Aromatic-substituted xanthene dyes

Details Aromatic-substituted xanthene dyes Aromatic-substituted xanthene dyes

1997-10-01

1999-12-28

Houtteman, Scott W.

Organic compounds -- part of the class 532-570 series

Organic compounds

Heterocyclic carbon compounds containing a hetero ring...

435 6, 536 266, C07D31182

Patent

active

060083794

ABSTRACT:
A class of aromatic-substituted xanthene compounds useful as fluorescent dyes is disclosed, the compounds having the general structure where Y.sub.1 and Y.sub.2 taken separately are selected from the group consisting of hydroxyl, oxygen, imminium, linking group and amine, or Y.sub.1 taken together with R.sub.2 is cyclic imine, or Y.sub.2 taken together with R.sub.3 is cyclic amine; R.sub.2, R.sub.3, R.sub.5, and R.sub.7 taken separately are selected from the group consisting of hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, imminium, amido, nitrile, lower alkoxy, phenyl, and linking group; R.sub.1 taken separately is selected from the group consisting of phenyl, substituted phenyl, polycyclic aromatic, substituted polycyclic aromatic, linking group and electron-rich heterocycle, or when taken together with R.sub.7 is selected from the group consisting of electron-rich heterocycle and indene; R.sub.4 taken separately is selected from the group consisting of amino, amido, phenyl, substituted phenyl, polycyclic aromatic, substituted polycyclic aromatic, indene, linking group and electron-rich heterocycle, or when taken together with R.sub.5 is selected from the group consisting of phenyl, substituted phenyl, polycyclic aromatic, substituted polycyclic aromatic, indene, and electron-rich heterocycle; and R.sub.6 is selected from the group consisting of acetylene, lower alkyl, lower alkene, cyano, phenyl, substituted phenyl, and heterocyclic aromatic. In another aspect, the invention includes methods for synthesizing the above dye compounds and intermediates. In yet another aspect, the present invention includes reagents labeled with the asymmetric benzoxanthene dye compounds, including deoxynucleotides, dideoxynucleotides, phosphoramidites, and polynucleotides. In an additional aspect, the invention includes methods utilizing such dye compounds and reagents including dideoxy polynucleotide sequencing and fragment analysis methods.

REFERENCES:
patent: 5188934 (1993-02-01), Menchen et al.
patent: 5654419 (1997-08-01), Mathies et al.
patent: 5750409 (1998-05-01), Hermann et al.
Lee et al., Nuc. Acids Res. 20(10):2471-83, Abstract and Xanthylium structure, RN=142975-78-8, 1992.

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