Methods and compositions for inhibiting undesired cleaving of labels

• US 9,765,384 B2
• Filed: 08/28/2013
• Issued: 09/19/2017
• Est. Priority Date: 03/19/2008
• Status: Active Grant

• Current Assignee: IsoPlexis Corporation (Bruker Corporation)
• Original Assignee: Intelligent Bio-Systems Incorporated. (Qiagen NV)
• Inventors: Olejnik, Jerzy, Guggenheim, Evan, Visalakshi, Visalakshi
• Primary Examiner(s): WOOLWINE, SAMUEL C
• Application Number:
  US14/012,622
• Publication Number:
  US 20140234832A1
• Time in Patent Office: 1,483 Days
• Field of Search: None
• 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 composition comprising a cleaving agent scavenger and one or more nucleotide analogues in solution, said scavenger comprising cystamine, said analogues labeled with a unique label attached through a cleavable linker.

2. The composition of claim 1, wherein said unique label is attached through a cleavable disulfide linker.

3. The composition of claim 1, wherein said unique label is attached through a cleavable azido linker.

4. The composition of claim 1, wherein said one or more nucleotide analogues comprise a removable chemical moiety capping the 3′

-OH.

5. The composition of claim 4, wherein said chemical moiety comprises a disulfide bond.

6. The composition of claim 4, wherein said chemical moiety comprises an azido group.

7. The composition of claim 4, wherein said chemical moiety comprises an azidomethyl ether.

8. The composition of claim 1, further comprising a polymerase.

9. A system comprising reservoirs in fluid communication with a reaction chamber, at least one of said reservoirs comprising a solution comprising a cleaving agent scavenger and one or more nucleotide analogues, said scavenger comprising cystamine, said analogues labeled with a unique label attached through a cleavable linker.

10. The system of claim 9, wherein said unique label is attached through a cleavable disulfide linker.

11. The system of claim 9, wherein said unique label is attached through a cleavable azido linker.

12. The system of claim 9 wherein said one or more nucleotide analogues comprise a removable chemical moiety capping the 3′

-OH.

13. The system of claim 12, wherein said chemical moiety comprises a disulfide bond.

14. The system of claim 12, wherein said chemical moiety comprises an azido group.

15. The system of claim 12, wherein said chemical moiety comprises an azidomethyl ether.