Labeled nucleotide analogs having protein shields

• US 10,023,605 B2
• Filed: 06/01/2015
• Issued: 07/17/2018
• Est. Priority Date: 02/15/2012
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Bjornson, Keith, Hanes, Jeremiah, Miller, Erik, Kamtekar, Satwik, Sebo, Lubomir, Brogley, Louis
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US14/727,553
• Publication Number:
  US 20150330987A1
• Time in Patent Office: 1,142 Days
• Field of Search: 435 61, 435 911, 536 266
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/16 Purine radicals
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C07K 14/36 from Actinomyces; from Streptomyces (G)
• CPC Class Codes: C09B 23/083 five >CH- groups
• CPC Class Codes: C09B 69/105 containing a methine or polymethine dye
• CPC Class Codes: C12N 9/10 Transferases (2.) ribonucleases C12N9/22
• 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: C12Q 2523/313 Irradiation, e.g. UV irradiation
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: G01N 33/582 with fluorescent label
• CPC Class Codes: G01N 33/583 with non-fluorescent dye label

Abstract

Compositions, methods, and systems are provided for nucleotide analogs comprising protein shields for improving enzyme photostability in single molecule real time sequencing. Nucleotide analogs of the invention have a protein shield between the dye moieties and nucleotide moieties of the analog. The nucleotide analogs have two avidin proteins connected by a central dye component, and each avidin protein is further connected to a nucleotide component. The protein can prevent the direct interaction of the dye moiety with the enzyme carrying out nucleotide synthesis preventing photodamage to the enzyme. The nucleotide analogs of the invention can have multiple dyes and multiple nucleotide moieties.

Claims

1. A labeled nucleotide analog comprising:

two avidin proteins connected through a central dye component, the central dye component comprising one or more dye moieties, the central dye component further comprising two bis-biotin moieties, each of the bis-biotin moieties bound to one of the avidin proteins,

wherein one of the avidin proteins is also bound to a first nucleotide component through a bis-biotin moiety, wherein the first nucleotide component comprises one or more phospholinked nucleotides, and

wherein the other avidin protein is also bound to a second nucleotide component through a bis-biotin moiety, wherein the second nucleotide component comprises one or more phospholinked nucleotides.

2. The labeled nucleotide analog of claim 1 wherein the first nucleotide component and second nucleotide component each comprise the same type of nucleotide.

3. The labeled nucleotide analog of claim 1 wherein the number of dye moieties is between 1 and 18 and the number of nucleotide moieties is between 1 and 18.

4. The labeled nucleotide analog of claim 1 wherein the number of dye moieties is 1, 2, 3, 5, 6, 7 or 8 and the number of nucleotide moieties is 4, 5, 6, 7, or 8.

5. The labeled nucleotide analog of claim 1 wherein the number of bonds between biotins on the bis-biotin moiety is between 15 and 50.

6. The labeled nucleotide analog of claim 1 wherein the avidin protein comprises streptavidin, tamavidin, traptavidin, xenavidin, bradavidin, AVR2, AVR4, and homologs thereof.

7. The labeled nucleotide analog of claim 1 wherein the avidin protein comprises either streptavidin or tamavidin.

8. The labeled nucleotide analog of claim 1 wherein the dye moieties comprise fluorescent labels.

9. The labeled nucleotide analog of claim 1 wherein the nucleotide analog comprises multiple sulfonate groups.

10. The labeled nucleotide analog of claim 1 wherein the nucleotide analog comprises from 6 to 50 sulfonate groups.

11. A reaction mixture for sequencing a nucleic acid template comprising:

a polymerase enzyme complex comprising a polymerase enzyme, a template nucleic acid, and optionally a primer hybridized to the template nucleic acid, wherein the polymerase enzyme complex is immobilized on a surface; and

sequencing reagents in contact with the surface comprising reagents for carrying out nucleic acid synthesis including 1 or more labeled nucleotide analogs of claim 1.

12. The reaction mixture of claim 11 wherein the number of dye moieties is between 1 and 18 and the number of nucleotide moieties is between 1 and 18 in each nucleotide analog.

13. The reaction mixture of claim 11 wherein the number of dye moieties is 1, 2, 3, 4, 5, 6, 7 or 8 and the number of nucleotide moieties is 4, 5, 6, 7, or 8 in each nucleotide analog.

14. The reaction mixture of claim 11 wherein the number of bonds between biotins on a bis-biotin moiety is between 15 and 50.

15. The reaction mixture of claim 11 wherein the avidin protein in an analog comprises either streptavidin or tamavidin.

16. The reaction mixture of claim 11 wherein the dye moieties comprise fluorescent labels.

17. A method for sequencing a nucleic acid template comprising:

providing a polymerase enzyme complex comprising a polymerase enzyme, a template nucleic acid, and optionally a primer hybridized to the template nucleic acid, wherein the polymerase enzyme complex is immobilized on a surface;

adding sequencing reagents in contact with the surface comprising reagents for carrying out nucleic acid synthesis including 1 or more labeled nucleotide analogs of claim 1; and

determining the sequential addition of nucleotides to a nucleic acid strand complementary to a strand of the template nucleic acid by observing the interaction of the labeled nucleotide analogs with the polymerase enzyme complex.

18. The method of claim 17 wherein the number of dye moieties is between 1 and 18 and the number of nucleotide moieties is between 1 and 18 in each nucleotide analog.

19. The method of claim 17 wherein the number of dye moieties is 1, 2, 3, 4, 5, 6, 7 or 8 and the number of nucleotide moieties is 4, 5, 6, 7, or 8 in each nucleotide analog.

20. The method of claim 17 wherein the number of bonds between biotins on a bis-biotin moiety is between 15 and 50.

21. The method of claim 17 wherein the avidin protein in an analog comprises either streptavidin or tamavidin.

22. The method of claim 17 wherein the dye moieties comprise fluorescent labels.

23. A system for sequencing nucleic acids comprising:

a chip comprising a plurality of polymerase enzyme complexes bound thereto, each polymerase enzyme complex individually optically resolvable, each polymerase enzyme complex comprising a polymerase enzyme, a template nucleic acid, and optionally a primer hybridized to the template nucleic acid,

sequencing reagents in contact with the surface comprising reagents for carrying out nucleic acid synthesis including 1 or more labeled nucleotide analogs of claim 1; and

an illumination system for illuminating the polymerase enzyme complexes; and

an optical detection system for detecting fluorescence from the labeled nucleotide analogs while they are interacting with the polymerase enzyme complexes; and

a computer for analyzing the signals detected by the detection system to determine the sequential addition of nucleotides to a nucleic acid strand complementary to a strand of the template nucleic acid.