Cyanine dyes
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.
1. A compound of Formula I:
wherein
n is selected from the integers 1 and 2;
R a is selected from H, a moiety according to Formula II:
and a moiety joined with R b , together with the atoms to which R a and R b are attached, forming substituted phenyl ring C:
wherein
each y is an independently selected integer from 0 to 10;
R u and R v are independently selected from —SO 3 H, a moiety according to Formula II, and
wherein
R 8 is selected from H and substituted or unsubstituted alkyl;
x is an integer from 1 to 10
R b is selected from H,
and a moiety joined with R a forming, together with the atoms to which R a and R b are attached, substituted phenyl ring C;
z is an integer from 0 to 10;
R 8 is selected from H and substituted or unsubstituted alkyl;
R c is selected from H,
q is an integer from 0 to 10;
wherein R a , R b and R c are not all H;
R d is selected from H and OCH 3 ;
R e and R e ′ are independently selected from
wherein t is an integer from 1 to 10;
R a ′ is selected from H, C(O)-M, a moiety according to Formula II, and a moiety joined with R b ′ forming, together with the atoms to which R a ′ and R b ′ are attached, substituted phenyl ring C′;
M is selected from OH, a carboxylic acid activating moiety, a polyvalent scaffold and a carrier molecule;
R u ′ and R v ′ are independently selected from H, a moiety according to Formula II, —SO 3 H, and
wherein each x is an integer independently selected from 0 to 10;
R 10 is selected from H and substituted or unsubstituted alkyl;
R w ′ is selected from H and a moiety according to Formula II;
R b ′ is selected from H, C(O)-M, a moiety according to Formula II, a moiety joined with R a ′, together with the atoms to which R a ′ and R b ′ are attached, forming substituted phenyl ring C′, and
wherein p is an integer from 0 to 10;
R c ′ is selected from H, C(O)-M and —SO 3 H,
wherein R a ′, R b ′ and R c ′ are not all H;
R d ′ is selected from H and OCH 3 ; and
R f , R g , R f ′ and R g ′ are independently selected from CH 3 ,
wherein each t is an independently selected integer from 1 to 10.
2. The compound according to claim 1 , having the formula:
3. The compound according to claim 1 , having the formula:
4. The compound according to claim 1 , having the formula:
5. The compound according to claim 1 , wherein R e is:
6. The compound according claim 1 , wherein a member selected from R a ′, and R b ′ is:
7. The compound according to claim 1 , wherein M comprises biotin.
8. The compound according to claim 7 , wherein biotin is bound to streptavidin.
9. The compound according to claim 1 , wherein a member selected from R a , R a ′, R b , R b ′, R c , R c ′, R d and R d ′ is a moiety comprising poly(ethylene glycol).
10. The compound according to claim 1 in which two, three, four, five or six of R a , R a ′, R b , R b ′, R c , R c ′, R d and R d ′, in any combination, include an independently selected dye moiety or dye linker moiety.
11. The compound according to claim 1 in which two, three, four, five or six of R a , R a ′, R b , R b ′, R c , R c ′, R d and R d ′, in any combination, include an independently selected polyvalent moiety.
12. The compound according to claim 1 wherein said polyvalent scaffold has bound thereto one or more member selected from a dye, a dye-linker moiety, and a nucleotide polyphosphate.
13. A method of monitoring an enzyme reaction, said method comprising:
(a) forming a reaction mixture by contacting said enzyme with a fluorescent dye according to claim 1 wherein said dye is a substrate for said enzyme under conditions sufficient for said enzyme and said dye to react; and
(b) monitoring fluorescence of said reaction mixture.
14. The method according to claim 13 wherein said enzyme is a DNA polymerase and said dye comprises a nucleic acid moiety which is said substrate for said enzyme.
15. The method according to claim 13 wherein said enzyme reaction is template directed DNA synthesis.
16. The method according to any of claim 13 wherein said reaction is a component of a single molecule DNA sequencing analysis.
17. A compound of Formula IA:
wherein
n is selected from the integers 1 and 2;
R u and R v are independently selected from —SO 3 H,
and
a moiety according to Formula II:
wherein
R 8 is selected from H and substituted or unsubstituted alkyl; and
x is an integer from 1 to 10;
each y is an independently selected integer from 0 to 10;
R e and R e′ are independently selected from:
wherein t is an integer from 1 to 10; and
each M is independently OH,
R f , R g , R f ′ and R g ′ are independently selected from CH 3 ,
wherein each t is an independently selected integer from 1 to 10;
R u ′ and R v ′ are independently selected from H, —SO 3 H, a moiety according to Formula II, and
wherein each x is an integer independently selected from 0 to 10;
R 10 is selected from H and substituted or unsubstituted alkyl;
R w ′ is selected from H and a moiety according to Formula II;
R f , R g , R f ′ and R g ′ are independently selected from CH 3 ,
wherein each t is an independently selected integer from 1 to 10.