Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron–Electron Double Resonance and Molecular Dynamics

Abstract

Pulsed electron-electron double resonance (PELDOR/DEER) experiments of nucleic acids with rigid spin labels provide highly accurate distance and orientation information. Here we combine PELDOR experiments with molecular dynamics (MD) simulations to arrive at an atomistic view of the conformational dynamics of DNA. The MD simulations closely reproduce the PELDOR time traces, and demonstrate that bending, in addition to twist-stretch motions, underpin the sub-μs dynamics of DNA. PELDOR experiments correctly rank DNA force fields and resolve subtle differences in the conformational ensembles of nucleic acids, on the order of 1-2 Å. Long-range distance and angle measurements with rigid spin labels provide critical input for the refinement of computer models and the elucidation of the structure and dynamics of complex biomolecules.