Single-Stranded DNA is not a Worm-Like Chain

Abstract

The structure of unfolded, flexible polyelectrolytes in solution, while an important subject for understanding various biological and technological phenomena such as RNA and protein folding and the self-assembly of DNA nanostructures, is poorly understood. While it is well-known and tested that semi-flexible polyelectrolytes, such as dsDNA, behave as Worm-Like Chains (WLC) with a scale-dependent electrostatic persistence length, validity of this model for flexible polyelectrolytes is doubtful. However, throughout the literature, data on flexible polyelectrolytes are naively fit to WLC models due to the simplicity of the analytical expressions. Here, we examine the validity of the WLC model for flexible polyelectrolytes using single-molecule force spectroscopy on ssDNA. We find that the force-extension data cannot be adequately fit to the Marko-Siggia prediction for the WLC even after accounting for electrostatic effects. Rather, our data reveal a self-avoiding walk regime consistent with scaling predictions at low force followed by a regime where the extension scales as a logarithm with force over a broad range of moderate forces and monovalent salt concentrations. Further, we run molecular dynamics simulations on a bead-spring model polyelectrolyte under tension and reproduce this logarithmic behavior in monovalent salt, indicating that it is indeed a general behavior for flexible polyelectrolytes. Examining the structure factor of the simulated polymer reveals a highly wrinkled, ion-stabilized structure at length scales smaller than a Debye length which defies characterization as a WLC. Addition of divalent salt to either the simulation or experiment results in enhanced flexibility indicating increased wrinkling or polymer “wrapping” around the divalent ions.