Modified polymerases for improved incorporation of nucleotide analogues

• US 10,150,954 B2
• Filed: 06/01/2017
• Issued: 12/11/2018
• Est. Priority Date: 09/30/2014
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Bomati, Erin, Previte, Michael, Kellinger, Matthew William, Chen, Cheng-Yao, He, Molly
• Primary Examiner(s): Raghu, Ganapathirama
• Application Number:
  US15/610,875
• Publication Number:
  US 20170298327A1
• Time in Patent Office: 558 Days
• CPC Class Codes: C12N 9/1252 DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Y 207/07007 DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase

Abstract

Presented herein are polymerase enzymes for improved incorporation of nucleotide analogs, in particular nucleotides which are modified at the 3′ sugar hydroxyl, as well as methods and kits using the same.

Claims

1. A recombinant DNA polymerase comprising an amino acid sequence that is at least 80% identical to SEQ ID NO:

10, which recombinant DNA polymerase comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Thr144, Gly153, Lys476, Leu478, Thr590, Ala639 or Asp718 in the 9°

N DNA polymerase amino acid sequence, wherein the mutation at the position functionally equivalent to Lys476 comprises a mutation to a hydrophobic amino acid, wherein the mutation at the position functionally equivalent to Lys478 comprises a mutation to a polar amino acid, wherein the mutation at the position functionally equivalent to Gly153 comprises a mutation to a polar amino acid, and which recombinant DNA polymerase further comprises at least one amino acid substitution mutation at one or more positions functionally equivalent to Cys223, Thr514, Lys477, or Ile521 in the 9°

N DNA polymerase amino acid sequence, and wherein the DNA polymerase is a family B DNA polymerase.

2. The altered polymerase of claim 1, wherein said substitution mutation at position Thr144 comprises a mutation to a nonpolar amino acid.

3. The altered polymerase of claim 1, wherein said substitution mutation at position Thr144 comprises a mutation homologous to Thr144Ala, Thr144Gly, or Thr144Leu.

4. The altered polymerase of claim 1, wherein said substitution mutation at position Gly153 comprises a mutation homologous to Gly153Asp.

5. The altered polymerase of claim 1, wherein said substitution mutation at position Lys476 comprises a mutation homologous to Lys476Trp.

6. The altered polymerase of claim 1, wherein said substitution mutation at position Leu478 comprises a mutation homologous to Leu478Ser, Leu478Arg, or Leu478Thr.

7. The altered polymerase of claim 1, wherein said substitution mutation at position Thr590 comprises a mutation to a non-polar amino acid.

8. The altered polymerase of claim 1, wherein said substitution mutation at position Thr590 comprises a mutation homologous to Thr590Ile or Thr590Gly.

9. The altered polymerase of claim 1, wherein said substitution mutation at position Ala639 comprises a mutation homologous to Ala639Val or Ala639Phe.

10. The altered polymerase of claim 1, wherein said substitution mutation at position Asp718 comprises a mutation to an uncharged amino acid.

11. The altered polymerase of claim 1, wherein said substitution mutation at position Asp718 comprises a mutation homologous to Asp718Asn.

12. The altered polymerase of claim 1, wherein the altered polymerase further comprises substitution mutations at positions functionally equivalent to Leu408, Tyr409, Pro410, or a combination thereof, in the 9°

N DNA polymerase amino acid sequence.

13. The altered polymerase of claim 1, wherein the altered polymerase comprises substitution mutations at positions functionally equivalent to Asp141, Glu143, or a combination thereof, in the 9°

N DNA polymerase amino acid sequence.

14. The altered polymerase of claim 1, wherein the altered polymerase further comprises substitution mutations at positions functionally equivalent to Ala485 in the 9°

N DNA polymerase amino acid sequence.

15. The altered polymerase of claim 1, wherein said substitution mutation comprises a mutation homologous to Thr144Ala, Thr144Gly, Thr144Leu, Gly153Asp, Lys476Trp, Leu478Ser, Leu478Arg, Leu478Thr, Thr590Ile, Thr590Gly, Ala639Val, Ala639Phe, or Asp718Asn, relative to SEQ ID NO:

10.

16. The altered polymerase of claim 1, wherein amino acid sequence is at least 90% identical to SEQ ID NO:

10.

17. The altered polymerase of claim 1, wherein amino acid sequence is at least 95% identical to SEQ ID NO:

10.

18. The altered polymerase of claim 1, wherein amino acid sequence is at least 99% identical to SEQ ID NO:

10.

19. The altered polymerase of claim 1, wherein said substitution mutation at Cys223 comprises a mutation homologous to Cys223Ser.

20. The altered polymerase of claim 1, wherein said substitution mutation at Thr514 comprises a mutation homologous to Thr514Ala or Thr514Ser.

21. The altered polymerase of claim 1, wherein said substitution mutation at Lys477 comprises a mutation homologous to Lys477Met.

22. The altered polymerase of claim 1, wherein said substitution mutation at Ile521 comprises a mutation homologous to Ile521Leu.

23. A method for incorporating modified nucleotides into DNA comprising allowing the following components to interact:

(i) the polymerase of claim 1, (ii) a DNA template; and

(iii) a nucleotide solution.

24. The method of claim 23, wherein the DNA template comprises a clustered array.

25. The method of claim 23, wherein the nucleotide solution comprises nucleotides modified at the 3′

sugar hydroxyl.

26. A kit for performing a nucleotide incorporation reaction comprising:

the polymerase of claim 1 and a nucleotide solution.

27. The kit of claim 26, wherein the nucleotide solution comprises labelled nucleotides.

28. The kit of claim 26, wherein the nucleotides comprise synthetic nucleotides.

29. The kit of claim 26, wherein the nucleotides comprise modified nucleotides.

30. The kit of claim 26, wherein the modified nucleotides have been modified at the 3′

sugar hydroxyl such that the substituent is larger in size than the naturally occurring 3′

hydroxyl group.

31. The kit of claim 29, wherein modified nucleotides comprise a modified nucleotide or nucleoside molecule comprising a purine or pyrimidine base and a ribose or deoxyribose sugar moiety having a removable 3′

-OH blocking group covalently attached thereto, such that the 3′

carbon atom has attached a group of the structure

—

O—

Z

wherein Z is any of —

C(R′

)₂—

O—

R″

, —

C(R′

)₂—

N(R″

)₂, —

C(R′

)₂—

N(H)R″

, —

C(R′

)₂—

S—

R″ and

—

C(R′

)₂—

F,

wherein each R″

is or is part of a removable protecting group;

each R′

is independently a hydrogen atom, an alkyl, substituted alkyl, arylalkyl, alkenyl, alkynyl, aryl, heteroaryl, heterocyclic, acyl, cyano, alkoxy, aryloxy, heteroaryloxy or amido group, or a detectable label attached through a linking group;

or (R′

)₂ represents an alkylidene group of formula ═

C(R′

″

)₂ wherein each R′

″

may be the same or different and is selected from the group comprising hydrogen and halogen atoms and alkyl groups; and

wherein said molecule may be reacted to yield an intermediate in which each R″

is exchanged for H or, where Z is —

C(R′

)₂—

F, the F is exchanged for OH, SH or NH₂, preferably OH, which intermediate dissociates under aqueous conditions to afford a molecule with a free 3′

OH;

with the proviso that where Z is —

C(R′

)₂—

S—

R″

, both R′

groups are not H.

32. The kit of claim 31, wherein R′

of the modified nucleotide or nucleoside is an alkyl or substituted alkyl.

33. The kit of claim 31, wherein —

Z of the modified nucleotide or nucleoside is of formula —

C(R′

)₂—

N₃.

34. The kit of claim 31, wherein Z is an azidomethyl group.

35. The kit of claim 29, wherein the modified nucleotides are fluorescently labelled to allow their detection.

36. The kit of claim 29, wherein the modified nucleotides comprise a nucleotide or nucleoside having a base attached to a detectable label via a cleavable linker.

37. The kit of claim 31, wherein the detectable label comprises a fluorescent label.

38. The kit of claim 31 further comprising one or more DNA template molecules, or primers, or a combination thereof.