Discrimination of the binding mode of DNA ligands by single-photon timing

We perform time-correlated single-photon counting measurements with 30-ps resolution of the fluorescence emitted by the donor fluorophores of donor-acceptor pairs covalently labeling DNA synthetic oligonucleotides by using a non-commercial single-photon avalanche diode. The measurements allow us to precisely assess the fluorescence resonant energy transfer efficiency of the pairs in solutions containing the oligonucleotides and DNA-ligands, for different ratios of the DNA base-pair to ligand concentrations. A quantitative evaluation of the deformations of DNA double strands following the ligand binding is obtained, as the transfer efficiency is a steep function of the donor-to-acceptor distance. The results lead to an easy and cheap method to discriminate between the binding modes of minor groove and base intercalating ligands. © 2009 - IOS Press. All rights reserved.