Multimeric protected fluorescent reagents

• US 10,150,872 B2
• Filed: 02/04/2016
• Issued: 12/11/2018
• Est. Priority Date: 02/04/2015
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Zheng, Frank, Hanes, Jeremiah, Shen, Gene, Brogley, Louis, Yue, Stephen, Lapin, Yuri, Lyle, John, Osuna, Honey, Fedorov, Andrei, Sebo, Lubomir
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US15/015,602
• Publication Number:
  US 20160237279A1
• Time in Patent Office: 1,041 Days
• Field of Search: 435 61
• CPC Class Codes: C09B 23/06 three >CH- groups, e.g. carbocyanines
• CPC Class Codes: C09B 23/105 two >CH- groups
• CPC Class Codes: C09B 69/00 Dyes not provided for by a single group of this subclass
• CPC Class Codes: C09B 69/10 Polymeric dyes; Reaction products of dyes with monomers or with macromolecular compounds addition products of alkylene oxide to dyes, C09B69/00; dyeing with polymeric dyes D06P1/0056
• CPC Class Codes: C09B 69/105 containing a methine or polymethine dye
• CPC Class Codes: G01N 33/533 with fluorescent label

Abstract

Multimeric protected fluorescent reagents and their methods of synthesis are provided. The reagents are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The reagents contain fluorescent dye elements, that allow the compounds to be detected with high sensitivity at desirable wavelengths, binding elements, that allow the compounds to be recognized specifically by target biomolecules, and protective shield elements, that decrease undesirable contacts between the fluorescent dye elements and the bound target biomolecules and that therefore decrease photodamage of the bound target biomolecules by the fluorescent dye elements. The reagents also contain coupling elements connect monomeric compounds into multimeric forms, thereby increasing brightness.

Claims

1. A reagent of structural formula (IV):

JB″

—

S″

—

ZS′

—

B′

]_m′

]_q 

 

(IV);

wherein

each Z is independently a multivalent central core element comprising a fluorescent dye element;

each S′

is independently an intermediate chemical group, wherein at least one S′

comprises a shield element;

each S″

is independently an intermediate chemical group, wherein S″

optionally comprises a shield element;

each B′

is independently a terminal chemical group, wherein at least one B′

comprises a binding element;

each B″

is independently a terminal chemical group or a bond;

J is a joining element;

each m′

is independently an integer from 1 to 23; and

q is an integer from 2 to 10.

2. The reagent of claim 1, wherein the shield element decreases photodamage of the reagent or of a biomolecule associated with the binding element.

3. The reagent of claim 1, wherein the shield element decreases contact between the fluorescent dye and the binding element.

4. The reagent of claim 1, wherein the shield element comprises a plurality of side chains.

5. The reagent of claim 1, wherein the shield element comprises the structure:

6. The reagent of claim 1, wherein the shield element comprises an inner layer and an outer layer.

7. The reagent of claim 1, wherein at least one S′

—

B′

group comprises the structure;

8. The reagent of claim 1, wherein the binding element comprises a nucleotide.

9. The reagent of claim 1, wherein the binding element comprises biotin.

10. The reagent of claim 1, wherein the binding element comprises a polyphosphate.

11. The reagent of claim 1, wherein Z comprises a branching element.

12. The reagent of claim 1, wherein each m′

is independently an integer from 1 to 11.

13. The reagent of claim 1, wherein each B″

is a terminal group, and J and each B″

are connected non-covalently.

14. The reagent of claim 1, wherein each B″

is a bond.

15. The reagent of claim 1, wherein each S′

comprises a shield element.

16. The reagent of claim 1, wherein q is an integer from 2 to 4.

17. The reagent of claim 1 having structural formula (VI):

18. The reagent of claim 17, wherein X comprises a polyamine.

19. The reagent of claim 17, wherein X comprises a substituted cyclohexane.

20. The reagent of claim 17, wherein X comprises a substituted 1,3,5-triazine.

21. The reagent of claim 17, wherein X comprises a substituted benzene.

22. The reagent of claim 17, comprising at least one donor fluorophore and at least one acceptor fluorophore.

23. The reagent of claim 17, wherein the shield element comprises a plurality of side chains.

24. The reagent of claim 17, wherein the shield element comprises the structure:

25. The reagent of claim 17, wherein the shield element comprises an inner layer and an outer layer.

26. The reagent of claim 17, wherein at least one S′

—

B′

group comprises the structure;

27. The reagent of claim 17, wherein the binding element comprises a nucleotide.

28. The reagent of claim 17, wherein the binding element comprises biotin.

29. The reagent of claim 17, wherein the binding element comprises a polyphosphate.

30. The reagent of claim 17, wherein the branching element comprises a substituted phenyl group.

31. The reagent of claim 17, wherein each B″

is a terminal group, and J and B″

are connected non-covalently.

32. The reagent of claim 17, wherein each B″

is a bond.