Quenching oligonucleotides

• US 6,323,337 B1
• Filed: 05/12/2000
• Issued: 11/27/2001
• Est. Priority Date: 05/12/2000
• Status: Expired due to Term

• Current Assignee: Molecular Probes Incorporated (Thermo Fisher Scientific Incorporated)
• Original Assignee: Molecular Probes Incorporated (Thermo Fisher Scientific Incorporated)
• Inventors: Haugland, Richard P., Singer, Victoria L.
• Primary Examiner(s): Houtteman, Scott W.
• Application Number:
  US09/570,343
• Time in Patent Office: 564 Days
• Field of Search: 435/6, 536/26.6
• US Class Current: 536/26.6
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2563/103 luminescence
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels

Abstract

The invention relates to oligonucleotides labeled with an energy transfer acceptor useful in conjunction with fluorescent nucleic acid stains. The resulting oligonucleotides are useful for decreasing background fluorescence during amplification assays and in ligation assays, and for detecting hybridization.

Claims

1. A method for decreasing detectable luminescence of nucleic acid stain molecules that are noncovalently associated with an oligonucleotide, said method comprising:

a) preparing the oligonucleotide by covalently attaching a quenching moiety to the oligonucleotide, wherein said quenching moiety is essentially nonfluorescent;

b) combining said oligonucleotide with a plurality of nucleic acid stain molecules such that the nucleic acid stain molecules associate noncovalently with said oligonucleotide;

wherein said nucleic acid stain molecules normally exhibit a luminescence when associated noncovalently with nucleic acids, and said nucleic acid stain molecules undergo energy transfer to said quenching moiety, such that said luminescence is detectably decreased.

2. A method, as claimed in claim 1, wherein said nucleic acid stain is a phenanthridinium dye, an acridine dye, an indole dye, an imidazole dye, a cyanine dye, or a homo- or heterodimer thereof.

3. A method, as claimed in claim 1, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye.

4. A method, as claimed in claim 1, wherein said oligonucleotide has 6-60 bases.

5. A method, as claimed in claim 1, wherein the oligonucleotide is a primer useful for the amplification of a nucleic acid.

6. A method, as claimed in claim 5, wherein the amplification of the nucleic acid results from a polymerase chain reaction.

7. A method, as claimed in claim 1, wherein the oligonucleotide possesses secondary structure, tertiary structure, or both secondary and tertiary structure.

8. A method, as claimed in claim 1, wherein said covalently bound quenching moiety is a xanthene dye, a phenoxazine dye, a triarylmethane dye, or an azo dye.

9. A method, as claimed in claim 8, wherein said covalently bound quenching moiety is an N-aryl rhodamine dye, an N-heteroaryl rhodamine dye, an N-aryl rhodol dye, an N-aryl phenoxazine dye, a 4′

,5′

-dialkoxyluorescein dye, a triarylmethane dye, or an azo dye.

10. A method, as claimed in claim 1, wherein said covalently bound quenching moiety is an N,N′

-diaryl rhodamine dye.

58. A method, as claimed in claim 5, wherein said nucleic acid stain is a phenanthridinium dye, an acridine dye, an indole dye, an imidazole dye, a cyanine dye, or a homo- or heterodimer thereof;

and said quenching moiety is a xanthene dye, a phenoxazine dye, a triarylmethane dye, or an azo dye.

59. A method, as claimed in claim 6, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye and said quenching moiety is a xanthene dye.

60. A method, as claimed in claim 10, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye.

11. A method of amplifying a target nucleic acid sequence, comprising:

a) preparing a reaction mixture comprising one or more polymerase enzymes, the target nucleic acid sequence, and a quenching primer;

wherein said quenching primer is an oligonucleotide having 6-60 nucleotides that is covalently bound to a quenching moiety;

b) incubating said reaction mixture under conditions such that the target nucleic acid sequence is amplified to produce an amplification product mixture;

c) adding a nucleic acid stain before, during, or after said incubating step, such that the nucleic acid stain associates noncovalently with the nucleic acids present in said amplification product mixture;

wherein said nucleic acid stain normally exhibits a luminescence when associated noncovalently with nucleic acids, and the luminescence of said nucleic acid stain that is associated with said quenching primer or a dimer of said quenching primer is detectably quenched; and

d) illuminating said amplification product mixture to yield a luminescence response.

12. A method, as claimed in claim 11, further comprising quantitating said resulting amplification products.

13. A method, as claimed in claim 11, wherein said amplification product mixture is electrophoretically separated.

14. A method, as claimed in claim 11, wherein said polymerase enzyme is a DNA polymerase, an RNA polymerase, a reverse transcriptase, or a combination thereof.

15. A method, as claimed in claim 11, wherein said luminescence response of said amplification product mixture is used to determine the presence or activity of the amplification enzyme.

16. A method, as claimed in claim 11, wherein said luminescence response of said amplification product mixture is used to determine the rate or extent of amplification.

17. A method, as claimed in claim 11, wherein the covalently bound quenching moiety is a xanthene, a coumarin, naphthalene, an anthracene, a pyrene, a stilbene, a carbostyryl, a pyridine, a quinoline, an acridine, a cyanine, a polyazaindacene, an oxazine, a styryl, or an azo dye.

18. A method, as claimed in claim 11, wherein said covalently bound quenching moiety is a xanthene dye, a phenoxazine dye, a triarylmethane dye, or an azo dye.

19. A method, as claimed in claim 11, wherein said covalently bound quenching moiety is an N,N′

-diaryl rhodamine dye or a 4′

,5′

-dialkoxyfluorescein dye.

61. A method, as claimed in claim 19, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye.

20. A method of elongating an oligonucleotide comprising:

a) preparing a mixture comprising an elongation enzyme and a quenching primer;

wherein said quenching primer is an oligonucleotide having 6-60 nucleotides that is covalently bound to a quenching moiety;

b) incubating said mixture under conditions such that the quenching primer is extended to produce an elongation product;

c) adding a nucleic acid stain before, during, or after said incubating step, such that the nucleic acid stain associates noncovalently with the nucleic acids present in said mixture;

wherein said nucleic acid stain normally exhibits a luminescence when associated noncovalently with nucleic acids, and said luminescence due to nucleic acid stain associated with said primer or a dimer of said primer is detectably quenched; and

d) illuminating said mixture to yield a luminescence response.

21. A method, as claimed in claim 20, further comprising quantitating said resulting elongation products.

22. A method, as claimed in claim 20, wherein said elongation enzyme is a terminal transferase.

23. A method, as claimed in claim 20, wherein said elongation enzyme is a telometase.

24. A method, as claimed in claim 20 wherein said luminescence response of said mixture is used to determine the presence or activity of the elongation enzyme.

25. A method, as claimed in claim 20, wherein said luminescence response of said mixture is used to determine the extent or rate of elongation.

26. A method, as claimed in claim 20, wherein said quenching moiety is a xanthene dye, a triarylmethane dye, or an azo dye.

27. A method, as claimed in claim 20, wherein said quenching moiety is an N-aryl rhodamine dye, an N-heteroaryl rhodamine dye, an N-aryl rhodol dye, and N-aryl phenoxazine dye, or an azo dye.

62. A method, as claimed in claim 27, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye, and wherein said luminescence response of the mixrure is used to determine presence or activity of the elongation enzyme, or extent or rate of elongdtion.

28. A method of assaying for a protein, comprising:

a) preparing a mixture comprising

i) a quenching oligonucleotide, wherein said quenching oligonucleotide is an oligonucleotide having 6-60 nucleotides that is covalently bound to a quenching moiety; and

ii) a nucleic acid stain, wherein said nucleic acid stain normally exhibits a luminescence when associated noncovalently with nucleic acids;

such that said nucleic acid stain associates noncovalently with the oligonucleotide, and the luminescence due to the nucleic acid stain associated with said oligonucleotide is detectably quenched;

c) adding a sample that contains or is thought to contain said protein to said mixture;

d) incubating the mixture for a time sufficient for said protein to interact with said oligonucleotide;

e) illuminating said mixture to yield a luminescence response; and

f) correlating said luminescence response with the presence or activity of said protein.

29. A method, as claimed in claim 28, wherein said protein is an enzyme.

30. A method, as claimed in claim 29, wherein said enzyme is a nuclease enzyme or a ligase enzyme.

31. A method, as claimed in claim 28, wherein said protein is a nucleic acid binding factor.

63. A method, as claimed in claim 28, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye and said quenching moiety is an N-aryl rhodamine dye.

32. A composition, comprising

an oligonucleotide having 6-60 bases;

a quenching moiety that is covalently bound to said oligonucleotide, wherein said quenching moiety is essentially nonfluorescent; and

a plurality of nucleic acid stain molecules, which may be the same or different, that are associated non-covalently with said oligonucleotide;

wherein said nucleic acid stain molecules normally exhibit a luminescence when associated noncovalently with nucleic acids;

wherein at least one of said nucleic acid stain molecules undergoes energy transfer of said luminescence to said quenching moiety.

33. A composition, as claimed in claim 32, wherein the quenching moiety has a maximum absorbance at about 450 to about 650 nm.

34. A composition, as claimed in claim 32, wherein the quenching moiety is a xanthene dye, a triarylmethane dye, or an azo dye.

35. A composition, as claimed in claim 34, wherein the covalently bound quenching moiety is a 4′

,5′

-dialkoxyfiluorescein or a triarylmethane dye.

36. A composition, as claimed in claim 35, wherein said quenching moiety has the formula

wherein

R¹ is H, or R¹ taken in combination with R² is a fuised six-membered aromatic ring;

R² and R⁵ are independently H, F, Cl, Br, I, CN;

or C₁-C₁₈ alkyl, or C₁-C₁₈ alkoxy, where each alkyl or alkoxy is optionally further substituted by F, Cl, Br, I, a carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alcohol;

or —

SO₃X where X is H or a counterion;

or R² taken in combination with R¹ is a fused six-membered aromatic ring;

or R⁵ taken in combination with R⁶ is a fused six-membered aromatic ring;

R³ and R⁴ are independently C₁-C₆ alkoxy, the alkyl portions of which are linear or branched, saturated or unsaturated;

R⁶ is H, or R⁶ taken in combination with R⁵ is a fused six-membered aromatic ring;

R¹⁰ is H, CN, a carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alcohol;

or R¹⁰ is a saturated or unsaturated C₁-C₁₈ alkyl that is optionally substituted one or more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alcohol, —

SO₃X, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;

or R¹⁰ has the formula

 

where R¹², R¹³, R¹⁴, R¹⁵ and R¹⁶ are independently H, F, Cl, Br, I, —

SO₃X, a carboxylic acid, a salt of carboxylic acid, CN, hydroxy, amino, hydrazino;

or C₁-C₁₈ alkyl, C₁-C₁₈ alkoxy, C₁-C₁₈ alkylthio, C₁-C₁₈ alkanoylamino, C₁-C₁₈ alkylaminocarbonyl, C₂-C₃₆ dialkylaminocarbonyl, C₁-C₁₈ alkyloxycarbonyl, or C₆-C₁₈ arylcarboxamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alcohol, —

SO₃X, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;

or one pair of adjacent substituents R₁₃ and R¹⁴, R¹⁴ and R¹⁵ or R¹⁵ and R¹⁶, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, or a salt of carboxylic acid;

or one of R¹², R¹³, R¹⁴, R¹⁵ and R¹⁶ is a covalent linkage L;

provided that at least one of R¹⁰, R¹², R¹³, R¹⁴, R¹⁵, R¹⁶, R¹⁸, or R¹⁹ is a covalent linkage to said oligonucleotide, L, wherein L is a single covalent bond, or a linear or branched, cyclic or heterocyclic, saturated or unsaturated covalent linkage having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds.

37. A composition, as claimed in claim 35, wherein the covalently bound quenching moiety is a triarylmethane dye having the formula

wherein

R¹, R², R³, R⁴, R⁵, R⁶, R⁷, and R⁸ are independently H, F, Cl, Br, I, CN;

or C₁-C₁₈ alkyl, or C₁-C₁₈ alkoxy, where each alkyl or alkoxy is optionally further substituted by F, Cl, Br, I, a carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alcohol;

or —

SO₃X where X is H or a counterion;

or R¹ and R², R³ and R⁴, R⁵ and R⁶, or R⁷ and R⁸, taken in combination form a fused six-membered aromatic ring;

A is OH or NR¹⁴R¹⁵;

wherein R¹⁴ and R¹⁵ are independently H, C₁-C₆ alkyl, C₁-C₆ carboxyalkyl, C₁-C₆ sulfoalkyl, a salt of C₁-C₆ carboxyalkyl, or a salt of C₁-C₆ sulfoalkyl, wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or R¹⁴ taken in combination with R¹⁵ forms a saturated 5- or 6-membered heterocycle that is optionally further substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alkyl, or a covalent linkage L;

or R¹⁴ in combination with R², or R¹⁵ in combination with R³, or both, form a 5- or 6-membered ring that is saturated or unsaturated, and is optionally substituted by one or more C₁-C₆ alkyls or —

CH₂SO₃X;

B is O or N⁺R¹⁶R¹⁷;

wherein R¹⁶ and R¹⁷ are independently H, C₁-C₆ alkyl, C₁-C₆ carboxyalkyl, C₁-C₆ sulfoalkyl, a salt of C₁-C₆ carboxyalkyl, or a salt of C₁-C₆ sulfoalkyl, wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or R¹⁶ taken in combination with R¹⁷ forms a saturated 5- or 6-membered heterocycle that is optionally further substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or R¹⁶ in combination with R⁶, or R¹⁷ in combination with R⁷, or both, form a 5- or 6-membered ring that is saturated or unsaturated, and is optionally substituted by one or more C₁-C₆ alkyls or —

CH₂SO₃X;

where R⁹, R¹⁰, R¹¹, R¹² and R¹³ are independently H, F, Cl, Br, I, —

SO₃X, a carboxylic acid, a salt of carboxylic acid, CN, hydroxy, amino, hydrazino;

or C₁-C₁₈ alkyl, C₁-C₁₈ alkoxy, C₁-C₁₈ alkylthio, C₁-C₁₈ alkanoylamino, C₁-C₁₈ alkylaminocarbonyl, C₂-C₃₆ dialkylaminocarbonyl, C₁-C₁₈ alkyloxycarbonyl, or C₆-C₁₈ arylcarboxamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alcohol, —

SO₃X, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;

or one pair of adjacent substituents R¹⁰ and R¹¹, R¹¹ and R¹² or R¹² and R¹³, when taken in combination, form a fuised 6-membered aromatic ring that is optionally further substituted by carboxylic acid, or a salt of carboxylic acid;

or one of R⁹, R¹⁰R¹¹, R¹², R¹³ and R¹⁴ is a covalent linkage L;

provided that at least one of R¹⁴, R¹⁵, R¹⁶, R¹⁷, R⁹, R¹⁰, R¹¹, R¹², R₁₃, R¹⁴, or R¹⁵ is a covalent linkage to said oligonucleotide, L, wherein L is a single covalent bond, or a linear or branched, cyclic or heterocyclic, saturated or unsaturated covalent linkage having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds.

38. A composition, as claimed in claim 34, wherein the covalently bound quenching moiety has the formula

wherein

R¹ is H, or R¹ taken in combination with R² is a fused six-membered aromatic ring;

R², R³, R⁴ and R⁵ are independently H, F, Cl, Br, I, CN;

or C₁-C₁₈ alkyl, or C₁-C₁₈ alkoxy, where each alkyl or alkoxy is optionally further substituted by F, Cl, Br, I, a carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alcohol;

or —

SO₃X where X is H or a counterion;

or R² taken in combination with R¹ is a fused six-membered aromatic ring;

or R⁵ taken in combination with R⁶ is a fused six-membered aromatic ring;

R⁶ is H, or R⁶ taken in combination with R⁵ is a fused six-membered aromatic ring;

R⁸ and R⁹ are independently H, C₁-C₆ alkyl, C₁-C₆ carboxyalkyl, C₁-C₆ sulfoalkyl, a salt of C₁-C₆ carboxyalkyl, or a salt of C₁-C₆ sulfoalkyl, wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or one or more of R⁸ and R⁹ is a Q moiety;

or R⁸ taken in combination with R⁹ forms a saturated 5- or 6-membered heterocycle that is optionally fused to a Q moiety and optionally further substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alkyl, or a covalent linkage L;

or R⁸ in combination with R², or R⁹ in combination with R³, or both, form a 5- or 6-membered ring that is saturated or unsaturated, and is optionally substituted by one or more C₁-C₆ alkyls or —

CH₂SO₃X;

wherein each Q moiety is 1-4 fused aromatic or heteroaromatic rings that is optionally substituted by halogen, cyano, sulfo, alkali or ammonium salt of sulfo, carboxy, alkali or ammonium salt of carboxy, nitro, alkyl, perfluoroalkyl, alkoxy, alkylthio, amino, monoalkylamino, dialkylamino;

alkylamidol;

or a covalent linkage L;

wherein each heteroaromatic ring in Q is a 5- or 6-membered aromatic heterocycle having 1 to 3 heteroatoms selected from the group consisting of O, N or S in any combination; and

K is O or N⁺R¹⁸R¹⁹;

wherein R¹⁸ and R¹⁹ are independently H, C₁-C₆ alkyl, C₁-C₆ carboxyalkyl, C₁-C₆ sulfoalkyl, a salt of C₁-C₆ carboxyalkyl, or a salt of C₁-C₆ sulfoalkyl, wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, or a w carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or one or more of R¹⁸ and R¹⁹ is a Q moiety;

or R¹⁸ taken in combination with R¹⁹ forms a saturated 5- or 6-membered heterocycle that is a piperidine, or a pyrrolidine that is optionally fused to a Q moiety, and optionally further substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or R¹⁸ in combination with R⁴, or R¹⁹ in combination with R⁵, or both, form a 5- or 6-membered ring that is saturated or unsaturated, and is optionally substituted by one or more C₁-C₆ alkyls or —

CH₂SO₃X moieties;

R¹⁰ is H, CN, a carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alcohol;

or R¹⁰ is a saturated or unsaturated C₁-C₁₈ alkyl that is optionally substituted one more times by F, Cl, Br, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester a C₁-C₆ alcohol, —

SO₃X, amino, alkylamino, or dialkylamino, the alkyl groups of which have 1-6 carbons;

or R¹⁰ has the formula

 

where R¹², R¹³, R¹⁴, R¹⁵ and R¹⁶ are independently H, F, Cl, Br, I, —

SO₃X;

a carboxylic acid, a salt of carboxylic acid, CN, hydroxy, amino, hydrazino;

or C₁-C₁₈ alkyl, C₁-C₁₈ alkoxy, C₁-C₁₈ alkylthio, C₁-C₁₈ alkanoylamino, C₁-C₁₈ alkylaminocarbonyl, C₂-C₃₆ dialkylaminocarbonyl, C₁-C₁₈ alkyloxycarbonyl, or C₆-C₁₈ arylcarboxamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alcohol, —

SO₃X, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;

or one pair of adjacent substituents R¹³ and R¹⁴, R¹⁴ and R¹⁵ or R¹⁵ and R¹⁶, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, or a salt of carboxylic acid;

or one of R¹², R¹³, R¹⁴, R¹⁵ and R¹⁶ is a covalent linkage L;

provided that at least one of R⁸, R⁹, R¹⁸, and R¹⁹ is, or is fused to, a Q moiety; and

further provided that at least one of R⁸, R⁹, R¹², R¹³, R¹⁴, R¹⁵, R¹⁶, R¹⁸, or R¹⁹ is a covalent linkage to said oligonucleotide, L, wherein L is a single covalent bond, or a linear or branched, cyclic or heterocyclic, saturated or unsaturated covalent linkage having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds.

39. A composition, as claimed in claim 38, wherein for said covalently bound quenching moiety:

each Q moiety is a substituted or unsubstituted phenyl, naphthyl, anthracenyl, benzothiazole, benzoxazole, or benzimidazole;

K is N⁺R¹⁸R¹⁹;

R⁸═

R¹⁹ and R⁹═

R¹⁸; and

R¹⁰ has the formula

 

wherein one of R¹²-R¹⁶ is the covalent linkage L.

40. A composition, as claimed in claim 39, wherein each Q moiety is a phenyl or substituted phenyl;

and R¹² is the covalent linkage L;

wherein L is bound to the oligonucleotide at the 5′

-terminus, a base, a sugar, or a phosphate.

41. A composition, as claimed in claim 40, wherein the covalent linkage L is bound to the oligonucleotide at one or more purine or pyrimidine bases through an amide, ester, ether or thioether bond, or a transition metal complex.

42. A composition, as claimed in claim 40, wherein the covalent linkage L is bound to the oligonucleotide at the 5′

-terminus.

43. A composition, as claimed in claim 32, further comprising a second oligonucleotide that is hybridized to said oligonucleotide.

44. A composition, as claimed in claim 32, wherein the nucleic acid stain is a monomeric cyanine dye, a dimeric cyanine dye, a phenanthridinium dye, an acridine dye, an indole dye, or a Hoechst dye.

45. A composition, as claimed in claim 42, wherein the nucleic acid stain is Hoechst 33258, Hoechst 33342, Hoechst 34580, ethidium, ethidium dimer, propidium, aminoactinomycin, DAPI, or acridine orange.

46. A composition, as claimed in claim 42, wherein the nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye.

47. A composition, as claimed in claim 44, wherein the nucleic acid stain exhibits a maximum absorption at from about 350 nm to about 520 nm when associated noncovalently with a nucleic acid.

48. A composition, as claimed in claim 32, further comprising additional nucleotides covalently attached at the 3′

-terminus of said oligonucleotide.

49. A composition, as claimed in claim 32, wherein said oligonucleotide is covalently bound to one or more additional quenching moieties, that may be the same or different.

50. A kit, comprising:

a) a nucleic acid stain that normally exhibits a luminescence when associated noncovalently with nucleic acids; and

b) an oligonucleotide having 6-60 bases that is covalently bound to a quenching moiety capable of accepting energy transfer of said luminescence from said nucleic acid stain, wherein said quenching moiety is essentially nonfluorescent.

51. A kit, as claimed in claim 50, wherein said quenching moiety is a xanthene dye, a phenoxazine dye, a triarylmethane dye, or an azo dye.

52. A kit, as claimed in claim 51, wherein said quenching moiety is an N-aryl rhodamine dye, an N-heteroaryl rhodamine dye, an N-aryl rhodol dye, an N-aryl phenoxazine dye, a 4′

,5′

-dialkoxyfluorescein dye, a triarylmethane dye, or an azo dye.

53. A kit, as claimed in claim 50, wherein said quenching moiety has the formula

wherein

R¹ is H, or R¹ taken in combination with R² is a fused six-membered aromatic ring;

R², R³, R⁴ and R⁵ are independently H, F, Cl, Br, I, CN;

or C₁-C₁₈ alkyl, or C₁-C₁₈ alkoxy, where each alkyl or alkoxy is optionally further substituted by F, Cl, Br, I, a carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alcohol;

or —

SO₃X where X is H or a counterion;

or R² taken in combination with R¹ is a fused six-membered aromatic ring;

or R⁵ taken in combination with R⁶ is a fused six-membered aromatic ring;

R⁶ is H, or R⁶ taken in combination with R⁵ is a fused six-membered aromatic ring;

R⁸ and R⁹ are independently H, C₁-C₆ alkyl, C₁-C₆ carboxyalkyl, C₁-C₆ sulfoalkyl, a salt of C₁-C₆ carboxyalkyl, or a salt of C₁-C₆ sulfoaLkyl, wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or one or more of R⁸ and R⁹ is a Q moiety;

or R⁸ taken in combination with R⁹ forms a saturated 5- or 6-membered heterocycle that is optionally fused to a Q moiety and optionally further substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alkyl, or a covalent linkage L;

or R⁸ in combination with R², or R⁹ in combination with R³, or both, form a 5- or 6-membered ring that is saturated or unsaturated, and is optionally substituted by one or more C₁-C₆ alkyls or —

CH₂SO₃X;

wherein each Q moiety is a substituted or unsubstituted phenyl, naphthyl, anthracenyl, benzothiazole, benzoxazole, or benzimidazole that is optionally substituted by halogen, cyano, sulfo, alkali or ammonium salt of sulfo, carboxy, alkali or ammonium salt of carboxy, nitro, alkyl, perfluoroalkyl, alkoxy, alkylthio, amino, monoalkylamino, dialkylamino;

alkylamido;

or a covalent linkage L;

wherein each heteroaromatic ring in Q is a 5- or 6-membered aromatic heterocycle having 1 to 3 heteroatoms selected from the group consisting of O, N or S in any combination; and

wherein R¹⁸ and R¹⁹ are independently H, C₁-C₆ alkyl, C₁-C₆ carboxyalkyl, C₁-C₆ sulfoalkyl, a salt of C₁-C₆ carboxyalkyl, or a salt of C₁-C₆ sulfoalkyl, wherein the alkyl portions are optionally substituted by amino, hydroxy, carboxylic acid, a salt of carboxylic acid, or a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or one or more of R¹⁸ and R¹⁹ is a Q moiety;

or R¹⁸ taken in combination with R¹⁹ forms a saturated 5- or 6-membered heterocycle that is a piperidine, or a pyrrolidine that is optionally fused to a Q moiety, and optionally further substituted by methyl, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alkyl;

or a covalent linkage L;

or R¹⁸ in combination with R⁴, or R¹⁹ in combination with R⁵, or both, form a 5- or 6-membered ring that is saturated or unsaturated, and is optionally substituted by one or more C₁-C₆ alkyls or —

CH₂SO₃X moieties;

R¹², R¹³, R¹⁴, R¹⁵ and R¹⁶ are independently H, F, Cl, Br, I, —

SO₃X, a carboxylic acid, a salt of carboxylic acid, CN, hydroxy, amino, hydrazino;

or C₁-C₁₈ alkyl, C₁-C₁₈ alkoxy, C₁-C¹⁸ alkylthio, C₁-C₁₈ alkanoylamino, C₁-C₁₈ alkylaminocarbonyl, C₂-C₃₆ dialkylaminocarbonyl, C₁-C₁₈ alkyloxycarbonyl, or C₆-C₁₈ arylcarboxamido, the alkyl or aryl portions of which are optionally substituted one or more times by F, Cl, Br, I, hydroxy, carboxylic acid, a salt of carboxylic acid, a carboxylic acid ester of a C₁-C₆ alcohol, —

SO₃X, amino, alkylamino, dialkylamino or alkoxy, the alkyl portions of each having 1-6 carbons;

or one pair of adjacent substituents R¹³ and R¹⁴, R¹⁴ and R¹⁵ or R¹⁵ and R¹⁶, when taken in combination, form a fused 6-membered aromatic ring that is optionally further substituted by carboxylic acid, or a salt of carboxylic acid;

or one of R¹², R¹³, R¹⁴, R¹⁵ and R¹⁶ is a covalent linkage L;

provided that at least one of R⁸, R⁹, R¹⁸, and R¹⁹ is, or is fused to, a Q moiety; and

further provided that at least one of R⁸, R⁹, R¹², R¹³, R¹⁴, R¹⁵, R¹⁶, R¹⁸, or R¹⁹ is a covalent linkage to said oligonucleotide, L, wherein L is a single covalent bond, or a linear or branched, cyclic or heterocyclic, saturated or unsaturated covalent linkage having 1-16 nonhydrogen atoms selected from the group consisting of C, N, P, O and S, such that the linkage contains any combination of ether, thioether, amine, ester, amide bonds;

or single, double, triple or aromatic carbon-carbon bonds;

or phosphorus-oxygen, phosphorus-sulfur bonds, nitrogen-nitrogen or nitrogen-oxygen bonds;

or aromatic or heteroaromatic bonds.

54. A kit, as claimed in claim 53, wherein each Q moiety is a phenyl or substituted phenyl;

and R¹² is the covalent linkage L;

wherein L is bound to the oligonucleotide at the 5′

-terminus, a base, a sugar, or a phosphate.

55. A kit, as claimed in claim 50, wherein the covalently bound quenching moiety is bound to the oligonucleotide at one or more purine or pyrimidine bases through an amide, ester, ether or thioether bond, or a transition metal complex.

56. A kit, as claimed in claim 50, wherein the covalently bound quenching moiety is bound to the oligonucleotide at the 5′

-terminus.

57. A kit, as claimed in claim 50, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye.

64. A kit, as claimed in claim 54, wherein said nucleic acid stain is an unsymmetrical cyanine dye or a dimer of an unsymmetrical cyanine dye.