Continuous extension and deblocking in reactions for nucleic acids synthesis and sequencing

• US 10,378,051 B2
• Filed: 09/26/2012
• Issued: 08/13/2019
• Est. Priority Date: 09/29/2011
• Status: Active Grant

• Current Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Inventors: Meuleman, Wouter, Cressina, Elena, Smith, Geoffrey Paul, Jackson, Rosamond, Liu, Xiaohai
• Primary Examiner(s): Vivlemore, Tracy
• Assistant Examiner(s): Kaup, Sahana S
• Application Number:
  US13/627,134
• Publication Number:
  US 20130085073A1
• Time in Patent Office: 2,512 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2565/1015 labels being on the same oligonucleotide

Abstract

A reaction mixture including (a) a nucleic acid having a primer hybridized to a template, (b) nucleotide analogs, wherein the nucleotide analogs have a blocking moiety; (c) a polymerase that is capable of forming an extended primer by adding the nucleotide analogs to the primer, and (d) a deblocking agent that is capable of removing the blocking moiety from the extended primer. Also provided is a method of synthesizing a polynucleotide including sequentially adding a plurality of the different nucleotides analogs to the nucleic acid via several reaction cycles in the reaction mixture, wherein each reaction cycle includes (i) the polymerase adding a nucleotide analog to the nucleic acid to form a transient nucleic acid species comprising a blocking moiety, and (ii) the deblocking agent modifying the transient nucleic acid species to remove the blocking moiety.

Claims

1. A method of synthesizing a polynucleotide, comprising

(a) providing a mixture comprising a nucleic acid, a collection of different nucleotide analogs, a polymerase having activity to incorporate a nucleotide analog comprising a blocking moiety into a nucleic acid, and a deblocking agent having activity to selectively remove a blocking moiety that has been incorporated into a nucleic acid

compared to a blocking moiety attached to a monomeric nucleotide analog, wherein each different nucleotide analog comprises a blocking moiety, and

(b) allowing sequential addition of a plurality of the different nucleotide analogs to the nucleic acid to proceed via several reaction cycles in the mixture, wherein the polymerase and the deblocking agent are simultaneously present in the mixture to carry out the reaction cycles,

wherein each reaction cycle comprises:

(i) the polymerase adding a nucleotide analog from the collection of different nucleotide analogs to the nucleic acid to form a transient nucleic acid species comprising the blocking moiety, and

(ii) the deblocking agent modifying the transient nucleic acid species to remove the blocking moiety;

wherein the blocking moiety is attached to the nucleotide analog at a 3′

carbon of a pentose moiety of the nucleotide analog, and the blocking moiety comprises a phosphodiester moiety or a phosphotriester moiety.

2. The method of claim 1, wherein the blocking moiety further comprises a label moiety.

3. The method of claim 2, further comprising detecting the label in the mixture during each reaction cycle.

4. The method of claim 3, further comprising determining the sequence of the nucleic acid from a sequence of labels detected during the several reaction cycles.

5. The method of claim 2, wherein the different nucleotide analogs comprise different base moieties and different label moieties, individual label moieties of the different label moieties being correlated with a specific base moiety.

6. The method of claim 2, wherein the different nucleotide analogs further comprise a label-modifier moiety.

7. The method of claim 6, wherein the label moiety comprises a fluorophore and the label-modifier moiety comprises a quencher of the fluorophore, a FRET donor to the fluorophore or a FRET acceptor to the fluorophore.

8. The method of claim 6, further comprising detecting a signal from the label in the absence of the label-modifier moiety during each reaction cycle.

9. The method of claim 6, wherein each reaction cycle further comprises the polymerase removing the label-modifier moiety from the nucleotide analog.

10. The method of claim 6, wherein the nucleotide analog comprises a triphosphate moiety and wherein the label-modifier moiety is attached to the triphosphate moiety.

11. The method of claim 1, wherein the deblocking agent comprises a phosphoesterase enzyme.

12. The method of claim 1, wherein the phosphoesterase selectively removes the phosphodiester moiety or the phosphotriester moiety from the transient nucleic acid species.

13. The method of claim 1, wherein the phosphoesterase is selected from the group consisting of Endonuclease IV and AP endonuclease.

14. The method of claim 1, wherein the nucleic acid is one of a plurality of different nucleic acids in the mixture, wherein the plurality of the different nucleotides analogs are sequentially added to several of the different nucleic acids in the mixture by several reaction cycles in the mixture, wherein each reaction cycle comprises the polymerase adding nucleotide analogs to the several different nucleic acids to form several transient nucleic acid species comprising a blocking moiety and the deblocking agent modifies the several transient nucleic acid species to remove the blocking moiety.

15. The method of claim 14, wherein the several different nucleic acids in the mixture are attached to a solid-phase support.

16. The method of claim 14, wherein the blocking moiety of the several transient nucleic acid species further comprises a label moiety.

17. The method of claim 16, further comprising detecting the label during each reaction cycle.

18. The method of claim 17, wherein individual nucleic acids of the several different nucleic acids are individually resolved on the solid-phase support by the detecting.

19. The method of claim 17, wherein nucleic acids of the several different nucleic acids are detected as features on the solid-phase support during the detecting, wherein individual features comprise several copies having the same nucleic acid sequence.

20. The method of claim 14, wherein the several different nucleic acids comprise at least 1,000 different nucleic acid sequences.

21. The method of claim 1, wherein the transient nucleic acid species is present for at least 1 millisecond before the deblocking agent modifies the transient nucleic acid species to remove the blocking moiety.

22. The method of claim 21, wherein the transient nucleic acid species is present for no more than 30 seconds before the deblocking agent modifies the transient nucleic acid species to remove the blocking moiety.

23. The method of claim 1, wherein the several reaction cycles comprises at least 100 reaction cycles, whereby the nucleic acid is extended by addition of at least 100 nucleotide analogs.

24. The method of claim 23, further comprising adding any one of a nucleotide analog, a polymerase or a deblocking agent to the mixture after the first reaction cycle is complete and before the last reaction cycle is complete.

25. A method of synthesizing a polynucleotide, comprising

(a) providing a mixture comprising a nucleic acid, a collection of different nucleotide analogs, a polymerase having activity to incorporate a nucleotide analog comprising a blocking moiety into a nucleic acid, a phosphotriesterase and a phosphodiesterase, wherein the phosphotriesterase and the phosphodiesterase together have activity to selectively remove a blocking moiety that has been incorporated into a nucleic acid compared to a blocking moiety attached to a monomeric nucleotide analog,

wherein the different nucleotide analogs each comprise a phosphotriester blocking moiety, and

(b) sequentially adding a plurality of the different nucleotide analogs to the nucleic acid by several reaction cycles in the mixture, wherein the polymerase, phosphotriesterase and phosphodiesterase are simultaneously present in the mixture to carry out the reaction cycles,

wherein each reaction cycle comprises:

(i) the polymerase adding a nucleotide analog of the collection of different nucleotide analogs to the nucleic acid to form a transient nucleic acid species comprising the phosphotriester blocking moiety,

(ii) the phosphotriesterase converting the phosphotriester blocking moiety to a phosphodiester blocking moiety, and

(iii) the phosphodiesterase removing the phosphodiester blocking moiety from the nucleic acid.

26. The method of claim 25, wherein the phosphotriester blocking moiety further comprises a label moiety.

27. The method of claim 26, further comprising detecting the label in the mixture during each reaction cycle.

28. The method of claim 27, further comprising determining the sequence of the nucleic acid from a sequence of labels detected during the several reaction cycles.

29. The method of claim 26, wherein the different nucleotide analogs further comprise a label-modifier moiety.

30. The method of claim 29, further comprising detecting a signal from the label in the absence of the label-modifier moiety during each reaction cycle.

31. The method of claim 29, wherein each reaction cycle further comprises the polymerase removing the label-modifier moiety from the nucleotide analog.

32. The method of claim 25, wherein the nucleic acid is one of a plurality of different nucleic acids in the mixture,

wherein the plurality of the different nucleotide analogs are sequentially added to several of the different nucleic acids in the mixture by several reaction cycles in the mixture,

wherein each reaction cycle comprises the polymerase adding nucleotide analogs to the several different nucleic acids to form several transient nucleic acid species comprising a phosphotriester blocking moiety, the phosphodiesterase converts the phosphotriester blocking moiety on the several transient nucleic acid species to a phosphodiester blocking moiety and the phosphodiesterase removes the phosphodiester blocking moiety from the several transient nucleic acid species.

33. The method of claim 32, wherein the several different nucleic acids in the mixture are attached to a solid-phase support.

34. The method of claim 32, wherein the phosphotriester blocking moiety of the several transient nucleic acid species further comprises a label moiety.

35. The method of claim 34, further comprising detecting the label during each reaction cycle.

36. The method of claim 35, wherein individual nucleic acids of the several different nucleic acids are individually resolved on the solid-phase support by the detecting.

37. The method of claim 25, wherein, the several reaction cycles comprise a single pot reaction.

38. The method of claim 25, wherein the several reaction cycles comprise a single pot reaction.