Fluorescence probing of nucleic acids: I. singly and doubly labeled dithymidine phosphate: fluorescence and energy transfer studies

Dithymidine phosphate labeled at its 5' end with a naphthalene-carbamate has been prepared,DTpT. It is shown to exist in several conformations which are characterized by chromatography and absorption and fluorescence measurements. Models for three possible conformers where the dye is solvated, stacked on the first thymine or intercalated between the two thymines are given with their absorption and fluorescence spectra. The doubly labeled molecule,DTpTA, where D and A form a donor-acceptor energy transfer pair has also been prepared. The energy transfer rate has been measured from the donor fluorescence lifetime decay.