Cyanine dyes

• US 10,392,659 B2
• Filed: 09/12/2016
• Issued: 08/27/2019
• Est. Priority Date: 08/25/2010
• Status: Active Grant

• Current Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Original Assignee: Pacific Bioscience of California Incorporated (L'Oreal SA)
• Inventors: Yue, Stephen, Shen, Gene, Sun, Wei-Chuan (David)
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US15/262,546
• Publication Number:
  US 20170183501A1
• Time in Patent Office: 1,079 Days
• Field of Search: 548455, 536 266, 435 61
• CPC Class Codes: C07D 209/14 Radicals substituted by nitrogen atoms, not forming part of a nitro radical
• CPC Class Codes: C07D 401/14 containing three or more hetero rings
• CPC Class Codes: C07D 405/14 containing three or more hetero rings
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07K 5/0815 with the first amino acid being basic
• CPC Class Codes: C07K 5/1019 with the first amino acid being basic
• CPC Class Codes: C09B 23/0025 the substituent being bound through an oxygen atom
• CPC Class Codes: C09B 23/0033 the substituent being bound through a sulfur atom
• CPC Class Codes: C09B 23/0066 the polymethine chain being part of a carbocyclic ring,(e.g. benzene, naphtalene, cyclohexene, cyclobutenene-quadratic acid)
• CPC Class Codes: C09B 23/06 three >CH- groups, e.g. carbocyanines
• CPC Class Codes: C09B 23/083 five >CH- groups
• CPC Class Codes: C09B 23/105 two >CH- groups
• CPC Class Codes: C09B 23/164 containing one nitrogen atom
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: G01N 2333/9126 DNA-directed DNA polymerase (2.7.7.7)
• CPC Class Codes: G01N 33/52 Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper and including single- and multilayer analytical elements immunological elements G01N33/54386; involving labelled immunochemicals G01N33/58; for haemoglobin or occult blood G01N33/72
• CPC Class Codes: G01N 33/582 with fluorescent label

Abstract

The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.

Claims

1. A cyanine compound or conjugate having the structure of Formula (I) or (II):

2. The cyanine compound or conjugate according to claim 1, wherein said linker bound to a carrier molecule is a linker bound to a moiety having the structure of Formula III:

3. The cyanine compound or conjugate according to claim 1, said compound or conjugate having the structure of Formula IV:

4. The cyanine compound or conjugate according to claim 1, said compound or conjugate having the structure of Formula V:

5. The cyanine compound or conjugate according to claim 1, said compound or conjugate having the structure of Formula VI:

6. The cyanine compound or conjugate of claim 1, comprising at least one M moiety, wherein the linker of this moiety comprises the structure C(O)NH(CH₂)_t, wherein the index t is an integer selected from 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12.

7. The cyanine compound or conjugate of claim 1, comprising at least one M moiety, wherein said linker of this moiety comprises a polyvalent scaffold.

8. The cyanine compound or conjugate according to claim 7, wherein said polyvalent scaffold is a polyvalent arylene scaffold.

9. The cyanine compound or conjugate of claim 7, wherein the polyvalent scaffold comprises a second cyanine moiety bound thereto, said second cyanine moiety having a structure according to Formula I or Formula II.

10. The cyanine compound or conjugate of claim 1, comprising at least one M, wherein the linker comprises biotin bound to streptavidin.

11. The cyanine compound or conjugate according to claim 1, wherein said cyanine compound or conjugate has a structure selected from the following formulae:

12. The cyanine compound according to claim 1, wherein the linker of the M moiety includes a —

C(O)—

.

13. The cyanine compound or conjugate according to claim 2, having a structure selected from the following formulae:

14. The cyanine compound or conjugate according to claim 1, having the formula:

M-(R^D)₂

wherein

each R^D has a structure independently selected from Formula I and Formula II.

15. The cyanine compound or conjugate according to claim 7, wherein M comprises the polyvalent arylene scaffold moiety:

16. The cyanine compound or conjugate according to claim 13, having the formula:

17. The cyanine compound or conjugate according to claim 2, having at least one Y moiety comprising a natural nucleobase.

18. The cyanine compound or conjugate according to claim 1, wherein the carrier molecule comprises a member selected from a nucleic acid, a protein, a glycoprotein, a peptide, a saccharide, a hormone, a receptor, an antigen, a substrate, metabolite, a transition state analog, a cofactor, an inhibitor, a drug, a dye, a nutrient, and a growth factor.

19. The cyanine compound or conjugate according to claim 1, wherein the carrier molecule comprises a member selected from a solid support, a virus and a microorganism.

20. A method of monitoring an enzyme reaction, said method comprising:

(a) forming a reaction mixture by contacting said enzyme with a cyanine compound or conjugate according to claim 1, wherein said cyanine compound or conjugate is a substrate for said enzyme under conditions sufficient for said enzyme and said cyanine compound or conjugate to react; and

(b) monitoring fluorescence of said reaction mixture, thereby monitoring said enzyme reaction.

21. The method according to claim 20, wherein said enzyme is a DNA polymerase and said cyanine compound or conjugate comprises a nucleic acid moiety, which is said substrate for said enzyme.

22. The method according to claim 20, wherein said enzyme reaction is template directed DNA synthesis.

23. The method according to claim 20, wherein said reaction is a component of a single molecule DNA sequencing analysis.

24. A cyanine compound or conjugate having the structure of Formula (I) or (II):

25. A cyanine compound or conjugate having the structure of Formula (I) or (II):