FLUORESCENCE CHARACTERISTICS OF 5-CARBOXYTETRAMETHYLRHODAMINE LINKED COVALENTLY TO THE 5' END OF OLIGONUCLEOTIDES - MULTIPLE CONFORMERS OF SINGLE-STRANDED AND DOUBLE-STRANDED DYE-DNA COMPLEXES

Fluorescence steady-state and lifetime experiments have been carried o ut on duplex and single-stranded DNA molecules labeled at the 5' ends with 5-carboxytetramethylrhodamine (TMRh). The temperature and ionic s trength of the solutions were varied over large ranges. The results re veal at least three well-defined states of the TMRh-DNA molecules for the single-stranded as well as for the double-stranded DNA molecules. Two states are fluorescent, with lifetimes in the range of 0.5-1 ns an d 2.5-3 ns. A third state of TMRh-DNA does not fluoresce (a dark speci es of TMRh-DNA). The distribution of the TMRh-DNA molecules among thes e three slates is strongly temperature and ionic strength dependent. E stimates are made of some reaction parameters of the multistate model. The results are discussed in terms of the photophysics of TMRh, and c onsequences of the multiple conformers of TMRh-DNA for studies involvi ng fluorescence studies with TMRh-labeled DNA are considered.