Fluorescent quenching detection reagents and methods

An oligonucleotide conjugate of the formula

• wherein R0, R1, R2, R3 and R4 are independently —H, halogen,—O(CH2)n*CH3, —(CH2)n*CH3 where n*=0 to 5, —NO2, —SO3, —N[(CH2)n′CH3]2 where n′=0 to 5 or —CN;
• FL is a fluorophore moiety with emission wavelengths in the range of about 300 to about 800 nm;
• K is a linker from 1 to approximately 30 atoms in length;
• [A-B]n symbolizes an ODN, DNA, RNA or PNA or any combination thereof, where A is the sugar phosphate backbone where the sugar and the phosphate may independently be modified;
• B is a heterocyclic base, where B is independently selected from purine, pyrimidine, pyrazolo[3,4-d]pyrimidine, 7-substituted pyrazolo[3,4-d]pyrimidine-, 7-deazapurine, 7-substituted 7-deazapurine, and modified purine- and pyrimidine-bases, and where the DNA, RNA, PNA or ODN can include any combinations of these bases,
• and n, the number of nucleotide units in said DNA, RNA, PNA or ODN, is from about 5 to 100;
• W is a linker of a length of 1 to approximately 30 atoms, selected from the group consisting of C, O, N, S, and P;
• and
• m is an integer having the values of 1 to 20.

An oligonucleotide conjugate having the formula

• FL-ODN-MGB
• where ODN is an oligonucleotide or nucleic acid;
• MGB is minor groove binder moiety covalently attached to the ODN moiety or to the quencher moiety through a linker having the length of 0 to approximately 30 atoms;
• FL is a fluorophore covalently attached to the ODN through a linker having the length of 0 to approximately 30 atoms, said fluorophore moiety having the structure:
• R10 and R11 independently are H, —OR12, —NH(R13), —N(R12)2, halogen,—O(CH2)nCH3, —(CH2)nCH3, —NO2, —SO3, —C(═O)NH2, —N[(CH2)nCH3]2 or —CN where n=0 to 5 and R12 and R13 are each independently alkyl of 1 to 10 carbons or alkanoyl of 1 to 10 carbons;
• and
• the valence bond designated a symbolizes covalent attachment of the fluorophore to the linker.