Nucleic acid labeling compounds

1. A method for converting a pseudoisocytidine base to a pseudouridine base, said method comprising the steps of providing a pseudoisocytidine molecule having the formula

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

X is O, S, NR 1 or CHR 2 , wherein R 1 and R 2 are, independently, H, alkyl, or aryl;

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

L is a linker group 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, alkynyl alkyl, and amido alkyl, amino alkyl, alkoxy, amino, aryl, and thio;

Q is a detectable moiety selected from the group consisting of a radiolabel, a magnetic particle, colloidal gold, fluorescein, texas red, rhodamine, green fluorescent protein, luminol, lophine, acridine salts, luciferin, vanadium spin labels, copper spin labels, iron spin labels, manganese spin labels, nitroxide free radicals, quinoline dyes, triarylmethane dyes, acridine dyes, colored glass beads, polystyrene beads, polypropylene beads, latex beads, biotin, horseradish peroxidase, alkaline phosphatase, 1-aminoaphthalene, 2-aminoaphthalene, p,p′-diaminostilbenes, pyrenes, quaternary 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-3,a4a-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-methyl-2-aminoaphthalene-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, sulfonaphthylhydrazone 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, merocyanaine 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, —CO(CH 2 ) 5 NH—, —CO—, —CO(O)—, —CO(NH)—, —CO(CH 2 ) 5 NHCO(CH 2 ) 5 NH—, —NH(CH 2 CH 2 O) g 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, and wherein m is an integer ranging from about 0 to about 3; and

incubating said pseudoisocytidine molecule with EDC to provide a pseudouridine molecule having the formula:

2. A method according to claim 1 wherein A is selected from the group consisting of H, α-thiotriphosphate and H 4 O 9 P 3 —; X is O; Y is H or OH; Z is H or OR 10 , wherein R 10 is H, alkyl or aryl.

3. A method 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, quaternary 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, rhodamineisothiocyanate, 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-pheny,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) bis benzoxazole, 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-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 method according to claim 3 wherein Q is a biotin.

5. A method according to claim 3 having a first M and a second M, wherein said first M is —NH(CH 2 ) n NH—, wherein n is an integer from about 2 to about 10, and said second M is —CO(CH 2 ) p NH—, wherein p is an integer from about 2 to about 10 and m is 2.

6. A method according to claim 5 wherein said first M is —NH(CH 2 ) n NH— and said second M is —CO(CH 2 ) p NH—.

7. A method according to claim 1 wherein A is a triphosphate group having appropriate counterions and Y is OH and Z is OH.

8. A method according to claim 7 wherein said appropriate counterions are selected from the group consisting of H +, Na + , Li + , K + , (CH 3 CH 2 ) 3 NH + and NH 4 + .

9. A method for converting a pseudoisocytidine base to a biotinylated pseudouridine, said method comprising the steps of providing a pseudoisocytidine base having the formula

condensing said pseudoisocytidine molecule with one the equivalent of (biotin-ε-aminocaprolamido)ethylamine using excess EDC (1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride) to form a biotinylated pseudouridine coupled having the formula:

10. A method according to claim 9 wherein said step of condensing is carried out at a pH 5.5 in MES buffer.