Polymethine compounds and their use as fluorescent labels

Patent metadata

Field	Value
Publication number	US-9309409-B2
Application number	US-201514705844-A
Country	US
Kind code	B2
Filing date	May 6, 2015
Priority date	May 7, 2014
Publication date	Apr 12, 2016
Grant date	Apr 12, 2016

Abstract

The present disclosure relates to new compounds and their use as fluorescent labels. The compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

First claim

The invention claimed is:

1. A compound of formula (I) or mesomeric forms thereof:

wherein mCat+ or mAn− is an organic or inorganic positively/negatively charged counterion and
m is an integer 0-3;
n is an integer 1-5;
Rf represents OH or O − ; or an ester or amine conjugate linked to a substrate moiety;
each of Ra 1 and Ra 2 is independently H, SO 3 − , sulfonamide, halogen, or a further ring fused to an adjacent carbon atom; wherein either Ra 1 or Ra 2 is sulphonamide or SO 3 − ; and
each of Rc 1 and Rc 2 is independently alkyl or substituted alkyl;
wherein when Ra 1 or Ra 2 is SO 3 − , either i) Rc 1 or Rc 2 is an alkyl sulfonic acid group, or ii) Ra 1 or Ra 2 is a sulphonamide.

2. A compound according to claim 1 wherein Ra 1 is sulphonamide.

3. A compound according to claim 1 wherein Ra 2 is sulphonamide.

4. A compound according to claim 2 wherein Ra 2 is H or SO 3 − .

5. A compound according to claim 3 wherein Ra 1 is H or SO 3 − .

6. A compound according to claim 1 wherein Rc 1 or Rc 2 is methyl, ethyl, propyl or —(CH 2 ) q SO 3 − where q is 1-6.

7. A compound according to claim 6 wherein either Rc 1 or Rc 2 is (CH 2 ) 4 —SO 3 − .

8. A compound according to claim 1 wherein the sulphonamide is part of a structure of formula (II):

wherein Rc 1 is alkyl or substituted alkyl.

9. A compound according to claim 1 wherein the sulphonamide is part of a structure of formula (III):

wherein m is an integer 0-3, n is an integer 1-5, Rf is OH or O − ; and Rc 2 is alkyl or substituted alkyl.

10. A compound according to claim 1 which is represented by formula (IV):

or a salt thereof wherein mCat+ or mAn− is an organic or inorganic positively/negatively charged counterion and
m is an integer 0-3;
n is an integer 1-5; and
each of Rc 1 and Rc 2 is independently alkyl or substituted alkyl.

11. A compound according to claim 1 wherein the substrate moiety comprises a nucleotide or oligonucleotide.

12. A method of synthesizing a compound according to claim 1 , the method comprising reacting one of the following starting materials under conditions suitable for formation of a compound according to claim 1 :

or a salt thereof wherein Ra is H, SO 3 − , sulfonamide, halogen, or a further ring fused to an adjacent carbon atom; R1, R2, R3 and R4 are independently H, alkyl or aryl; R c is alkyl or substituted alkyl; Ar is an aromatic group and R is an alkyl group.

13. A method of synthesising a compound according to claim 1 , the method comprising reacting one of the following starting materials under conditions suitable for formation of a compound according to claim 1 :

or a salt thereof wherein n is an integer 1-5; Rc 2 is alkyl or substituted alkyl; Ar is an aromatic group and R is an alkyl group.

14. A compound according to claim 11 wherein the substrate moiety comprises a nucleotide.

15. A compound according to claim 11 wherein the substrate moiety comprises an oligonucleotide.

16. A compound according to claim 1 , wherein Rf represents an amine conjugate linked to a substrate moiety.

17. A compound according to claim 1 , wherein Rf represents an ester conjugate linked to a substrate moiety.

Assignees

• Illumina Cambridge Ltd

Inventors

• Liu Xiaohai
• Romanov Nikolai Nikolaevich

Classifications

• C12Q1/6876 Primary

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title

• C09B23/02

  the polymethine chain containing an odd number of >CH- {or >C[alkyl]-} groups · CPC title

• C09B23/083 Primary

  five >CH- groups · CPC title

• C07D403/06 Primary

  linked by a carbon chain containing only aliphatic carbon atoms · CPC title

• C07D209/08 Primary

  with only hydrogen atoms or radicals containing only hydrogen and carbon atoms, directly attached to carbon atoms of the hetero ring · CPC title