Modular nucleotide compositions and uses therefor

• US 9,879,319 B2
• Filed: 12/14/2016
• Issued: 01/30/2018
• Est. Priority Date: 11/19/2008
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Korlach, Jonas, Wegener, Jeffrey
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US15/379,168
• Publication Number:
  US 20170159116A1
• Time in Patent Office: 412 Days
• Field of Search: 435 61
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

Abstract

Nucleic acid compositions, methods of making and using such compositions that comprise modular functional groups that can be configured to provide desired functionality to different nucleotide types through a swappable and preferably non-covalent linkage component. Such compositions are useful in a variety of applications including nucleic acid analyses.

Claims

1. A sequencing reaction mixture comprising a nucleoside polyphosphate coupled to a functional group by a non-covalent linkage component through a phosphate group of the polyphosphate, wherein the functional group comprises a detectable label.

2. The sequencing reaction mixture of claim 1, further comprising a polymerase enzyme complexed with a template and a primer.

3. The sequencing reaction mixture of claim 1, wherein the functional group is coupled to the terminal phosphate group of the polyphosphate.

4. The sequencing reaction mixture of claim 1, wherein incorporation of the nucleoside polyphosphate during nucleic acid polymerization removes the functional group.

5. The sequencing reaction mixture of claim 1, wherein the mixture comprises multiple different nucleoside polyphosphates coupled to corresponding different functional groups by non-covalent linkage components through a phosphate group of their respective polyphosphates, wherein each different functional group comprises a different detectable label.

6. The sequencing reaction mixture of claim 1, wherein the detectable label is selected from the group consisting of:

an optically detectable label, an electrically detectable label, an enzymatically detectable label, an electrochemically detectable label, a magnetic label, and a mass label.

7. The sequencing reaction mixture of claim 1, wherein the detectable label is selected from the group consisting of:

a fluorescent label, a FRET label, and combinations thereof.

8. The sequencing reaction mixture of claim 1, wherein the functional group comprises multiple detectable labels.

9. The sequencing reaction mixture of claim 8, wherein the multiple detectable labels comprise a mixture of different types of detectable labels.

10. The sequencing reaction mixture of claim 1, wherein the non-covalent linkage component comprises an affinity binding pair.

11. The sequencing reaction mixture of claim 1, wherein the affinity binding pair is selected from the group consisting of:

an avidin/biotin pair, an antibody/antigen or epitope pair, a complementary nucleic acid pair, a nucleic acid/nucleic acid binding protein pair, an associative protein or polypeptide pair, a carbohydrate/lectin pair, a GST/glutathione pair, and an RNA/aptamer pair.

12. The sequencing reaction mixture of claim 11, wherein the affinity binding pair is an avidin/biotin pair, wherein the avidin is selected from the group consisting of:

avidin, streptavidin, neutravidin, and biotin-binding subunits thereof.

13. The sequencing reaction mixture of claim 1, wherein the non-covalent linkage component is polyvalent.

14. The sequencing reaction mixture of claim 13, wherein multiple functional groups are coupled to the nucleoside polyphosphate through the polyvalent linkage component.

15. The sequencing reaction mixture of claim 14, wherein the multiple functional groups are different.

16. The sequencing reaction mixture of claim 14, wherein multiple nucleoside polyphosphates are coupled to the functional group through the polyvalent linkage component.

17. The sequencing reaction mixture of claim 1, wherein the nucleoside polyphosphate is coupled to multiple functional groups through multiple linkage groups.

18. The sequencing reaction mixture of claim 17, wherein the multiple linkage groups are different.

19. The sequencing reaction mixture of claim 18, wherein a different functional group is coupled to each different linkage group.

20. The sequencing reaction mixture of claim 1, wherein multiple nucleoside polyphosphates are coupled to the functional group through multiple linkage groups, wherein the multiple nucleoside polyphosphates are the same.

21. The sequencing reaction mixture of claim 1, wherein the non-covalent linkage component comprises a photo-induced damage mitigating agent.

22. The sequencing reaction mixture of claim 21, wherein the photo-induced damage mitigating agent comprises a triplet state quencher, an antioxidant, or combinations thereof.