Dark quenchers for donor-acceptor energy transfer

1. A quencher of excited state energy having the formula:

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, 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 is a member selected from CH 3 , —OH, COOH, —NR′R″, —SH, and —OP(OX 3 )(N(X 4 ) 2 );

X 2 is OP(OX 3 )(N(X 4 ) 2 )

wherein,

R′, R″, are members independently selected from H, and substituted or unsubstituted alkyl; and

X 3 and X 4 are members independently selected from substituted and unsubstituted alkyl;

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

s is a number from 1 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.

2. The compound according to claim 1 wherein at least one member selected from the group consisting of m, n and f is at least 1.

3. The quencher according to claim 1 , wherein a member selected from R 9 , R 10 and combinations thereof comprises a polyether.

4. The quencher according to claim 1 , wherein said polyether is a member selected from poly(ethylene glycol), poly(propyleneglycol) and copolymers thereof.

5. The quencher according to claim 1 , wherein

at least one of X, Y and Y′ is:

wherein,

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

6. The quencher according to claim 5 , wherein

X 3 is cyanoethyl; and

X 4 is isopropyl.

7. The quencher according to claim 5 , wherein p and q are numbers independently selected from 2 to 16, inclusive.

8. The quencher according to claim 1 , wherein R 1 and R 2 are members independently selected from aryl substituted with a member selected from the group consisting of —NR′R″, nitro, substituted or unsubstituted C 1 –C 6 alkyl, substituted or unsubstituted C 1 –C 6 alkoxy and combinations thereof, wherein R′ and R″ are members independently selected from H, and substituted or unsubstituted C 1 –C 6 alkyl.

9. The quencher according to claim 1 , wherein at least one member selected from the group consisting of R 1 , R 2 and R 3 comprises:

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

10. A quencher of excited state energy having the formula:

X and Y are members independently selected from reactive functional groups, 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 is a member selected from —CH 3 , H, —COOH, —NR′R″, —SH, 9 and —OP(OX 3 )(N(X 4 ) 2 );

X 2 is —OP(OX 3 )(N(X 4 ) 2 )

wherein,

R′, R″, are members independently selected from H, and substituted or unsubstituted alkyl; and

X 3 and X 4 are members independently selected from substituted and unsubstituted alkyl;

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 indpendently selected from substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.

11. The quencher according to claim 10 , wherein a member selected from R 9 , R 10 and combinations thereof comprises a polyether.

12. The quencher according to claim 11 , wherein said polyether is a member selected from poly(ethylene glycol), poly(propyleneglycol) and copolymers thereof.

13. The quencher 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.

14. The quencher according to claim 13 , wherein

X 3 is cyanoethyl; and

X 4 is isopropyl.

15. The quencher according to claim 13 , wherein p and q are numbers independently selected from 2 to 16, inclusive.

16. The quencher according to claim 10 , wherein R 1 and R 2 are members independently selected from aryl substituted with a member selected from the group consisting of —NR′R″, nitro, substituted or unsubstituted C 1 –C 6 alkyl, substituted or unsubstituted C 1 –C 6 alkoxy and combinations thereof

wherein R′ and R″ are members independently selected from H, and substituted or unsubstituted C 1 –C 6 alkyl.

17. A quencher of excited state energy having the structure:

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 independently selected from substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and combinations thereof;

X and Y are members independently selected from reactive functional groups, 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 is a member selected from CH 3 , —OH, —COOH, —NR′R″, —SH, and OP(OX 3 )(N(X 4 ) 2 );

X 2 is —OP(OX 3 )(N(X 4 ) 2 )

wherein,

R′, R″, are members independently selected from H, and substituted or unsubstituted alkyl; and

X 3 and X 4 are members independently selected from substituted and unsubstituted alkyl;

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, inclusive, such that when v is greater than 1 the R 2 groups are the same or different.

18. The quencher according to claim 17 , wherein a member selected from R 9 , R 10 and combinations thereof comprises a polyether.

19. The quencher according to claim 18 , wherein said polyether is a member selected from poly(ethylene glycol), poly(propyleneglycol) and copolymers thereof.

20. The quencher according to claim 17 , wherein

at least one of X and Y is:

wherein

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

21. The quencher according to claim 20 , wherein p and q are numbers independently selected from 2 to 16, inclusive.

22. The quencher according to claim 17 , wherein R 1 , R 2 and R 3 are members independently selected from the group consisting of aryl substituted with a member selected from —NR′R″, nitro, substituted or unsubstituted C 1 –C 6 alkyl, substituted or unsubstituted C 1 –C 6 alkoxy and combinations thereof,

wherein R′ and R″ are members independently selected from H, and substituted or unsubstituted C 1 –C 6 alkyl.

23. A quencher of excited state energy having the structure:

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, wherein at least one of X and Y is:

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

X 1 is a member selected from —CH 3 , H, —COOH, —NH2, —SH, and P(OX 3 )(N(X 4 ) 2 );

X 2 is —OP(OX 3 )(N(X 4 ) 2 )

wherein, X 3 and X 4 are members independently selected from substituted and unsubstituted alkyl;

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.

24. A quencher of excited state energy according to claim 23 having the structure:

25. The quencher according to claim 24 , wherein X 3 is cyanoethyl; and

X 4 is isopropyl.

26. A quencher of excited state energy 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, ER′, DOOR′, —NR′R″ —SH, —OP(OX 3 )N(X 4 ) 2 , wherein at least one of X 5 and X 6 is a reactive functional group;

R′ is a member selected from the group consisting of H, and alkyl or substituted alkyl;

R″ is a member selected from the group consisting of H and substituted alkyl; and

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

27. A compound having a formula which is a member selected from:

28. A compound having a formula which is a member selected from:

wherein

R 20 is a protecting group; and

PAM is a phosphoramidite.

29. A compound having a formula which is a member selected from:

wherein

R 20 is a protecting group; and

PAM is a phosphoramidite.

30. A compound having a formula which is a member selected from:

31. The quencher according to claim 3 , wherein

X 3 is cyanoethyl; and

X 4 is isopropyl.

32. The quencher according to claim 5 , wherein R 1 and R 2 are members independently selected from aryl substituted with a member selected from the group consisting of —NR′R″, nitro, substituted or unsubstituted C 1 –C 6 alkyl, substituted or unsubstituted C 1 –C 6 alkoxy and combinations thereof,

wherein R′ and R″ are members independently selected from H, and substituted or unsubstituted C 1 –C 6 alkyl.

33. The quencher according to claim 5 , wherein at least one member selected from the group consisting of R 1 , R 2 and R comprises:

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

34. The quencher according to claim 26 wherein at least one of X 5 and X 6 has the formula:

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

X 1 is a member selected from —CH 3 , H, —COOH, —NH2, H, and —OP(OX 3 )(N(X 4 ) 2 ); and

X 2 is —OP(OX 3 )(N(X 4 ) 2 )

wherein,

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

35. A quencher of excited state energy having a structure which is a member selected from:

wherein

at least one of X 5 and X 6 is a bond conjugating said quencher to a nucleic acid carrier molecule.