Nucleic acid labeling compounds

• US 7,282,327 B2
• Filed: 08/15/2003
• Issued: 10/16/2007
• Est. Priority Date: 01/23/1996
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Barone, Anthony D., McGall, Glenn H.
• Primary Examiner(s): Jiang; Shaojia
• Application Number:
  US10/641,677
• Publication Number:
  US 20040101892A1
• Time in Patent Office: 1,523 Days
• Field of Search: 435/6, 536/23.1, 536/25.1
• US Class Current: 435/6.18
• CPC Class Codes: A61K 47/557 the modifying agent being biotin
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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

Abstract

Compounds of the following structure:

are useful as nucleic labeling compounds.

Claims

1. A nucleic acid labeling compound of the following structure:

2. A nucleic acid labeling compound according to claim 1 wherein A is selected from the group consisting of H, α

-thiotriphosphate and H₄O₉P₃—

;

Y is H or OH;

Z is H or OR₁₀, wherein R₁₀ is H, alkyl or aryl.

3. A nucleic acid labeling compound according to claim 2 wherein Q is selected from the group consisting of colloidal gold, fluorescein, texas red, rhodamine, green fluorescent protein, 1-aminonaphthalene, 2-aminonaphthalene, p,p′

-diaminostilbenes, pyrenes, quatemary phenanthridine salts, 9-aminoacridines, p,p′

-diaminobenzophenone imines, anthracenes,oxacarbocyanines, marocyanine, 3-amino aminoequilenin, perylene,bisbenzoxazole, bis-p-oxazolyl benzene, 1,2-benzophenazin, retinol, bis-3-aminopridinium salts, hellebrigenin, tetracycline, sterophenol, benzimidazolyl phenylamine, 2-oxo-3-chromen, indole, xanthen, 7-hydroxycoumarin, phenoxazine, salycilate, strophanthidin, porphyrins, triarylmethanes, flavin, xanthene dyes, rhodamine dyes, cyanine dyes, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene dyes, phycobil iprotein, dansyl chloride, 3,6-dihydroxy-9-phenylxanthhydrol, rhodamineisothyocyanate, N-phenyl-1-amino-8-sulfonatonaphthalene, N-phenyl-2-amino-6-sulfonatonaphthalene, 4-acetamido-4-isothiocyanatostilbene-2,2′

-disulfonic acid, pyrene-3-sulfonic acid, 2-toluidinonaphthalene-6-sulphonate, N-phenyl, N-methyl-2-aminonaphthalene-6-sulphonate, ethidium bromide, stebrine, auromine-0,2-(9′

-anthroyl)palmitate, dansyl phosphatidylethanolamin, N,N′

-dioctadecyloxacarbocycanine, N,N′

-dihexyl oxacarbocyanine, merocyanine, 4-(3′

-pyrenyl)butyrate, d-3-aminodesoxy-equilenin, 12-(9′

-anthroyl)stearate, 2-methylanthracene, 9-vinylanthracene, 2,2′

-(vinylene-p-phenylene) bisbenzoxazole, p-bis [2-(4-methyl-5-phenyl oxazolyl)]benzene, 6-dimethylamino-1,2-benzophenzin, retinol, bis (3′

-aminopyridinium)-1,10-decandiyl diiodide, sulphonaphthylhydrazone of hellibrienin, chlorotetracycline, N-(7-dimethyl amino-4-methyl-2-oxo-3-chromenyl)maleimide ,N-[p-(2-benzimidazolyl)phenyl]maleimide, N-(4-fluoranthyl)maleimide, bis(homovanillic acid), resazarin, 4-chloro-7-nitro-2,1,3-benzooxadizole, merocyanine 540, resorufin, rose bengal, and 2,4-diphenyl-3(2H)-furanone, and biotin.

4. A nucleic acid labeling compound according to claim 3 wherein Q is a biotin.

5. A nucleic acid labeling compound according to claim 3 having a first M and a second M, wherein said first M is —

NH(CH₂)_nNH—

, wherein n is an integer from 2 to 10, and said second M is —

CO(CH₂)pNH—

, wherein p is an integer from 2 to 10 and m is 2.

6. A nucleic acid labeling compound according to claim 5 wherein said first M is —

NH(CH₂)₂NH— and

said second M is —

CO(CH₂)₅NH—

.

7. A nucleic acid labeling compound according to claim 1 wherein A is a triphosphate group having appropriate counterions and Y is OH and Z is OH.

8. A nucleic acid labeling compound according to claim 7 wherein said appropriate counterions are selected from the group consisting of H⁺, Na⁺, Li⁺, K⁺, (CH₃CH₂)₃NH⁺ and NH₄⁺.

9. A method of synthesizing a labeled nucleic acid comprising attaching a nucleic acid labeling compound according to claim 1 to a nucleic acid.

10. A method of detecting a nucleic acid comprising incubating a nucleic acid derivative with a complementary probe, wherein said nucleic acid derivative is prepared by coupling a nucleic acid labeling compound according to claim 1 with a nucleic acid.

11. A method according to claim 10, wherein the probe is attached to a solid support.

12. A method according to claim 11, wherein said solid support is glass.

14. A nucleic acid labeling compound according to claim 1 wherein L is —

CH═

CH—

R₁₁, wherein R₁₁ comprises a moiety selected from the group consisting of alkyl, functionalized alkyl, alkenyl alkyl, alkynyl alkyl, amido alkyl, amino alkyl, alkoxy, amino, aryl, and thio.

15. A nucleic acid labeling compound according to claim 14 where R₁₁ is C(O)R₁₂, where R₁₂ comprises a moiety selected from the group consisting of a bond, alkyl, functionalized alkyl, alkenyl alkyl, alkynyl alkyl, amido alkyl, amino alkyl, alkoxy, amino, aryl, and thio.

18. A nucleic acid labeling compound according to claim 15, wherein R₁₂ is a bond, having a first M and a second M, wherein said first M is —

NH(CH₂)_nNH—

, wherein n is an integer from 2 to 10, and second M is —

CO(CH₂)pNH—

, wherein p is an integer from 2 to 10 and m is 2.

19. A nucleic acid labeling compound according to claim 18 wherein said first M is —

NH(CH₂)₂NH— and

said second M is —

CO(CH₂)₅NH— and

m is 2, having the structure;

13. A nucleic acid labeling compound having the formula:

16. A nucleic acid labeling according to claim 13 wherein A is selected from the group consisting of H, α

-thiotriphosphate, and H₄O₉P₃—

;

Y is H or OH;

Z is H or OR₁₀, wherein R₁₀ is H, alkyl or aryl.

17. A nucleic acid labeling compound according to claim 13 wherein Q is selected from the group consisting of colloidal gold, fluorescein, texas red, rhodamine, green fluorescent protein, 1-aminonaphthalene, 2-aminonaphthalene, p,p′

-diaminostilbenes, pyrenes, quatemary phenanthridine salts, 9-aminoacridines, p,p′

-diaminobenzophenone imines, anthracenes, oxacarbocyanines, marocyanine, 3-amino aminoequilenin, perylene,bisbenzoxazole, bis-p-oxazolyl benzene, 1,2-benzophenazin, retinol, bis-3-aminopridinium salts, hellebrigenin, tetracycline, sterophenol, benzimidazolyl phenylamine, 2-oxo-3-chromen, indole, xanthen, 7-hydroxycoumarin, phenoxazine, salycilate, strophanthidin, porphyrins, triarylmethanes, flavin, xanthene dyes, rhodamine dyes, cyanine dyes, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene dyes, phycobil iprotein, dansyl chloride, 3,6-dihydroxy-9-phenylxanthhydrol, rhodamineisothyocyanate, N-phenyl-1-amino-8-sulfonatonaphthalene, N-phenyl-2-amino-6-sulfonatonaphthalene, 4-acetamido-4-isothiocyanatostilbene-2,2′

-disulfonic acid, pyrene-3-sulfonic acid, 2-toluidinonaphthalene-6-sulphonate, N-phenyl, N-methyl-2-aminonaphthalene-6-sulphonate, ethidium bromide, stebrine, auromine-0,2-(9′

-anthroyl)palmitate, dansyl phosphatidylethanolamin, N,N′

-dioctadecyloxacarbocycanine, N,N′

-dihexyl oxacarbocyanine, merocyanine, 4-(3′

-pyrenyl)butyrate, d-3-aminodesoxy-equilenin, 12-(9′

-anthroyl)stearate, 2-methylanthracene, 9-vinylanthracene, 2,2′

-(vinylene-p-phenylene) bisbenzoxazole, p-bis [2-(4-methyl-5-phenyl oxazolyl)]benzene, 6-dimethylamino-1,2-benzophenzin, retinol, bis (3′

-aminopyridinium)-1,10-decandiyl diiodide, sulphonaphthylhydrazone of hellibrienin, chlorotetracycline, N-(7-dimethyl amino-4-methyl-2-oxo-3-chromenyl)maleimide, N-[p-(2-benzimidazolyl)phenyl]maleimide, N-(4-fluoranthyl)maleimide, bis(homovanillic acid), resazarin, 4-chloro-7-nitro-2,1,3-benzooxadizole, merocyanine 540, resorufin, rose bengal, and 2,4-diphenyl-3(2H)-furanone, and biotin.

20. A nucleic acid labeling compound according to claim 13 wherein A is a triphosphate group having appropriate counterions.

21. A nucleic acid labeling compound according to claim 20 wherein said appropriate counterion is selected from the group consisting of H⁺, Na⁺, Li⁺, K⁺, (CH₃)₃NH⁺ and NH₄⁺.

22. A nucleic acid labeling compound according to claim 13 wherein L is —

CH═

CH—

R₁₁, where R₁₁ comprises a moiety selected from the group consisting of alkyl, functionalized alkyl, alkenyl alkyl, alkynyl alkyl, amido alkyl, amino alkyl, alkoxy, amino, aryl, and thio.

23. A nucleic acid labeling compound according to claim 13 where R₁₁ is C(O)R₁₂, where R₁₂ comprises a moiety selected from the group consisting of a bond, alkyl, functionalized alkyl, alkenyl alkyl, alkynyl alkyl, amido alkyl, amino alkyl, alkoxy, amino, aryl, and thio.

24. A nucleic acid labeling compound according to claim 13 wherein A is selected from the group consisting of H, α

-thiotriphosphate, and

H₄O₉P₃;

Y is H or OH;

Z is H or OR₁₀, wherein R₁₀ is H, alkyl or aryl.

25. A nucleic acid labeling compound according to claim 13 wherein Q is selected from the group consisting of colloidal gold, fluorescein, texas red, rhodamine, green fluorescent protein, 1-aminonaphthalene, 2-aminonaphthalene, p,p′

-diaminostilbenes, pyrenes, quatemary phenanthridine salts, 9-aminoacridines, p,p′

-diaminobenzophenone imines, anthracenes, oxacarbocyanines, marocyanine, 3-amino aminoequilenin, perylene,bisbenzoxazole, bis-p-oxazolyl benzene, 1,2-benzophenazin, retinol, bis-3-aminopridinium salts, hellebrigenin, tetracycline, sterophenol, benzimidazolyl phenylamine, 2-oxo-3-chromen, indole, xanthen, 7-hydroxycoumarin, phenoxazine, salycilate, strophanthidin, porphyrins, triarylmethanes, flavin, xanthene dyes, rhodamine dyes, cyanine dyes, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene dyes, phycobiliprotein, dansyl chloride, 3,6-dihydroxy-9-phenylxanthhydrol, rhodamineisothyocyanate, N-phenyl-1-amino-8-sulfonatonaphthalene, N-phenyl-2-amino-6-sulfonatonaphthalene, 4-acetamido-4-isothiocyanatostilbene-2,2′

-disulfonic acid, pyrene-3-sulfonic acid, 2-toluidinonaphthalene-6-sulphonate, N-phenyl, N-methyl-2-aminonaphthalene-6-sulphonate, ethidium bromide, stebrine, auromine-0,2-(9′

-anthroyl)palmitate, dansyl phosphatidylethanolamin, N,N′

-dioctadecyloxacarbocycanine, N,N′

-dihexyl oxacarbocyanine, merocyanine, 4-(3′

-pyrenyl)butyrate, d-3-aminodesoxy-equilenin, 12-(9′

-anthroyl)stearate, 2-methylanthracene, 9-vinylanthracene, 2,2′

-(vinylene-p-phenylene) bisbenzoxazole, p-bis [2-(4-methyl-5-phenyl oxazolyl)]benzene, 6-dimethylamino-1,2-benzophenzin, retinol, bis (3′

-aminopyridinium)-1,10-decandiyl diiodide, sulphonaphthylhydrazone of hellibrienin, chlorotetracycline, N-(7-dimethyl amino-4-methyl-2-oxo-3-chromenyl)maleimide, N-[p-(2-benzimidazolyl)phenyl]maleimide, N-(4-fluoranthyl)maleimide, bis(homovanillic acid), resazarin, 4-chloro-7-nitro-2,1,3-benzooxadizole, merocyanine 540, resorufin, rose bengal, and 2,4-diphenyl-3(2H)-furanone, and biotin.

26. A nucleic acid labeling compound according to claim 23, wherein R₁₂ is a bond, having a first M and a second M wherein said first M is —

NH(CH₂)_n,NH—

, wherein n is an integer from 2 to 10, and said second M is —

CO(CH₂)_pNH—

, wherein p is an integer from 2 to 10 and m is 2.

27. A nucleic acid labeling compound according to claim 24 wherein A is a triphosphate group having an appropriate counterion.

28. A nucleic acid labeling compound according to claim 24 wherein said appropriate counterion is selected from the group consisting of H⁺, Na⁺, Li⁺, K⁺, (CH₃)₃NH⁺ and NH₄⁺.

29. A nucleic acid derivative produced by coupling a nucleic acid labeling compound according to claim 24 with a nucleic acid.

30. A hybridization product comprising the nucleic acid derivative according to claim 29 bound to a complementary probe.

31. The hybridization product according to claim 30, wherein the complementary probe is attached to a solid support.

32. The hybridization product according to claim 31 wherein said solid support is glass.