4,7-dichlororhodamine dyes labeled polynucleotides

Abstract

A set of 4,7-dichlororhodamine compounds useful as fluorescent dyes are disclosed having the structures wherein R-Rare hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group, or, when taken together, Rand Ris benzo, or, when taken together, Rand Ris benzo; R-R, R-Rand Rmay be hydrogen, fluorine, chlorine, lower alkyl, lower alkene, lower alkyne, sulfonate, sulfone, amino, amido, nitrile, lower alkoxy, linking group; Rand Rmay be hydrogen, lower alkyl, lower alkene, lower alkyne, phenyl, aryl, linking group; Y-Yare hydrogen, lower alkyl, or cycloalkyl, or, when taken together, Yand R, Yand RYand R, and/or Yand Ris propano, ethano, or substituted forms thereof; and X-Xtaken separately are hydrogen, chlorine, fluorine, lower alkyl, carboxylate, sulfonate, hydroxymethyl, and linking group, or any combinations thereof. In another aspect, the invention includes reagents labeled with the 4,7-dichlororhodamine dye compounds, including deoxynucleotides, dideoxynucleotides, and polynucleotides. In an additional aspect, the invention includes methods utilizing such dye compounds and reagents including dideoxy polynucleotide sequencing and fragment analysis methods.