Methods and solutions for inhibiting undesired cleaving of labels

• US 9,605,301 B2
• Filed: 08/11/2014
• Issued: 03/28/2017
• Est. Priority Date: 03/19/2008
• Status: Active Grant

• Current Assignee: IsoPlexis Corporation (Bruker Corporation)
• Original Assignee: Intelligent Bio-Systems Incorporated. (Qiagen NV)
• Inventors: Meyyappan, Visalakshi, Olejnik, Jerzy, Guggenheim, Evan
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US14/456,321
• Publication Number:
  US 20150099647A1
• Time in Patent Office: 960 Days
• Field of Search: 435/6.1, 435/6.12, 435/91.2
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/117 incorporating modified base
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2527/137 Concentration of a component of medium
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/601 being a microscope, e.g. atomic force microscopy [AFM]
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

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.

Claims

1. A method of incorporating labeled nucleotides into nucleic acid, comprising:

a) providing i) a reaction chamber comprising 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 dCTP, dTTP, dUTP, dATP and dGTP, wherein each nucleotide analogue comprises a unique label attached through a cleavable linker, and wherein each nucleotide analogue contains a removable chemical moiety capping the 3′

-OH group, iii) a second solution comprising a cleaving agent, and iv) 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 and said cleavable linker is cleaved by said cleaving agent; and

e) introducing said cleaving agent scavenger into said reaction chamber under conditions so as to scavenge said cleaving agent.

2. The method of claim 1, wherein said cleavable linker comprises a disulfide bond.

3. The method of claim 1, wherein said removable chemical moiety comprises an azido group.

4. The method of claim 1, wherein said removable chemical moiety comprises an azidomethyl ether.

5. The method of claim 1, wherein said cleaving agent is a phosphine.

6. The method of claim 5, wherein said phosphine is Tris(2-carboxy-ethyl)phosphine.

7. The method of claim 1, wherein said cleaving agent scavenger does not contain a nucleic acid base.

8. The method of claim 1, wherein said cleaving agent scavenger is cystamine.

9. The method of claim 1, wherein said cleaving agent scavenger comprises an azidomethyl group.

10. A method of incorporating labeled nucleotides into nucleic acid, comprising:

a) providing i) a reaction chamber comprising 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 dCTP, dTTP, dUTP, dATP and dGTP, wherein each nucleotide analogue comprises a unique label attached through a cleavable linker, and wherein each nucleotide analogue contains a removable chemical moiety capping the 3′

-OH group, iii) a second solution comprising a cleaving agent, and iv) a cleaving agent scavenger, wherein said cleaving agent scavenger comprises a disulfide bond;

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 and said cleavable linker is cleaved by said cleaving agent; and

e) introducing said cleaving agent scavenger into said reaction chamber under conditions so as to scavenge said cleaving agent.

11. The method of claim 10, wherein said cleavable linker comprises a disulfide bond.

12. The method of claim 10, wherein said cleaving agent is a phosphine.

13. The method of claim 12, wherein said phosphine is Tris(2-carboxy-ethyl)phosphine.

14. The method of claim 10, wherein said cleaving agent scavenger does not contain a nucleic acid base.

15. The method of claim 10, wherein said cleaving agent scavenger is cystamine.