Dark quenchers for donor-acceptor energy transfer

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, R9 and R10 are members independently selected from alkyl and substituted alkyl;
• and
• X1 is a member selected from —CH3, H, —COOH, —NR′R″, —SH, 9 and —OP(OX3)(N(X4)2);
• X2 is —OP(OX3)(N(X4)2)
• wherein,
• R′, R″, are members independently selected from H, and substituted or unsubstituted alkyl;
• and
• X3 and X4 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 R3 groups are the same or different;
• R1, R2, and R3 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 R1, R2 and R3 are members indpendently selected from substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl.

A quencher of excited state energy having the structure:

• wherein
• R1, R2, and R3 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 R1, R2 and R3 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, R9 and R10 are members independently selected from alkyl and substituted alkyl;
• and
• X1 is a member selected from CH3, —OH, —COOH, —NR′R″, —SH, and OP(OX3)(N(X4)2);
• X2 is —OP(OX3)(N(X4)2)
• wherein,
• R′, R″, are members independently selected from H, and substituted or unsubstituted alkyl;
• and
• X3 and X4 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 R2 groups are the same or different.

A quencher of excited state energy having the structure:

• wherein
• R5, R6 and R7 are members independently selected from —NR′R″, substituted or unsubstituted aryl, nitro, substituted or unsubstituted C1–C6 alkyl, and substituted or unsubstituted C1–C6 alkoxy, wherein R′ and R″ are independently selected from H and substituted or unsubstituted C1–C6 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, R9 and R10 are members independently selected from substituted and unsubstituted alkyl;
• and
• X1 is a member selected from —CH3, H, —COOH, —NH2, —SH, and P(OX3)(N(X4)2);
• X2 is —OP(OX3)(N(X4)2)
• wherein, X3 and X4 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 R5 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 R6 groups are the same or different;
• c is a number from 0 to 5, inclusive, such that when c is greater than 1, the R7 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.

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

• wherein,
• X5 and X6 are members independently selected from H, substituted or unsubstituted C1–C6 alkyl, ER′, DOOR′, —NR′R″ —SH, —OP(OX3)N(X4)2, wherein at least one of X5 and X6 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
• X3 and X4 are members independently selected from CN, and substituted or unsubstituted C1–C6 alkyl.

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

• wherein
• R20 is a protecting group;
• and
• PAM is a phosphoramidite.

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

• wherein
• R20 is a protecting group;
• and
• PAM is a phosphoramidite.