Fluorescent quenching detection reagents and methods

1. An oligonucleotide probe compound having the formula:

wherein

Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group, and one of Ar 1 and Ar 2 is directly or indirectly substituted with a substituted aryl group (Ar 3 ), where Ar 3 extends the resonance ability of the Ar 1 —N═N—Ar 2 aromatic system and thereby increases the wavelength absorbance maximum of the compound;

MGB is a minor groove binding group;

FL is a fluorescent group having an emission maxima in the region from about 400 to about 900 nm;

K is a cyclic or acyclic linking group having from 1 to 30 backbone atoms selected from C, N, O, S and P;

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-B] n is a natural or modified oligonucleotide where the subscript n is an integer of from 4 to 100; and

the subscript zz is 0 or 1.

2. An oligonucleotide probe compound having the formula:

wherein

Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group;

MGB is a minor groove binding group;

FL is a fluorescent group having an emission maxima in the region from about 400 to about 900 nm;

K is a cyclic or acyclic linking group having from 1 to 30 backbone atoms selected from C, N, O, S and P;

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, where W modulates the absorption wavelength of the Ar 1 —N═N—Ar 2 moiety to increase the wavelength absorbance of the compound;

[A-B] n is a natural or modified oligonucleotide where the subscript n is an integer of from 4 to 100; and

the subscript zz is 0 or 1.

3. A probe compound for a hybridization assay comprising the formula FL-ODN—(W) d -Q wherein

FL is a fluorophore with an emission wavelength in the range of about 300 to about 800 nm, ODN is an oligonucleotide;

W is a linker group that has from 3 to 100 atoms other than hydrogen atoms, selected from C, N, O, S, P and Si, and is cyclic, acyclic, aromatic or a combination thereof, and d is 0 or 1;

Q is a quencher moiety comprising the structure —Ar 1 —N═N—Ar 2 wherein Ar 1 is joined to either ODN or W, and Q has a broader absorbance range than dabcyl (4-{[4-(dimethylamino)phenyl]diazenyl}benzoyl, absorbance max=453 nm), wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group.

4. A compound of claim 3 wherein one of Ar 1 and Ar 2 is directly or indirectly substituted with a substituted aryl group (Ar 3 ), where Ar 3 extends the resonance ability of the Ar 1 —N═N—Ar 2 aromatic system and thereby increases the wavelength absorbance maximum of the compound.

5. A compound of the formula

wherein

a solid support;

L is a cleavable linker;

q is 0 or 1;

MGB is a minor groove binder;

r is 0 or-1;

W is a linker group that has from 3 to 100 atoms other than hydrogen atoms, selected from C, N, O, S, P and Si, and is cyclic, acyclic, aromatic or a combination thereof;

Q is a quencher moiety comprising the formula Ar 1 —N═N—Ar 2 where Ar 1 is joined to W and wherein Ar 1 and Ar 2 are each independently a substituted or unsubstituted aryl group, and one of Ar 1 and Ar 2 is directly or indirectly substituted with a substituted aryl group (Ar 3 ), where Ar 3 extends the resonance ability of the Ar 1 —N═N—Ar 2 aromatic system and thereby increases the wavelength absorbance maximum of the compound; and

Y is selected from —O-J 1 where J 1 is a hydroxyl protecting group;

an oligonucleotide (—ODN); and

an oligonucleotide-fluorophore conjugate (—ODN-FL).