Methods and solutions for inhibiting undesired cleaving of labels
The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.
1. A method of incorporating labeled nucleotides into nucleic acid, comprising:
a) providing i) a reaction chamber comprising a plurality of nucleic acid template molecules bound to a solid support, ii) a first solution comprising polymerase and a plurality of nucleotide analogues wherein each nucleotide analogue is labeled with a unique label and contains a removable chemical moiety capping the 3′-OH group, iii) a second solution comprising a cleaving agent, iv) a cleaving agent scavenger, wherein said cleaving agent scavenger is cystamine, and v) a wash solution;
b) introducing said first solution into said reaction chamber under conditions wherein a first nucleotide analogue is incorporated by said polymerase;
c) detecting the label of the incorporated nucleotide analogue;
d) introducing said second solution into said reaction chamber under conditions such that the chemical moiety of the incorporated nucleotide analogue capping the 3′-OH group is removed by said cleaving agent leaving a 3′ hydroxyl group to enable the next nucleotide incorporation;
e) washing said reaction chamber with said wash solution under conditions where some leftover cleaving agent remains in said reaction chamber; and
f) introducing said cleaving agent scavenger into said reaction chamber under conditions where cystamine reacts with said leftover cleaving agent.
2. The method of claim 1 , wherein said reaction chamber is a flow cell.
3. The method of claim 1 , wherein said cleaving agent scavenger is in a third solution and said scavenger is introduced into said reaction chamber in step f) by introducing said third solution.
4. The method of claim 1 , further comprising the step of re-introducing said first solution into said reaction chamber under conditions such that a second nucleotide analogue is incorporated by said polymerase.
5. The method of claim 1 , wherein said cleaving agent scavenger is in said first solution and said introducing of steps b) and f) comprises introducing said first solution comprising said scavenger.
6. The method of claim 4 , wherein said second nucleotide analogue is incorporated in the presence of said cleaving agent scavenger.
7. The method of claim 1 , wherein a wash solution is introduced into said reaction chamber between steps b) and c).
8. The method of claim 1 , wherein said first nucleotide is incorporated at step b) into a plurality of primers hybridized to said plurality of nucleic acid template molecules.
9. The method of claim 1 , wherein each of said plurality of nucleic acid template molecules comprises a self-priming hairpin, and said first nucleotide is incorporated at step b) into said template.
10. The method of claim 1 , wherein said removable chemical moiety comprises a disulfide bond.
11. The method of claim 1 , wherein said removable chemical moiety comprises an azido group.
12. The method of claim 1 , wherein said removable chemical moiety comprises an azidomethyl ether.
13. The method of claim 1 , wherein said cleaving agent is a phosphine.
14. The method of claim 13 , wherein said phosphine is Tris(2-carboxy-ethyl)phosphine.
15. A method of incorporating labeled nucleotides into nucleic acid, comprising:
a) providing i) a reaction chamber comprising a plurality of nucleic acid template molecules bound to a solid support, ii) a first solution comprising polymerase and a plurality of nucleotide analogues selected from the group consisting of cytosine, thymine, deaza-adenine and deaza-guanine, wherein each nucleotide analogue comprises a unique label attached through a cleavable linker to a 5-position of cytosine or thymine or to a 7-position of deaza-adenine or deaza-guanine, and wherein each nucleotide analogue contains a removable chemical moiety capping the 3′-OH group, iii) a second solution comprising a cleaving agent, iv) a cleaving agent scavenger, wherein the cleaving agent scavenger is cystamine, and v) a wash solution;
b) introducing said first solution into said reaction chamber under conditions wherein a first nucleotide analogue is incorporated by said polymerase;
c) detecting the label of the incorporated nucleotide analogue;
d) introducing said second solution into said reaction chamber under conditions such that the chemical moiety of the incorporated nucleotide analogue capping the 3′-OH group is removed leaving a 3′ hydroxyl group to enable the next nucleotide incorporation, and said cleavable linker is cleaved by said cleaving agent;
e) washing said reaction chamber with said wash solution under conditions where some leftover cleaving agent remains in said reaction chamber; and
f) introducing said cleaving agent scavenger into said reaction chamber under conditions where cystamine reacts with said leftover cleaving agent.
16. The method of claim 15 , wherein said first nucleotide is incorporated at step b) into a plurality of primers hybridized to said plurality of nucleic acid template molecules.
17. The method of claim 15 , wherein each of said plurality of nucleic acid template molecules comprises a self-priming hairpin, and said first nucleotide is incorporated at step b) into said template.
18. The method of claim 15 , wherein said reaction chamber is a flow cell.
19. The method of claim 15 , wherein said cleaving agent scavenger is in a third solution and said scavenger is introduced into said reaction chamber in step f) by introducing said third solution.
20. The method of claim 15 , further comprising the step of re-introducing said first solution into said reaction chamber under conditions such that a second nucleotide analogue is incorporated by said polymerase.
21. The method of claim 15 , wherein said cleaving agent scavenger is in said first solution and said introducing of steps b) and f) comprises introducing said first solution comprising said scavenger.
22. The method of claim 20 , wherein said second nucleotide analogue is incorporated in the presence of said cleaving agent scavenger.
23. The method of claim 15 , wherein a wash solution is introduced into said reaction chamber between steps b) and c).
24. The method of claim 15 , wherein said removable chemical moiety comprises a disulfide bond.
25. The method of claim 15 , wherein said cleavable linker comprises a disulfide bond.
26. The method of claim 15 , wherein said removable chemical moiety comprises an azido group and said cleavable linker comprises a disulfide bond.
27. The method of claim 15 , wherein said removable chemical moiety comprises an azidomethyl ether.
28. The method of claim 15 , wherein said cleaving agent is a phosphine.
29. The method of claim 28 , wherein said phosphine is (Tris-carboxyethyl)phosphine.
30. A method of incorporating labeled nucleotides into nucleic acid, comprising:
a) providing i) a reaction chamber comprising a plurality of nucleic acid template molecules bound to a solid support, ii) a first solution comprising polymerase and a plurality of nucleotide analogues wherein each nucleotide analogue is labeled with a unique label, said label attached via a cleavable linker, wherein said cleavable linker comprises a disulfide bond, iii) a second solution comprising a cleaving agent, iv) a cleaving agent scavenger, wherein the cleaving agent scavenger comprises a disulfide bond, and v) a wash solution;
b) introducing said first solution into said reaction chamber under conditions wherein a first nucleotide analogue is incorporated by said polymerase;
c) detecting the label of the incorporated nucleotide analogue;
d) introducing said second solution into said reaction chamber under conditions such that the label of the incorporated nucleotide analogue is removed by cleaving said cleavable linker with said cleaving agent;
e) washing said reaction chamber with said wash solution under conditions where some leftover cleaving agent remains in said reaction chamber; and
f) introducing said cleaving agent scavenger into said reaction chamber under conditions wherein said scavenger reacts with said leftover cleaving agent.
31. The method of claim 30 , further comprising, prior to step b) hybridizing a primer to said plurality of nucleic acid template molecules, such that said first nucleotide analogue is incorporated into said primer at step b).
32. The method of claim 30 , wherein said nucleic acid template molecules comprise a self-priming hairpin, such that said first nucleotide analogue is incorporated into said template molecules at step b).
33. The method of claim 30 , wherein said cleaving agent is a phosphine.
34. The method of claim 33 , wherein said phosphine is (Tris-carboxyethyl)phosphine.
35. The method of claim 30 , wherein said scavenger is cystamine.
36. A method of incorporating labeled nucleotides into nucleic acid, comprising:
a) providing i) a reaction chamber comprising a plurality of nucleic acid template molecules bound to a solid support, ii) a first solution comprising polymerase and a plurality of nucleotide analogues wherein each nucleotide analogue is labeled with a unique label and contains a removable chemical moiety capping the 3′-OH group, iii) a second solution comprising a cleaving agent, iv) a cleaving agent scavenger, wherein said cleaving agent scavenger is cystamine, and v) a wash solution;
b) introducing said first solution into said reaction chamber under conditions wherein a first nucleotide analogue is incorporated by said polymerase;
c) detecting the label of the incorporated nucleotide analogue so that the identity of the base can be called;
d) introducing said second solution into said reaction chamber under conditions such that the chemical moiety of the incorporated nucleotide analogue capping the 3′-OH group is removed by said cleaving agent leaving a 3′ hydroxyl group to enable the next nucleotide incorporation;
e) washing said reaction chamber with said wash solution under conditions where some leftover cleaving agent remains in said reaction chamber; and
f) introducing said cleaving agent scavenger into said reaction chamber under conditions such that cystamine reacts with said leftover cleaving agent; and
g) repeating steps b) through f) such that additional nucleotide analogs are incorporated, wherein each additional nucleotide analog is incorporated after a cleaving agent scavenger has been introduced into said reaction chamber, whereby the accuracy of base calling at step c) is improved.
37. The method of claim 36 , wherein said cleaving agent is a phosphine.
38. A method of incorporating labeled nucleotides into nucleic acid, comprising:
a) providing i) a reaction chamber comprising a plurality of nucleic acid template molecules bound to a solid support, ii) a first solution comprising polymerase and a plurality of nucleotide analogues wherein each nucleotide analogue is labeled with a unique label and contains a removable chemical moiety capping the 3′-OH group, iii) a second solution comprising a cleaving agent, and iv) a wash solution comprising a cleaving agent scavenger;
b) introducing said first solution into said reaction chamber under conditions wherein a first nucleotide analogue is incorporated by said polymerase;
c) detecting the label of the incorporated nucleotide analogue;
d) introducing said second solution into said reaction chamber under conditions such that the chemical moiety of the incorporated nucleotide analogue capping the 3′-OH group is removed by said cleaving agent leaving a 3′ hydroxyl group to enable the next nucleotide incorporation; and
e) washing said reaction chamber with said wash solution under conditions where leftover cleaving agent from step d) reacts with said scavenger.
39. The method of claim 38 , wherein said cleaving agent scavenger is cystamine.