IP Library Granted Patent US 8,623,628
Granted Patent B2
US 8,623,628 · App. 11/431,939 · Granted Jan 7, 2014

Polymerases

Inventors: Tobias William Barr Ost (Saffron Walden, GB); Geoffrey Paul Smith (Saffron Walden, GB); Shankar Balasubramanian (Saffron Walden, GB); Roberto Rigatti (Saffron Walden, GB); Raquel Maria Sanches (Saffron Walden, GB)
Assignee: Illumina, Inc.
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Quick Facts
Patent No.
US 8,623,628
App. No.
11/431,939
Granted
Jan 7, 2014
Kind
B2
Abstract

Modified DNA polymerases have an affinity for DNA such that the polymerase has an ability to incorporate one or more nucleotides into a plurality of separate DNA templates in each reaction cycle. The polymerases are capable of forming an increased number of productive polymerase-DNA complexes in each reaction cycle. The modified polymerases may be used in a number of DNA sequencing applications, especially in the context of clustered arrays.

Claims (26)

1. A polymerase having amino acid sequence SEQ ID NO:22, having a substitution mutation from Arg713 to a nonpolar amino acid, whereby the polymerase has a reduced affinity for DNA.

2. The polymerase of claim 1 , wherein the polymerase is capable of incorporating a nucleotide or nucleotides into a plurality of separate DNA templates in each reaction cycle as compared to a control polymerase, wherein the control polymerase is the unaltered polymerase and is capable of incorporating a nucleotide or nucleotides into a single DNA template in each reaction cycle.

3. The polymerase of claim 1 , wherein the polymerase is capable of forming an increased number of productive polymerase-DNA complexes in each reaction cycle as compared to a control polymerase, wherein the control polymerase is the unaltered polymerase.

4. The polymerase of claim 1 , wherein the affinity of the polymerase for nucleotides and the fidelity of the polymerase is substantially unaffected by the substitution mutation.

5. The polymerase according to claim 1 , wherein the substitution mutation converts Arg713 to glycine (G) or methionine (M).

6. The polymerase according to claim 1 , wherein the substitution mutation converts Arg713 to alanine (A).

7. A kit for performing a nucleotide incorporation reaction comprising: a polymerase as defined in claim 1 , 5 , or 6 , and a nucleotide solution.

8. The kit of claim 7 , wherein the nucleotide solution comprises labelled nucleotides.

9. The kit of claim 7 , wherein the nucleotides comprise synthetic nucleotides.

10. The kit of claim 7 , wherein the nucleotides comprise modified nucleotides.

11. The kit of claim 10 , 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.

12. The kit according to claim 11 , wherein the modified nucleotides are 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 NH 2 , 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.

13. The kit according to claim 12 , wherein R′ of the modified nucleotide or nucleoside is an alkyl or substituted alkyl.

14. The kit according to claim 13 , wherein —Z of the modified nucleotide or nucleoside is of formula —C(R′) 2 —N 3 .

15. The kit according to claim 14 , wherein Z is an azidomethyl group.

16. The kit according to claim 11 , wherein the modified nucleotides are fluorescently labelled to allow their detection.

17. The kit according to claim 11 , wherein the modified nucleotides comprise a nucleotide or nucleoside having a base attached to a detectable label via a cleavable linker, wherein the cleavable linker contains a moiety selected from the group consisting of:

wherein X is selected from the group comprising O, S, NH and NQ wherein Q is a C 1-10 substituted or unsubstituted alkyl group, Y is selected from the group comprising O, S, NH and N(allyl), T is hydrogen or a C 1-10 substituted or unsubstituted alkyl group and * indicates where the moiety is connected to the remainder of the nucleotide or nucleoside.

18. The kit according to claim 17 , wherein the detectable label comprises a fluorescent label.

19. The kit of claim 7 further comprising one or more DNA template molecules and/or primers.

Assignments (2)
CHANGE OF NAME Recorded Feb 8, 2011
From: SOLEXA LIMITED
To: ILLUMINA CAMBRIDGE LIMITED
Reel/Frame 025759/0070 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded May 16, 2007
From: OST, TOBIAS WILLIAM BARR; SMITH, GEOFFREY PAUL; BALASUBRAMANIAN, SHANKAR; RIGATTI, ROBERTO; SANCHES, RAQUEL MARIA
To: SOLEXA LIMITED
Reel/Frame 019320/0658 →
Continuity (2)
Provisional Application 60757997 · Jan 11, 2006
Related Publication 20060281109A1 · Dec 14, 2006