Duplex stabilizing fluorescence quenchers for nucleic acid probes
Diaryl-azo derivatives are efficient fluorescence quenchers as well as nucleic acid duplex-stabilizing agents and are useful in oligonucleotide conjugates and probes. The oligonucleotide-quencher conjugates may be used in detection methods for nucleic acid targets.
1. An oligonucleotide conjugate comprising a fluorescence quenching compound and having the formula:
wherein ODN is an oligonucleotide;
L is a linking group;
R 1 is H, alkyl, or alkyl covalently connected to Ar 3
Ar 1 and Ar 2 are aromatic or hetero-aromatic moieties;
Ar 3 is an aromatic moiety selected from substituted or unsubstituted indole, benzofuran, benzothiophene and benzoselenophene;
R 3 is hydroxyl, a linking group, or a blocking group; and
n is from 1 to 5.
2. The oligonucleotide conjugate of claim 1 , wherein the oligonucleotide comprises a fluorophore connected to the oligonucleotide.
3. The oligonucleotide conjugate of claim 2 , wherein the fluorophore is FAM, AP525, AP559, AP593 or AP662.
4. The oligonucleotide conjugate of claim 1 , wherein the oligonucleotide comprises a minor groove binder connected to the oligonucleotide.
5. The oligonucleotide conjugate of claim 1 , wherein the oligonucleotide comprises one or more modified nucleobases or modified bases.
6. The oligonucleotide conjugate of claim 1 , wherein L is connected to the oligonucleotide at a 3′-end.
7. The oligonucleotide conjugate of claim 1 , wherein L is connected to the oligonucleotide at a 5′-end.
8. The oligonucleotide conjugate of claim 1 , wherein L is connected to the oligonucleotide at a position other than a 3′- or 5′-end.
9. The oligonucleotide conjugate of claim 1 having the formula:
wherein n is 1, 2, or 3.
10. The oligonucleotide conjugate of claim 1 having the formula:
wherein n is 1, 2, or 3.