Sorting out the structure of single-stranded DNA

Abstract

The mechanical properties of single stranded nucleic acids play a vital role in such dynamic processes as DNA replication and RNA folding. While experiments have demonstrated that duplex DNA molecules behave as ideal worm-like chains with a persistence length that can be measured accurately, the unfolded single-stranded form of DNA (ssDNA) has been surprisingly recalcitrant: different biophysical techniques lead to different conclusions. Making matters worse, all-atom molecular dynamics simulations of ssDNA do not agree with experiment. This has motivated new experimental and theoretical work. In recent force spectroscopy and computational studies, McIntosh, Stevens and Saleh propose models where excluded volume influences long-ranged structure, while specific ion interactions induce “wrinkles” at short length scales (“Single-stranded DNA is not a wormlike-chain”, Biophys. J. 104, 28). However, direct structural evidence for these models is lacking. Thus, we perform detailed investigations of ssDNA homopolymers using x-ray scattering, single molecule FRET, and quantitative characterization of the ion atmosphere in mono- and di-valent salt. We develop a novel data-driven ensemble optimization technique that allows us to visualize the conformational adaptation of the DNA backbone to changes in the ion atmosphere, including the distinct effects of base stacking and ion valence. Correlation functions obtained from the structure ensembles, without reference to polymer or electrostatic theories, nonetheless show signatures of electrostatic excluded volume and strong ion effects at short distances. We discuss the implications for new polyelectrolyte theories of ssDNA and the biological role of electrostatics in these systems.