Nucleic acid labeling compounds

A nucleic acid labeling compound having the formula:

• wherein A is hydrogen or, monophosphate, diphosphate, triphosphate, α-thiotriphosphate, phosphoramidite, or H-phosphonate;
• X1 is O, S, NR1 or CHR2,
• wherein R1 and R2 are, independently, hydrogen, alkyl or aryl;
• R15 is hydrogen, alkyl or aryl;
• Y1 is hydrogen, N3, F, OR9, SR9 or NHR9, wherein R9 is hydrogen, alkyl or aryl;
• Z1 is hydrogen, N3, F, OR9, SR9 or NHR10, wherein R10 is hydrogen, alkyl or aryl;
• wherein one of Y, or Z, is a group having the formula —X2L-(M), -Q;
• X2 is O, S, or NR16, and R16 is hydrogen, alkyl or aryl;
• L is a linker moiety selected from the group consisting of —CH═CH—R11, or C≡C—R11 wherein
• R1 comprises a moiety selected from the group consisting of alkyl, functionalized alkyl, alkenyl alkyl, alkynyl alkly, amido alkyl, amino alkyl, alkoxy, amino, aryl, and thio;
• Q is a detectable moiety 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, 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, 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;
• 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, —CO(CH2)5NH—, —CO—, —CO(O)—, CO(NH)—, —CO(CH2)5NHCO(CH2)5NH—, —NH(CH2CH2O)kNH—, NH(CH2CH2O)kCH2CH2NH— and —CO(CH2)5—, wherein m is an integer ranging from 0 to about 20.