2-aminopyrimidin-4-one nucleic acid labeling compounds

1. A nucleic acid labeling compound having the formula:

wherein A is H, monophosphate, diphosphate, triphosphate, α-thiotriphosphate, phosphoramidite, or H-phosphonate;

X is O;

Y is hydrogen, N 3 , F, OR 9 , SR 9 or NHR 9 , wherein R 9 is hydrogen, alkyl or aryl;

Z is hydrogen, N 3 , F, OR 9 , SR 9 or NHR 10 ,wherein R 10 is hydrogen, alkyl or aryl;

L is a linker moiety; selected from the group consisting of —CH═CH—R 11 , or C═C-R 11 wherein R 11 comprises a moiety selected from the group consisting of alkyl, functionalized alkyl, alkenyl alkyl, amido alkyl, amino alkyl, alkoxy, amino, aryl, and thio;

Q is selected from the group consisting of a raiolabel, a magnetic particle, colloidal gold, fluorescein, texas red, rhodamine, green fluorescent protein, luminal lophine, acridine salts, luciferin, vanadium spin labels, copper spin labels, iron spin labels, manganese spine labels, nitroxide free radicals, quinoline dyes, triarlmethane dyes, acridine dyes, colored glass beads, polystyrene beads, polypropylene beads, latex beads, biotin, horseradish peroxidase, alkaline phosphatase, 1-aminonapthalene, 2-aminonapthalene, 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, tetracyline, 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; rhodamineisothiocyanate; N-phenyl-1-amino-8-sulfonatonaphthalene; N-phenyl-2-amino-6- sulfonatonaphthanlene; 4-acetamido-4-isothiocyanatostilbene-2,2′-disulfonic acid; pyrene-3-sulfonic acid; 2-toluidinonapththalene-6-sulfonate; N-phenyl, N-methyl 2-aminonaphthalene-6-sulfonate; ethidium bromide; stebrine; auromine-0,2-(9′-anthroyl)palmitate; dansyl phosphatidylethanolamin; N,N′-dioctadecyl oxacarbocycanine; N,N′-dihexyl oxacarbocyanine; merocyanine, 4-(3′- pyrenyl)butryate; 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, sulfonaphthylhydrazone of hellibrienin; chlorotetracycline; N-(7-dimethylamino-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

M is a connecting group selected from the group consisting of amino alkyl, —O(CH 2 ) 5 NH—, —CO—, —CO(O)—, —CO(NH)—, —CO(CH 2 ) 5 NHCO(CH 2 ) 5 NH—, —NH(CH 2 CH 2 O) k NH—, NH(CH 2 CH 2 O) k CH 2 CH 2 NH— and —CO(CH 2 ) 5 —, wherein k is an integer from 1 to 5, wherein m is an integer ranging from 0 to 20.

2. The nucleic acid labeling compound of claim 1 , wherein A is H or H 4 O 9 P 3 —; Y is H or OR 9 , wherein R 9 is hydrogen, alkyl or aryl; z is hydrogen, N 3 , F or OR 10 , wherein R 10 is hydrogen, alkyl or aryl; and L is amido alkyl and M is -(M 1 ) a -(M 2 ) b - wherein a and b are independently integers from 0 to 5, and wherein M 1 and M 2 are connecting groups.

3. The nucleic acid labeling compound of claim 2 , wherein L is —(CH 2 ) n C(O)NR 3 —, wherein R 3 is hydrogen, alkyl or aryl and n is an integer ranging from 1 to 10; M 1 is —(CH 2 ) i O— and M 2 is —(CH 2 ) i NH—, wherein i and j are independently integers from 1 to 5.

4. The nucleic acid labeling compound of claim 3 , wherein Y is H or OH; Z is H or OH; -L is —CH 2 C(O)NH—; M 1 is —(CH 2 CH 2 O) 3 — and M 2 is —CH 2 CH 2 NH—; and Q is biotin or a carboxyfluorescein.

5. The nucleic acid labeling compound of claim 4 , wherein Y is OH; Z is OH; -L-(M) m - is —CH 2 C(O)NH—(CH 2 CH 2 O) 3 —CH 2 CH 2 NH—; and Q is biotin.

6. The nucleic acid labeling compound of claim 4 wherein Y is OH; Z is OH; -L-(M) m - is —CH 2 C(O)NH—(CH 2 CH 2 O) 3 —CH 2 CH 2 NH—; and Q is a carboxyfluorescein.

7. The nucleic acid labeling compound of claim 1 , wherein A is H 4 O 9 P 3 —; Y is H or OR 9 , wherein R 9 is hydrogen, alkyl or aryl; Z is hydrogen, N 3 , F or OR 10 , wherein R 10 is hydrogen, alkyl or aryl; and L is amido alkyl and M is -(M 1 ) a -(M 2 ) b - (M 3 ) c -(M 4 ) d - wherein a, b, c, and d are independently integers from 0 to 5 and the sum of a, b, c, and d is not greater than 15, and wherein M 1 , M 2 , M 3 , and M 4 are connecting groups.

8. The nucleic acid labeling compound of claim 7 , wherein L is —(CH 2 ) n C(O)NR 3 —, wherein R 3 is hydrogen, alkyl or aryl and n is an integer ranging from 1 to 10; M 1 , M 2 , M 3 , and M 4 are each independently —C(O)(CH 2 ) k O—, —(CH 2 ) i O— or —(CH 2 ) j NH—, wherein i, j and k are independently integers from 1 to 5.

9. The nucleic acid labeling compound of claim 8 , wherein L is —CH 2 C(O)NR 3 —, wherein R 3 is hydrogen or, alkyl; M 1 is —(CH 2 ) 2 NH—, M 2 is —C(O)(CH 2 ) 2 O—, M 3 is —(CH 2 CH 2 O) 3 —, and M 4 is —(CH 2 ) 2 NH—.

10. The nucleic acid labeling compound of claim 9 wherein Y is OH; Z is OH; L-(M) m - is —CH 2 C(O)NH—CH 2 CH 2 NH—C(O)CH 2 CH 2 O—(CH 2 CH 2 O) 3 —CH 2 CH 2 NH—; and Q is biotin.

11. The nucleic acid labeling compound of claim 9 , wherein Y is OH; Z is OH; -L-(M) m - is —CH 2 C(O)NH—CH 2 CH 2 NH—; m is 1; and Q is a carboxyfluorescein.

12. The nucleic acid labeling compound of claim 8 , wherein L is —(CH 2 ) 2 C(O)NR 3 —, wherein R 3 is hydrogen or, alkyl; M 1 is —(CH 2 ) 2 NH—, M 2 is —C(O)(CH 2 ) 2 O—, M 3 is —(CH 2 CH 2 O) 3 — and M 4 is (CH 2 ) 2 NH—.

13. The nucleic acid labeling compound of claim 12 , wherein Y is OH; Z is OH; L-(M) m - is —CH 2 C(O)NH—CH 2 CH 2 NH—C(O)CH 2 CH 2 O—(CH 2 CH 2 O) 3 —CH 2 CH 2 NH—; and Q is biotin.

14. The nucleic acid labeling compound of claim 12 , wherein Y is OH; Z is OH; -L-(M) m - is —CH 2 CH 2 C(O)NH—CH 2 CH 2 NH—; m is 1; and Q is a carboxyfluorescein.

15. The nucleic acid labeling compound of claim 1 , wherein A is H 4 O 9 P 3 —; Y is H or OR 9 , wherein R 9 is hydrogen, alkyl or aryl; Z is hydrogen, N 3 , F or OR 10 wherein R 10 is hydrogen, alkyl or aryl; and L is functionalized alkyl and M is -(M 1 ) a - (M 2 ) b -(M 3 ) c -(M 4 ) d - wherein a, b, c, and d are independently integers from 0 to 5 and the sum of a, b, c, and d is not greater than 15, and wherein M 1 , M 2 , M 3 , and M 4 are connecting groups.

16. The nucleic acid labeling compound of claim 15 , wherein L is —(CH 2 ) n O—, wherein n is an integer ranging from 1 to 10; M 1 , M 2 , M 3 , and M 4 are each independently —C(O)(CH 2 ) k O—, —(CH 2 ) i O— or —(CH 2 ) j NH—, wherein i, j and k are independently integers from 1 to 5.

17. The nucleic acid labeling compound of claim 16 , wherein L is —CH 2 O—; M 1 is —(CH 2 ) 2 NH—, M 2 is —C(O)(CH 2 ) 2 O—, M 3 is —(CH 2 CH 2 O) 3 — and M 4 is —(CH 2 ) 2 NH—.

18. The nucleic acid labeling compound of claim 17 , wherein Y is OH; Z is OH; L-(M) m - is —CH 2 O—CH 2 CH 2 NH—C(O)(CH 2 ) 2 O—(CH 2 CH 2 O) 3 —CH 2 CH 2 NH—; and Q is biotin.

19. The nucleic acid labeling compound of claim 17 , wherein Y is OH; Z is OH; L-(M) m - is —CH 2 O—CH 2 CH 2 NH—; m is 1; and Q is a carboxyfluorescein.

20. The nucleic acid labeling compound of claim 15 , wherein L is —(CH 2 ) n NR 3 —, wherein R 3 is hydrogen, alkyl or aryl and n is an integer ranging from 1 to 10; M 1 , M 2 , M 3 , and M 4 are each independently —C(O)(CH 2 ) k O—, —(CH 2 ) i O— or —(CH 2 ) j NH—, wherein i, j and k are independently integers from 1 to 5.

21. The nucleic acid labeling compound of claim 20 , wherein L is —(CH 2 ) 6 NH—; M 1 is —(CH 2 ) 2 NH—, M 2 is —C(O)(CH 2 ) 2 O—, and M 3 is —(CH 2 CH 2 O) 3 —.

22. The nucleic acid labeling compound of claim 21 , wherein Y is OH; Z is OH; -L-(M) m - is —(CH 2 ) 6 NH—C(O)(CH 2 ) 2 O—(CH 2 CH 2 O) 3 —CH 2 CH 2 NH—; and Q is biotin.

23. The nucleic acid labeling compound of claim 21 , wherein Y is OH; Z is OH; L is —(CH 2 ) 6 NH—; m is 0; and Q is a carboxyfluorescein.

24. The nucleic acid labeling compound of claim 1 , wherein A is H 4 O 9 P 3 —; Y is H or OR 9 , wherein R 9 is hydrogen, alkyl or aryl; Z is hydrogen, N 3 , F or OR 10 , wherein R 10 is hydrogen, alkyl or aryl; and L is alkenyl alkyl and M is -(M 1 ) a - (M 2 ) b -(M 3 ) c -(M 4 ) d - wherein a, b, c, and d are independently integers from 0 to 5 and the sum of a, b, c, and d is not greater than 15, and wherein M 1 , M 2 , M 3 , and M 4 are connecting groups.

25. The nucleic acid labeling compound of claim 7 , wherein L is—structure —CH═CH—(CH 2 ) n C(O)N(R 6 )—, wherein R 6 is hydrogen, alkyl or aryl and n is an integer ranging from 0 to 10; M 1 , M 2 , M 3 , and M 4 are each independently —C(O)(CH 2 ) k O—, —(CH 2 ) i O— or —(CH 2 ) j NH—, wherein i, j and k are independently integers from 1 to 5.

26. The nucleic acid labeling compound of claim 2 , wherein L is —CH═CH—C(O)N(H); M 1 is —(CH 2 ) 2 NH—, M 2 is —C(O)(CH 2 ) 2 O—, M 3 is (CH 2 CH 2 O) 3 — and M 4 is —(CH 2 ) 2 NH—.

27. The nucleic acid labeling compound of claim 12 , wherein -L-(M) m - is —CH═CH—C(O)NH—CH 2 CH 2 NH—C(O)CH 2 CH 2 O—(CH 2 CH 2 O) 3 —CH 2 CH 2 NH—; Y is OH; Z is OH; and Q is biotin.

28. The nucleic acid labeling compound of claim 12 , wherein Y is OH; Z is OH; L-(M)hd m - is —CH═CH—C(O)NH—CH 2 CH 2 NH—; m is 1; and Q is a carboxyfluorescein.

29. The nucleic acid labeling compound of claim 1 having the formula:

wherein A is hydrogen or a functional group that permits the attachment of the nucleic acid labeling compound to a nucleic acid;

X is O;

Y is hydrogen, N 3 , F, OR 9 , SR 9 or NHR 9 , wherein R 9 is hydrogen,

alkyl or aryl;

Z is hydrogen, N 3 , F, OR 9 , SR 9 or NHR 10 , wherein R 10 is hydrogen, alkyl or aryl;

L is a linker moiety;

M is a connecting group, wherein m is an integer ranging from 0 to 20; and Q is a detectable moiety which is detectable following coupling to a nucleic acid.

30. A nucleic acid labeling compound of claim 1 having the formula:

wherein A is hydrogen or a functional group that permits the attachment of the nucleic acid labeling compound to a nucleic acid;

X is O;

Y is hydrogen, N 3 , F, OR 9 , SR 9 or NHR 9 , wherein R 9 is hydrogen, alkyl or aryl;

Z is hydrogen, N 3 , F, OR 9 , SR 9 or NHR 10 , wherein R 10 is hydrogen, alkyl or aryl;

L is a linker moiety;

M is a connecting group, wherein m is an integer ranging from 0 to 20; and Q is a detectable moiety which is detectable following coupling to a nucleic acid.

31. The nucleic acid labeling compound according to claim 24 , wherein Y is H or OH; Z is H or OH; L is structure —CH═CH—(CH 2 ) n C(O)N(R 6 )—; M 1 is —(CH 2 ) j NH—; M 2 is —C(O)(CH 2 ) 5 NH—, c and d are each 0; and Q is biotin or a carboxyfluorescein.

32. The nucleic acid labeling compound of claim 31 , wherein L is —CH═CH—C(O)N(H); and M 1 is —(CH 2 ) 2 NH—.

33. A nucleic acid labeling compound according to claim 31 , wherein Y is OH; Z is OH; L is —CH═CH—C(O)N(H)—; and Q is biotin.

34. A nucleic acid labeling compound according to claim 1 , wherein:

A is selected from the group consisting of H; monophosphate; diphosphate; triphosphate; (R 2 N)(R′O)P, wherein R is linear, branched or cyclic alkyl, and R′is a protecting group; and HP(O)O—HNR, wherein R is linear, branched or cyclic alkyl;

L is selected from the group consisting of —C(O)—NR—, wherein R is H, alkyl, or aryl; —R′C(O)NR—, wherein R is H, alkyl, or aryl, and R′is alkyl or aryl; —(CH 2 ) n C(O)NH—, wherein n is an integer ranging from 1 to 10; —C(O)NRR′—, wherein R is H, alkyl, or aryl, and R′ is alkylene or arylene; —C(O)NH(CH 2 ) n R—, wherein R is —O—, —NR′—, or —C(O)—, and R′ is H, alkyl, or aryl, and n is an integer ranging from 2 to 10; —(CH 2 ) n R—, wherein n is an integer ranging from 1 to 10, and R is —O—, —S—, —NH—, or —C(O)—; —CH═CH—R—, wherein R is alkylene or arylene; —CH═CH(CH 2 ) n —R—, wherein n is an integer ranging from 1 to 10, R is —O—, —NR′—, —C(O)—, or —C(O)NR′—, and R′is H, alkyl, or aryl; —(CH 2 ) n C(O)—, wherein n is an integer ranging from 2 to 10; —O(CH 2 ) n R—, wherein n is an integer ranging from 2 to 10, and R is —O—, —S—, —NH—, or —C(O)—; —S(CH 2 ) n R—, wherein n is an integer ranging from 2 to 10, and R is —O—, —S—, —NH—, or —C(O)—; and —NH(CH 2 ) n NH—, wherein n is an integer ranging from 2 to 10;

Q is selected from the group consisting of radiolabels, magnetic particles, colloidal gold, fluorescent labels, chemiluminescent labels, bioluminescent labels, spin labels, dyes, and colored glass or plastic beads;

M is selected from the group consisting of amino alkyl groups, —C(O)(CH 2 ) 5 NH—, —C(O)—, —NH—, —C(O)O—, —C(O)NH—, —(CH 2 ) n O—, —(CH 2 ) n NH—, —C(O)(CH 2 ) n O—, —C(O)(CH 2 ) 5 NHC(O)(CH 2 ) 5 NH—, —NH(CH 2 CH 2 O) n NH—, and —C(O)(CH 2 ) 5 —, wherein n is an integer ranging from 1 to 5; and

m is an integer ranging from 0 to 5.

35. A method of synthesizing a labeled nucleic acid comprising attaching a nucleic acid labeling compound of claims 2 , 7 , 12 , 15 , 20 , or to a nucleic acid.