Reactive cyanine compounds
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Abstract
The invention provides compounds and compositions of Formulas I-VII, and methods of using the compounds. The compounds can be used to prepare dye conjugates that are uniformly and substantially more fluorescent on proteins, nucleic acids or other biopolymers, than conjugates labeled with structurally similar known carbocyanine dyes. In addition to having more intense fluorescence emission than structurally similar dyes at virtually identical wavelengths, and decreased artifacts in their absorption spectra upon conjugation to biopolymers, the compounds can have greater photostability and/or higher absorbance (extinction coefficients) at the wavelength(s) of peak absorbance than such structurally similar dyes.
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Citations
21 Claims
- 1. A compound of Formula I:
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15. A compound selected from the group consisting of
5-((1E,3E,5E)-5-(1,1-dimethyl-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)penta-1,3-dienyl)-6-(6-(2,5-dioxopyrrolidin-1-yloxy)-6-oxohexyl)-6-methyl-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium trifluoroacetate (3525); -
6-(6-((2-Cyanoethoxy)(diisopropylamino)phosphinooxy)hexyl)-5-((1E,3E,5E)-5-(1,1-dimethyl-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)penta-1,3-dienyl)-6-methyl-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium chloride (3742); (E)-2-((2E,4E)-5-(6-(6-(2,5-Dioxopyrrolidin-1-yloxy)-6-oxohexyl)-6-methyl-7-sulfo-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-5-yl)penta-2,4-dienylidene)-1,1-dimethyl-2,4,5,6-tetrahydro-1H-pyrrolo[3,2,1-ij]quinoline-9-sulfonate (3526); 6-(25-chloro-6-oxo-10,13,16,19-tetraoxa-7-azapentacosyl)-5-((1E,3E,5E)-5-(1,1-dimethyl-9-sulfo-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)penta-1,3-dienyl)-6-methyl-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-7-sulfonate (3665); 5-((1E,3E)-3-((E)-2-(1,1-Dimethyl-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)ethylidene)-6-hydroxyhex-1-enyl)-6,6-dimethyl-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium chloride (3688); (E)-2-((E)-3-((E)-2-(6,6-Dimethyl-7-sulfo-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-5-yl)vinyl)-6-hydroxyhex-2-enylidene)-1,1-dimethyl-2,4,5,6-tetrahydro-1H-pyrrolo[3,2,1-ij]quinoline-9-sulfonate (3786); 5-((1E,3E)-3-(1,1-Dimethyl-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)prop-1-enyl)-6-(6-hydroxyhexyl)-6-methyl-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium chloride (3785); Sodium 2-((1E,3Z)-3-(1-(5-carboxypentyl)-1-methyl-9-sulfonato-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)prop-1-enyl)-1-methyl-1-(4-sulfonatobutyl)-1,4,5,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-9-sulfonate (3845); Sodium 2-((1E,3Z)-3-(1-(6-(2-(2-(6-chlorohexyloxy)ethoxy)ethylamino)-6-oxohexyl)-1-methyl-9-sulfonato-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)prop-1-enyl)-1-methyl-1-(4-sulfonatobutyl)-1,4,5,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-9-sulfonate (3838); 6-((Z)-5-((2E,4E)-5-(6,6-Dimethyl-1,2,3,6-tetrahydrobenzo[f]pyrrolo[3,2,1-ij]quinolinium-5-yl)penta-2,4-dienylidene)-6-methyl-2,3,5,6-tetrahydro-1H-benzo[f]pyrrolo[3,2,1-ij]quinolin-6-yl)hexanoate (3846); Sodium 2-((1E,3E,5Z)-5-(1-(6-(2-(2-(6-chlorohexyloxy)ethoxy)ethylamino)-6-oxohexyl)-1-methyl-9-sulfonato-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)penta-1,3-dienyl)-1-methyl-1-(4-sulfonatobutyl)-1,4,5,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-9-sulfonate (3847); Sodium 5-((1E,3E,5Z)-5-(1-(5-carboxypentyl)-1-methyl-9-sulfonato-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)penta-1,3-dienyl)-6-methyl-6-(4-sulfonatobutyl)-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-7-sulfonate (3848); Sodium 5-((E)-2-((E)-2-(4-carboxyphenoxy)-3-((E)-2-(1-methyl-9-sulfonato-1-(4-sulfonatobutyl)-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)ethylidene)cyclohex-1-enyl)vinyl)-6-methyl-6-(4-sulfonatobutyl)-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-7-sulfonate (3855); Sodium 2-((E)-2-((E)-2-(4-(2-(2-(6-chlorohexyloxy)ethoxy)ethylcarbamoyl)phenoxy)-3-((E)-2-(1-methyl-9-sulfonato-1-(4-sulfonatobutyl)-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)ethylidene)cyclohex-1-enyl)vinyl)-1-methyl-1-(4-sulfonatobutyl)-1,4,5,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-9-sulfonate (3856);
or5-((E)-2-((E)-3-((Z)-2-(1-(25-Chloro-6-oxo-10,13,16,19-tetraoxa-7-azapentacosyl)-1-methyl-9-sulfo-5,6-dihydro-1H-pyrrolo[3,2,1-ij]quinolin-2(4H)-ylidene)ethylidene)-2-(4-sulfophenoxy)cyclohex-1-enyl)vinyl)-6-methyl-6-(4-sulfobutyl)-1,2,3,6-tetrahydropyrrolo[3,2,1-ij]quinolinium-7-sulfonate (3921).
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Specification