A covalent conjugate of a nucleic acid and a quencher of Formula or Formula, optionally wherein the conjugate also bears a fluorophore having an emission matching the absorbance of the quencher, wherein Formula is defined as: 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, and wherein X has a structure according to Formula VIII: wherein X 1 and X 2 are members independently selected from -CH 3, -OH, -COOH, -NH 2, -SH, -OP(OX 3)N(X 4) 2 wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl; p and q are numbers independently selected from 1 to 20, inclusive; 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 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 Formula is defined as: wherein R 1 is a structure of the formula: R 2 is aryl or 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 4 is a member selected from alkyl, substituted alkyl, aryl, substituted aryl, heteroaryl and substituted heteroaryl; X and Y are each independently a reactive functional group, and wherein X has a structure according to Formula VIII: wherein X 1 and X 2 are members independently selected from -CH 3, -OH, -COOH, -NH 2, -SH, -OP(OX 3)N(X 4) 2 wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl; and p and q are numbers independently selected from 1 to 20, inclusive; m is a member selected from 1 to 4, the X groups being the same or different when m is greater than 1; and n is a number from 0 to 6 inclusive, the Y groups being the same or different when n is greater than 1. 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, and wherein X has a structure according to Formula VIII: wherein X 1 and X 2 are members independently selected from -CH 3, -OH, -COOH, -NH 2, -SH, -OP(OX 3)N(X 4) 2 wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl; p and q are numbers independently selected from 1 to 20, inclusive; 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 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; X 1 and X 2 are members independently selected from -CH 3, -OH, -COOH, -NH 2, -SH, -OP(OX 3)N(X 4) 2 wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl; p and q are numbers independently selected from 1 to 20, inclusive; 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 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; R 1 is a structure of the formula: R 2 is aryl or 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 4 is a member selected from alkyl, substituted alkyl, aryl, substituted aryl, heteroaryl and substituted heteroaryl; X and Y are each independently a reactive functional group, and wherein X has a structure according to Formula VIII: wherein X 1 and X 2 are members independently selected from -CH 3, -OH, -COOH, -NH 2, -SH, -OP(OX 3)N(X 4) 2 wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl; and p and q are numbers independently selected from 1 to 20, inclusive; m is a member selected from 1 to 4, the X groups being the same or different when m is greater than 1; and n is a number from 0 to 6 inclusive, the Y groups being the same or different when n is greater than 1. X 1 and X 2 are members independently selected from -CH 3, -OH, -COOH, -NH 2, -SH, -OP(OX 3)N(X 4) 2 wherein X 3 and X 4 are members independently selected from alkyl and substituted alkyl; and p and q are numbers independently selected from 1 to 20, inclusive; m is a member selected from 1 to 4, the X groups being the same or different when m is greater than 1; and n is a number from 0 to 6 inclusive, the Y groups being the same or different when n is greater than 1.