Methods of sequencing polynucleotides by ligation of multiple oligomers

• US 6,013,456 A
• Filed: 02/05/1999
• Issued: 01/11/2000
• Est. Priority Date: 07/24/1998
• Status: Expired due to Term

• Current Assignee: Lumigen, Inc. (Danaher Corporation)
• Original Assignee: Lumigen, Inc. (Danaher Corporation)
• Inventors: Akhavan-Tafti, Hashem
• Primary Examiner(s): Myers, Carla J.
• Assistant Examiner(s): JOHANNSEN, DIANA B
• Application Number:
  US09/245,984
• Time in Patent Office: 340 Days
• Field of Search: 435/6, 435/91.52, 536/25.32, 536/25.3
• US Class Current: 435/6.14
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2563/167 Mass label

Abstract

Methods of synthesizing polynucleotides are disclosed involving the simultaneous ligation of a set of oligomer 5'"'"'-phosphates onto a template-bound primer. The set of these oligomers can be preselected to contain oligomers which are complementary to the template strand or the oligomers can be supplied as a library and allowed to self select. The synthesis by ligation can proceed unidirectionally or bidirectionally from the primer and can be used to synthesize both strands simultaneously by the use of two primers. The ligation is preferably performed with a ligase enzyme. The methods of synthesis are useful in a variety of applications, including cloning, amplification, labeling, diagnostic assays, mutation analysis and screening, gene expression monitoring and sequence analysis.

Claims

1. A method for determining the base sequence of a portion of a single stranded nucleic acid by determining the base sequence of a complementary strand comprising the steps of:

a) providing a reaction mixture comprising a single stranded nucleic acid, a capture probe/primer which is complementary to a portion of the single stranded nucleic acid, and a plurality of labeled identical length oligonucleotide 5'"'"'-monophsphates wherein each opligonucleotide 5'"'"'-monophophate compxises a label that is specific for and identifies that oligonucleotide 5'"'"'-monophosphate;

b) hybridizing the capture probe/primer with the single stranded nucleic acid to form a captured probe-nucleic acid hybrid;

c) ligating more than one of the plurality of the oligonucleotide 5'"'"'-monophosphates in a contiguous manner onto the capture probe/primer in one continuous process to synthesize the complementary strand, wherein ligation of oligonucleotide 5'"'"'-monophosphates only occurs in the presence of the hybridized primer;

d) removing all nonligated oligonucleotide 5'"'"'-monophosphates;

e) detecting the plurality of labels which were attached in the ligation;

f) relating the plurality of detected labels to the identity of their corresponding oligonucleotide 5'"'"'-monophosphates; and

g) determining the base sequence of the portion of the nucleic acid from the identity of the plurality of oligonucleotide 5'"'"'-monophosphates identified in step f.

2. The method of claim 1 wherein the capture probe/primer is immobilized onto a solid support before hybridizing with the single stranded nucleic acid.

3. The method of claim 1 wherein the capture probe/primer is immobilized onto a solid support after ligating the oligonucleotide 5'"'"'-monophosphates in step c).

4. The method of claim 1 wherein the ligation is performed by means of a ligase enzyme.

5. The method of claim 4 wherein the ligase enzyme is T4 DNA ligase.

6. The method of claim 1 wherein the number of bases, n, in each of the plurality of identical length oligonucleotide 5'"'"'-monophosphates is an integer in the range of 4 to 8.

7. The method of claim 6 wherein the number of bases in each of the plurality of identical length oligonucleotide 5'"'"'-monophosphates is either 5 or 6.

8. The method of claim 6 wherein the plurality of oligonucleotide 5'"'"'-monophosphates contains all possible oligonucleotide 5'"'"'-monophosphates of the same number of bases.

9. The method of claim 1 wherein each label has a unique molecular mass.

10. The method of claim 9 wherein at least a portion of each label is cleaved from the synthesized complementary nucleic acid strand and the cleaved portions of each label are detected.

11. The method of claim 10 wherein the labels are detected by determining the molecular mass of the cleaved portions of the labels.

12. The method of claim 9 wherein the labels comprise 1,2-dioxetanes and the dioxetanes are cleaved thermally, chemically or enzymatically.

13. The method of claim 1 wherein the ligation proceeds from the 3'"'"' end of the primer.

14. The method of claim 1 wherein the primer contains a 5'"'"'-phosphate group and ligation proceeds from the 5'"'"' end of the primer.

15. The method of claim 1 wherein the single stranded nucleic acid is produced by separating a double stranded nucleic acid.

16. A method for determining the base sequence of a portion of a single stranded nucleic acid by determining the base sequence of a complementary strand comprising the steps of:

a) providing a capture probe/primer which is complementary to a portion of the single stranded nucleic acid;

b) forming a plurality of sets of labeled identical length oligonucleotide 5'"'"'-monophosphates, each oligonucleotide 5'"'"'-monophosphate comprising a label that is specific for and identifies that oligonucleotide 5'"'"'-monophosphhate and each set containing a plurality of oligonucleotide 5'"'"'-monophosphates wherein one labeled oligonucleotide 5'"'"'-monophosphate which is present in all other sets is excluded from each set;

c) for each set of labeled oligonucleotide 5'"'"'-monophosphates, hybridizing the capture probe/primer with the single stranded nucleic acid;

d) for each set of labeled oligonucleotide 5'"'"'-monophosphates, contacting the set with the captured hybrid in a separate reaction;

e) ligating each set of labeled oligonucleotide 5'"'"'-monophosphates in a contiguous manner onto the capture probe/primer in one continuous process, wherein ligation of oligonucleotide 5'"'"'-monophosphates only occurs in the presence of the hybridized primer;

f) removing all nonligated oligonucleotide 5'"'"'-mononophosphates in each set;

g) for each set, identifying all labels which were attached in the ligation, thereby determining the number and base sequence of all oligonucleotide 5'"'"'-monophosphates ligated in each set and determining the relative position of the excluded oligonucleotide 5'"'"'-monophosphate in the base sequence of the complementary strand; and

h) deducing the base sequence of the portion of the single stranded nucleic acid from either the relative positions of each of the excluded oligonucleotide 5'"'"'-monophosphates in the comlementary strand, or the number and base sequence of ligated oligonucleotide 5'"'"'-monophosphates of all sets combined.

17. The method of claim 16 wherein the number of sets in the plurality of sets is equal N/n where n is the number of bases in each of the oligonucleotide 5'"'"'-monophosphates and N is the number of bases in the portion of the single stranded nucleic acid to be sequenced.

18. The method of claim 16 wherein all possible sets of oligonucleotide 5'"'"'-monophosphates, 4ⁿ, are employed, where n is the number of bases in each of the oligonucleotide 5'"'"'-monophosphates.

19. The method according to claim 16 wherein each set in the plurality of sets of oligonucleotide 5'"'"'-monophosphates further comprises a unique nonextendable oligomer which contains the same base sequence as the excluded oligonucleotide 5'"'"'-monophosphate.

20. The method of claim 16 wherein the ligation is performed by means of a ligase enzyme.

21. The method of claim 20 wherein the ligase enzyme is T4 DNA ligase.

22. The method of claim 16 wherein the number of bases, n, in each of the identical length oligonucleotide 5'"'"'-monophosphates is an integer in the range of 4 to 8.

23. The method of claim 22 wherein the number of bases in each of the identical length oligonucleotide 5'"'"'-monophosphates is either 5 or 6.

24. The method of claim 16 wherein the capture probe/primer is immobilized onto a solid support before hybridizing with the single stranded nucleic acid.

25. The method of claim 16 wherein the capture probe/primer is immobilized onto a solid support after ligating the oligonucleotide 5'"'"'-monophosphates in step e.

26. The method of claim 16 wherein each label has a unique molecular mass.

27. The method of claim 26 wherein at least a portion of each label is cleaved from the synthesized complementary nucleic acid strand and the cleaved portions of each label are detected.

28. The method of claim 27 wherein the labels are detected by determining the molecular mass of the cleaved portions of the labels.

29. The method of claim 27 wherein the labels comprise 1,2-dioxetanes and the dioxetanes are cleaved thermally, chemically or enzymatically.

30. The method of claim 16 wherein the ligation proceeds from the 3'"'"' end of the primer.

31. The method of claim 16 wherein the primer contains a 5'"'"'-phosphate group and ligation proceeds from the 5'"'"' end of the primer.

32. The method of claim 16 wherein the single stranded nucleic acid is produced by separating a double stranded nucleic acid.

33. A method for determining the sequence of a portion of a single stranded nucleic acid by determining the base sequence of a complementary strand comprising the steps of:

a) providing a capture probe/primer which is complementary to a portion of the single stranded nucleic acid;

b) forming a plurality of sets of labeled identical length oligonucleotide 5'"'"'-monophosphates, each oligonucleotide 5'"'"'-monophosphate having the same detectable label and each set containing a plurality of oligonucleotide 5'"'"'-monophosphates wherein one labeled oligonucleotide 5'"'"'-monophosphate which is present in all other sets is excluded from each set;

c) hybridizing the capture probe/primer with the single stranded nucleic acid to form a captured probe-nucleic acid hybrid;

d) for each set of labeled oligonucleotide 5'"'"'-monophosphates, contacting the set with the captured hybrid in a separate reaction;

e) ligating each set of labeled oligonucleotide 5'"'"'-monophosphates in a contiguous manner onto the capture probe/primer in one continuous process, wherein ligation of oligonucleotide 5'"'"'-monophosphates only occurs in the presence of the hybridized primer;

f) removing all nonligated oligonucleotide 5'"'"'-monophosphates in each set;

g) determining the number of labels which were attached in the ligation in each set thereby determining the relative position of the excluded oligonucleotide 5'"'"'-monophosphate in the base sequence of the complementary strand; and

h) deducing the base sequence of the portion of the single stranded nubleic acid from the relative positions of each of the excluded oligonucleotide 5'"'"'-monophosphates in the complementary strand.

34. The method of claim 33 wherein the ligation is performed by means of a ligase enzyme.

35. The method of claim 34 wherein the ligase enzyme is T4 DNA ligase.

36. The method of claim 33 wherein the number of bases, n, in each of the identical length oligonucleotide 5'"'"'-monophosphates is an integer in the range of 4 to 8.

37. The method of claim 33 wherein the number of bases in each of the identical length oligonucleotide 5'"'"'-monophosphates is either 5 or 6.

38. The method of claim 33 wherein the capture probe/primer is immobilized onto a solid support before hybridizing with the single stranded nucleic acid.

39. The method of claim 33 wherein the capture probe/primer is immobilized onto a solid support after ligating the oligonucleotide 5'"'"'-monophosphates in step e.

40. The method of claim 33 wherein the detectable label is selected from radioisotopes, chemiluminescent labels, fluorescent labels, chromogenic labels, enzymes, binding proteins, antigens, antibodies and haptens.

41. The method of claim 33 wherein the ligation proceeds from the 3'"'"' end of the primer.

42. The method of claim 33 wherein the primer contains a 5'"'"'-phosphate group and ligation proceeds from the 5'"'"' end of the primer.

43. The method of claim 33 wherein the single stranded nucleic acid is produced by separating a double stranded nucleic acid.