FRET by FET and dynamics of polymer folding

Abstract

Fluorescence resonance energy transfer (FRET) is a powerful tool for the investigation of the conformational and dynamic properties of macromolecules. In this work, we report Brownian dynamics simulations of FRET during polymer folding. The polymer molecule is modeled as a necklace of beads that interact via a site-site Lennard-Jones interaction, and FRET occurs via Forster energy transfer between the ends of the chain. The simulations demonstrate that FRET can act as a good marker of polymer folding only when the Forster radius (R_F) is smaller than the root-mean-square radius (R0) of the polymer. FRET is sensitive to the early stages of polymer folding for R_F ≤ R₀ and to the late stages of polymer folding for R_F « R₀. This suggests that it might be necessary to employ more than one donor-acceptor pair in experiments aimed at probing the entire dynamics of polymer folding.