Functionalized cyanine dyes (PEG)

Patent metadata

Field	Value
Publication number	US-9920365-B2
Application number	US-201514729988-A
Country	US
Kind code	B2
Filing date	Jun 3, 2015
Priority date	Aug 25, 2010
Publication date	Mar 20, 2018
Grant date	Mar 20, 2018

Abstract

The invention provides a novel class of cyanine dyes that are functionalized with 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.

First claim

What is claimed is:

1. A compound of formula:

wherein
Q is:

R m is a member selected from substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl;
n is an integer selected from 1, 2, 3, 4 and 5;
R c , and R d are independently selected from alkyl and heteroalkyl, substituted with a member selected from sulfonic acid, carboxylic acid, phosphonic acid, and phosphoric acid;
each R a and each R e , is independently selected from C(O)R 9 , OR 12 , NR 12 R 13 , CR 12 C(O)R 13 , NR 12 C(O) 2 R 13 , SO 3 H, and C(O)NR 12 R 13 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl, and a ring structure formed by joining a member selected from two R a moieties together with the atoms to which they are attached, two R e moieties together with the atoms to which they are attached, and a combination thereof, to form said ring structure, which is a member selected from a substituted or unsubstituted aryl and a substituted or unsubstituted heteroaryl, said ring substituted with at least one SO 3 H,
wherein
R 9 is a member selected from OR 10 , and NH(CH 2 ) t OR 11
wherein
R 10 is a member selected from H and substituted or unsubstituted alkyl;
t is selected from the integers from 1 to 12;
R 11 is a member selected from H, and

wherein
 u is selected from the integers from 1 to 8; and
 Y is a naturally occurring nucleobase; and

R 12 and R 13 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl;

a is an integer selected from 1, 2, 3 and 4;
e is an integer selected from 0, 1, 2, 3 and 4
R f , R g , R h , and R i are independently selected from unsubstituted alkyl, alkylsulfonic acid, and

wherein
s is selected from the integers from 1 to 12; and
R 9a is a member selected from OH, and
—NH(CH 2 ) tt —O—R 10a

wherein
tt is selected from the integers from 1 to 12; and
R 10a is a member selected from H, a moiety comprising branched or linear poly(ethylene glycol), and

wherein
Y is a naturally occurring nucleobase; and
u is selected from the integers from 1 to 8; and

wherein
at least one of R a , R e , R f , R g , R h and R i comprises a branched poly(ethylene glycol) moiety, and said at least one of R a , R b , R e , R f , R g , R h , R i and R j is:

wherein
X 2 , X 3 and X 4 are linkage fragments independently selected from S, SC(O)NH, HNC(O)S, SC(O)O, O, NH, NHC(O), (O)CNH and NHC(O)O, and OC(O)NH, CH 2 S, CH 2 O, CH 2 CH 2 O, CH 2 CH 2 S, (CH 2 ) o O, (CH 2 ) o S or (CH 2 ) o Y′-PEG wherein, Y′ is S, NH, NHC(O), C(O)NH, NHC(O)O, OC(O)NH, or O;
and o is an integer from 1 to 50;
X 5 is selected from H, unsubstituted alkyl, unsubstituted heteroalkyl and polyethylene glycol; and
R 16 and R 17 are independently selected poly(ethylene glycol) moieties.

2. The compound according to claim 1 wherein said linear poly(ethylene glycol) moiety has the formula:

wherein
b and d are integers independently selected from 0 to 18; and
n is an integer from 2 to 10,000.

3. The compound according to claim 1 wherein said linear poly(ethylene glycol) moiety has the formula:

wherein
b, bb and d are integers independently selected from 0 to 18; and
n is an integer from 2 to 10,000.

4. The compound according to claim 1 , wherein at least two of R f , R g , R h , and R i are alkylsulfonic acid.

5. The compound according to claim 1 , wherein neither R c nor R d is unsubstituted alkyl.

6. The compound according claim 1 , wherein when two R a moieties are not joined to form said ring substituted with said at least one SO 3 H moiety, at least one R a is SO 3 H.

7. The compound according to claim 1 , wherein when two R e moieties are not joined to form said aryl ring substituted with said at least one SO 3 H moiety, at least one R e is SO 3 H.

8. The compound according to claim 2 , comprising the substructure:

9. The compound according to claim 2 , comprising the substructure:

10. The compound according to claim 2 , comprising the substructure:

wherein
q is selected from 0 and 1.

11. The compound according to claim 2 , comprising the substructure:

wherein
q is selected from 0 and 1.

12. The compound according to claim 1 , of a formula selected from:

wherein
each R b and each R j are members independently selected from C(O)R 29 , OR 32 , NR 32 R 33 , CR 32 C(O)R 33 , NR 32 C(O) 2 R 33 , SO 3 H, and C(O)NR 32 R 33 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted heterocycloalkyl
wherein
R 29 is a member selected from OR 31 , and NH(CH 2 ) t′ OR 30
wherein
R 31 is a member selected from H and substituted or unsubstituted alkyl;
t′ is selected from the integers from 1 to 12;
R 30 is a member selected from a moiety comprising branched or linear poly(ethylene glycol), and

wherein
 u′ is selected from the integers from 1 to 8; and
 Y is a naturally occurring nucleobase;

R 32 and R 33 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl

wherein
at least one of R a , R e , R f , R g , R h and R i comprises a branched poly(ethylene glycol) moiety, and said at least one of R a , R e , R f , R g , R h and

Assignees

• Pacific Biosciences California Inc

Inventors

• Shen Gene

Classifications

• G01N33/52

  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 title

• C09B23/0066

  the polymethine chain being part of a carbocyclic ring,(e.g. benzene, naphtalene, cyclohexene, cyclobutenene-quadratic acid) · CPC title

• C09B23/06

  three >CH- groups, e.g. carbocyanines · CPC title

• C09B23/0025

  the substituent being bound through an oxygen atom · CPC title

• C12Q1/6844

  Nucleic acid amplification reactions · CPC title