Direct measurement of thermodynamic and kinetic parameters of DNA triple helix formation by fluorescence spectroscopy

Abstract

Direct measurement of thermodynamic and kinetic parameters of oligonucleotide-directed DNA triple helix formation has been achieved by fluorescence spectroscopic methods. Fluorescence resonance energy transfer (FRET) was used to study the binding of an acceptor-labeled single-stranded oligonucleotide to a donor-labeled DNA duplex. Equilibrium binding constants and association rate constants for triplex formation between 5'-tetramethylrhodamine-labeled 11-mer, 13-mer, and 15-mer homopyrimidine oligonucleotides and a 5'-fluorescein-labeled, 25-bp DNA duplex containing a 15-bp homopurine site were determined by FRET measurements, and the values were in close agreement with those determined by established methods. The thermal dissociation profile of the triplex-to-duplex transition was also directly observed by FRET and was consistent with the triplex melting curves obtained by UV absorbance measurements. In addition, a homogeneous fluorescence anisotropy assay is described which enables determination of the binding constants between 5'-tetramethylrhodamine-labeled 11-mer and 13-mer homopyrimidine oligonucleotides and unlabeled 25-, 30-, and 50-bp double-stranded DNA containing a homopurine target site. These results demonstrate the utility of nonradioactive fluorescence measurements as an efficient method for studying triple helix formation under homogeneous solution conditions and highlight the uniqueness of the FRET method for obtaining equilibrium, kinetic, and thermal dissociation data in a straightforward manner.