Fluorescent quenching detection reagents and methods

A compound having the formula:

• wherein
• Ar1 and Ar2 are each independently a substituted or unsubstituted aryl group, where at least one of Ar1 and Ar2 is a substituted aryl;
• X1 is selected from the group consisting of H, (C1-C1-C12)alkyl, aryl, heteroaryl, and protected or unprotected functional group;
• X2 is selected from the group consisting of a phosphorous coupling moiety, a pentafluorophenoxy moiety and a succinimidyl moiety;
• and
• W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.

A compound having the formula:

• wherein
• Ar1 and Ar2 are each independently a substituted or unsubstituted aryl group,where at least one of Ar1 and Ar2 is a substituted aryl;
• X1, is selected from the group consisting of H, (C1-C12)alkyl, aryl, heteroaryl and protected or unprotected functional group;
• X2 is a phosphoramidite;
• and
• W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof.

A compound having the formula:

• wherein
• Ar1 and Ar2 are each independently a substituted or unsubstituted aryl group;
• X1 is selected from the group consisting of H, (C1-C12)alkyl, aryl, heteroaryl, and protected or unprotected functional group;
• X2 is a moiety reactive towards nucleophiles;
• W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof;
• and
• wherein one of Ar1 and A2 is directly or indirectly substituted with a substituted aryl group (A3), where Ar3 extends the resonance ability of the Ar1—N═N—A2 aromatic system and thereby increases the wavelength absorbance maximum of the compound.

A compound having the formula:

• wherein
• Ar1 and A2 are each independently a substituted or unsubstituted aryl group;
• X1, is selected from the, group consisting of H, (C1-C12)alkyl, aryl, heteroaryl, and protected or unprotected functional group;
• X2 is a phosphoramidite;
• W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof;
• and
• wherein Ar1 or Ar2 is indirectly substituted with an aryl group through a group selected from —(C═C)n— and —(CR′CR′)n— where n is 0 to 5 and R′ is independently selected from hydrogen, (C1-C8)alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C1-C4)alkyl, and (u nsubstituted aryl)oxy-(C1-C4)alkyl.

A compound having the formula:

• wherein
• Ar1 and Ar2 are each independently a substituted or unsubstituted aryl group;
• X1 is selected from the group consisting of H, (C1-C12)alkyl, aryl, heteroaryl, and protected or unprotected functional group;
• X2 is a phosphoramidite;
• W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof;
• and
• Ar1 or Ar2 is indirectly substituted with an aryl group (Ar3) through a double bond selected from carbon—carbon and nitrogen—nitrogen double bonds.

A compound having the formula:

• wherein
• Ar1 and A2 are each independently a substituted or unsubstituted aryl group;
• X1 is selected from the group consisting of H, (C1-C12)alkyl, aryl, heteroaryl, and protected or unprotected functional group;
• X2 is a phosphoramidite;
• W is a linking group having from 3 to 100 backbone atoms selected from C, N, O, S, Si and P, said linking group being cyclic, acyclic, aromatic or a combination thereof;
• wherein one of Ar1 and Ar2 is directly or indirectly substituted with a substituted aryl group (Ar3), where Ar3 extends the resonance ability of the Ar1—N═N—Ar2 aromatic system and thereby increases the wavelength absorbance maximum of the compound;
• and
• at least one of Ar1, A2and Ar3 is substituted with -halogen, —OR′, —OC(O)R′, —NR′R″, —SR′, —R′, —CN, —NO2, —CO2R′, —CONR′R″, —C(O)R′, —OC(O)NR′R″, —NR″C(O)R′, —NRC″C(O)2R′, —NR′—C(O)NR″R′″, —NH—C(NH2)NH, —NR′C(NH2)NH, —NH—C(NH2)═NR′, —S(O)R′, —S(O)2R′, —S(O)2NR′R″, —N3, —CH(Ph)2, perfluoro(C1-C4)alkoxy, and perfluoro(C1-C4)alkyl, in a number ranging from zero to the total number of open valences on the aromatic ring system;
• and where R′, R″ and R′″ are independently selected from hydrogen, (C1-C8)alkyl and heteroalkyl, unsubstituted aryl and heteroaryl, (unsubstituted aryl)-(C1-C4)alkyl, and (unsubstituted aryl)oxy-(C1-C4)alkyl.