Computer simulation to investigate the FRET application in DNA hybridization systems

Abstract

Molecular dynamics (MD) and quantum mechanics (QM) were used to investigate fluorescence resonance energy transfer (FRET) between coumarin and ethidium in two Mergny's DNA hybridization systems. By combining the transition dipoles calculated by the quantum semi-empirical method and the conformations of the FRET probes collected by MD, FRET efficiencies were derived from the Förster equation at five temperatures from 273 K to 313 K. The plotted efficiencies were compared with Mergny's experiments, and showed good agreement. The simulated orientation factor and isotropically averaged orientation factor were compared, and the results demonstrated that the assumption of isotropic orientations is invalid when FRET probes are close to each other. The first order kinetic assumptions were also used to calculate the transfer efficiencies, and the results show that this D-A FRET process approximates the first order kinetic reactions.