Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low k2 Values

Forster resonance energy transfer (FRET) is analyzed in terms of distance- and orientation-dependent interactions between the transition dipole moments of the involved donor and acceptor molecules. However, the ideal dipole approximation (IDA) is known to, fail at short donor-acceptor distances. In this work, we model FRET in a Cy5- and Alexa Fluor 488-labeled double-stranded RNA by means of combined molecular dynamics (MD) simulations and quantum-chemical calculations involving the IDA as well as the more sophisticated monomer transition density (MTD) approach. To this end, the relaxed ground:state geometries of the dyes were fitted to the MD-based structures. Although substantial deviations between IDA and MTD results can he observed for individual snapshots, the statistical impact of the failure on the FRET rates is negligible in the chosen examples. Our results clearly demonstrate that the IDA-based Forster model can-still be applied to systems with small donor-acceptor distances, provided that the dyes are not trapped. in arrangements with a high IDA failure and that the distribution of the relative transitions dipole orientations is fairly isotropic.