Dark quenchers for donor-acceptor energy transfer

1. A nucleic acid having linked thereto:

a quencher of excited state energy having a structure comprising at least three residues selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and combinations thereof, wherein at least two of said residues are covalently linked via an exocyclic diazo bond; and

a minor groove binder.

2. The nucleic acid according to claim 1 , wherein said quencher is covalently attached to said nucleic acid by reaction of a nucleic acid and a quencher precursor having a structure according to Formula (I)

wherein

R 1 , R 2 and R 3 are members independently selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted unsaturated alkyl, with the proviso that at least two of R 1 , R 2 and R 3 are members selected from substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl;

X, Y and Y′ are members independently selected from reactive functional groups;

f is a number selected from 0 to 4, inclusive, such that when (f x s) is greater than 1, the Y′ groups are the same or different;

m is a number selected from 1 to 4, inclusive, such that when m is greater than 1, the X groups are the same or different;

n is a number from 0 to 6, inclusive, such that when (n x t) is greater than 1, the Y groups are the same or different;

s is a number from 0 to 6, inclusive, such that when s is greater than 1 the R 3 groups are the same or different; and

t is a number from 1 to 6, inclusive, such that when t is greater than 1 the R 2 groups are the same or different, and when t is 1 and s is 0, a member selected from R′, R 2 and combinations thereof is a member selected from substituted or unsubstituted polycyclic aryl and substituted or unsubstituted polycyclic heteroaryl groups.

3. The nucleic acid according to claim 2 , wherein at least one of X, Y and Y′ is:

wherein

R 9 and R 10 are members independently selected from alkyl and substituted alkyl; and

X 1 and X 2 are members independently selected from —CH 3 , —OH, —COOH, —NH 2 , —SH, and —OP(OX 3 )N(X 4 ) 2 ,

wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl.

4. The nucleic acid according to claim 3 , wherein at least one of X, Y and Y′ is:

wherein p and q are numbers independently selected from 1 to 20, inclusive.

5. The nucleic acid according to claim 4 , wherein X 3 is cyanoethyl; and X 4 is isopropyl.

6. The nucleic acid according to claim 1 , wherein said quencher is covalently attached to said nucleic acid by reaction of a nucleic acid and a quencher precursor having a structure according to Formula (II)

wherein

X and Y are members independently selected from reactive functional groups;

m is a number selected from 1 to 5, inclusive, such that when m is greater than 1, the X groups are the same or different;

n is a number selected from 0 to 5, inclusive, such that when m is greater than 1, the Y groups are the same or different;

s is a number selected from 1 to 5, inclusive, such that when s is greater than 1, the R 3 groups are the same or different;

R 1 , R 2 , and R 3 are members independently selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, and substituted or unsubstituted unsaturated alkyl,

with the proviso that at least two of R 1 , R 2 and R 3 are members independently selected from substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.

7. The nucleic acid according to claim 6 , wherein at least one of X and Y is:

wherein

R 9 and R 10 are members independently selected from alkyl and substituted alkyl; and

X 1 and X 2 are members independently selected from —CH 3 , —OH, —COOH, —NH 2 , —SH, and —OP(OX 3 )N(X 4 ) 2 ,

wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl.

8. The nucleic acid according to claim 7 , wherein at least one of X and Y is:

wherein p and q are numbers independently selected from 1 to 20, inclusive.

9. The nucleic acid according to claim 8 , wherein X 3 is cyanoethyl; and X 4 is isopropyl.

10. The nucleic acid according to claim 6 , wherein

R 2 and R 3 are members independently selected from aryl and aryl substituted with a member selected from amino, amino derivatives, nitro, C 1 -C 6 alkyl, C 1 -C 6 alkoxy and combinations thereof;

R 1 includes a structure according to Formula III:

wherein R 4 is a member selected from alkyl, substituted alkyl, aryl, substituted aryl, heteroaryl and substituted heteroaryl.

11. The nucleic acid according to claim 10 , wherein at least one of X and Y is:

wherein

R 9 and R 10 are members independently selected from alkyl and substituted alkyl; and

X 1 and X 2 are members independently selected from —CH 3 , —OH, —COOH, —NH 2 , —SH, and —OP(OX 3 )N(X 4 ) 2 ,

wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl.

12. The nucleic acid according to claim 11 , wherein at least one of X and Y is:

wherein p and q are numbers independently selected from 1 to 20, inclusive.

13. The nucleic acid according to claim 12 , wherein X 3 is cyanoethyl; and X 4 is isopropyl.

14. The nucleic acid according to claim 1 , wherein said quencher is covalently attached to said nucleic acid by reaction of a nucleic acid and a quencher precursor having a structure according to Formula IV:

wherein

X and Y are members independently selected from reactive functional groups;

m is a number selected from 0 to 4, inclusive, such that when m is greater than 1, the X groups are the same or different;

v is a number from 1 to 10 and when v is greater than 1, the R 2 groups are the same or different;

R 1 , R 2 , and R 3 are members independently selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted unsaturated alkyl, with the proviso that at least two of R 1 , R 2 and R 3 are members selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and combinations thereof.

15. The nucleic acid according to claim 14 , wherein at least one of X and Y is:

wherein

R 9 and R 10 are members independently selected from alkyl and substituted alkyl; and

X 1 and X 2 are members independently selected from —CH 3 , —OH, —COOH, —NH 2 , —SH, and —OP(OX 3 )N(X 4 ) 2 ,

wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl.

16. The nucleic acid according to claim 15 , wherein at least one of X and Y is:

wherein p and q are numbers independently selected from 1 to 20, inclusive.

17. The nucleic acid according to claim 16 , wherein X 3 is cyanoethyl; and X 4 is isopropyl.

18. The nucleic acid according to claim 1 , wherein said quencher is covalently attached to said nucleic acid by reaction of a nucleic acid and a quencher precursor having a structure according to Formula V:

wherein

R 5 , R 6 and R 7 are members independently selected from —NR′R″, substituted or unsubstituted aryl, nitro, substituted or unsubstituted C 1 -C 6 alkyl, and substituted or unsubstituted C 1 -C 6 alkoxy,

wherein R′ and R″ are independently selected from H and substituted or unsubstituted C 1 -C 6 alkyl;

X and Y are independently selected from the group consisting of reactive functional groups;

n is a number from 0 to 1, inclusive;

a is a number from 0 to 4, inclusive, such that when a is greater than 1, the R 5 groups are the same or different;

b is a number from 0 to 4, inclusive, such that when (v×b) is greater than 1, the R 6 groups are the same or different;

c is a number from 0 to 5, inclusive, such that when c is greater than 1, the R 7 groups are the same or different; and

v is a number from 1 to 10, inclusive, such that when v is greater than 1, the value of b on each of the v phenyl rings is the same or different.

19. The nucleic acid according to claim 18 , wherein at least one of X and Y is:

wherein

R 9 and R 10 are members independently selected from alkyl and substituted alkyl; and

X 1 and X 2 are members independently selected from —CH 3 , —OH, —COOH, —NH 2 , —SH, and —OP(OX 3 )N(X 4 ) 2 ,

wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl.

20. The nucleic acid according to claim 19 , wherein at least one of X and Y is:

wherein p and q are numbers independently selected from 1 to 20, inclusive.

21. The nucleic acid according to claim 20 , wherein X 3 is cyanoethyl; and X 4 is isopropyl.

22. The nucleic acid according to claim 1 , wherein said quencher is covalently attached to said nucleic acid by reaction of a nucleic acid and a quencher precursor having a structure according to Formula VI:

wherein

R 5 , R 6 and R 7 are members independently selected from amine, alkyl amine, substituted or unsubstituted aryl, nitro, substituted or unsubstituted C 1 -C 6 alkyl, and substituted or unsubstituted C 1 -C 6 alkoxy;

a is a number between 0 and 5, inclusive, such that when a is greater than 1, the R 5 groups are the same or different;

b is a number between 0 and 4, inclusive, such that when b is greater than 1, the R 6 groups are the same or different;

c is a number between 0 and 4, inclusive, such that when c is greater than 1, the R 7 groups are the same or different; and

X 1 and X 2 are members independently selected from C 1 -C 6 alkyl and C 1 -C 6 substituted alkyl.

23. The nucleic acid according to claim 1 , wherein said quencher is covalently attached to said nucleic acid by reaction of a nucleic acid and a quencher precursor having a structure which is a member selected from:

wherein

X 5 and X 6 are members independently selected from H, substituted or unsubstituted C 1 -C 6 alkyl, —OR′, —COOR′, —NR′R″, —SH, and —OP(OX 3 )N(X 4 ) 2 , in which R′ and R″ are members independently selected from the group consisting of H, and alkyl or substituted alkyl, with the proviso that at least one of X 5 and X 6 is a reactive functional group

wherein

X 3 and X 4 are members independently selected from substituted or unsubstituted C 1 -C 6 alkyl.

24. The nucleic acid according to claim 23 , wherein at least one of X 5 and X 6 is:

wherein

R 9 and R 10 are members independently selected from alkyl and substituted alkyl; and

X 1 and X 2 are members independently selected from —CH 3 , —OH, —COOH, —NH 2 , —SH, and —OP(OX 3 )N(X 4 ) 2 ,

wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl.

25. The nucleic acid according to claim 24 , wherein at least one of X 5 and X 6 is:

wherein p and q are numbers independently selected from 1 to 20, inclusive.

26. The nucleic acid according to claim 25 , wherein X 3 is cyanoethyl; and X 4 is isopropyl.