11. The method of claim 10 wherein said step of ligating includes treating said polynucleotide with a ligase.

12. The method of claim 11 wherein said polynucleotides each contains a 5'"'"'-phosphoryl group on said end having said protruding strand and wherein said probe lacks a 5'"'"'-phosphoryl group on said end having said protruding strand.

13. The method of claim 12 wherein said step of ligating includes treating said polynucleotide in succession with a ligase, a kinase, and a ligase.

14. The method of claim 2 further including the step of removing unligated probe from said ligated complex after said step of ligating.

15. The method of claim 2 wherein the step of providing further includes blocking the recognition sites of said nuclease on said polynucleotides.

16. The method of claim 15 wherein said blocking said recognition sites includes treating said polynucleotides with a methylase.

17. The method of claim 15 wherein said nuclease is a type IIs restriction endonuclease and wherein said step of identifying includes identifying a nucleotide in each of said protruding strands of said polynucleotides by extending a strand of each of said polynucleotides with a nucleic acid polymerase in the presence of chain-terminating nucleoside triphosphates.

18. The method of claim 17 further including the step of removing unligated probe from said polynucleotide after said step of ligating.

19. The method of claim 18 wherein said chain-terminating nucleoside triphosphates are labeled dideoxynucleoside triphosphates and wherein said step of identifying includes identifying said nucleotide by the label on the labeled dideoxynucleoside triphosphates incorporated into said recessed strand of said polynucleotide.

20. The method of claim 19 further including the steps of excising said labeled dideoxynucleotides and extending said recessed strands with a nucleic acid polymerase.

21. The method of claim 20 wherein said step of excising is carried out with T4 DNA polymerase in the presence of deoxyribonucleoside triphosphates.