Understanding the structure of unfolded, flexible polyelectrolytes is important for our comprehension of basic processes in molecular biology (e.g., RNA and protein folding) and our ability to exploit the polymers in technology (e.g., in self-assembled nanostructures). Here, we investigate the structure of single single-stranded DNA molecules and their interactions with ions using magnetic tweezers.

Our data reveal that single-stranded DNA is not well-described by ideal polymer models such as the Worm-Like Chain. At low force, we report the first experimental observation of a nonlinear elastic regime revealing the relevance of long-range excluded volume effects. At high force, the extension scales as a logarithm in monovalent salt. Molecular dynamics simulations indicate that this logarithmic regime is the result of ion-stabilized wrinkles at short-length scales along the polymer backbone. Addition of divalent salt to the buffer results in enhanced elasticity indicating increased wrinkling or polymer ''wrapping" around the divalent ions. Using a thermodynamic identity, we are able to count ions as they are released into the bulk upon polymer elongation. We find that ssDNA releases significantly more ions than dsDNA. We posit that the recently termed ''Snake-Like Chain" model (Ullner, J. Phys. Chem B (2003)) for flexible polyelectrolytes may explain these observations.

As a first step towards characterizing biologically relevant nucleic acid structures, we measure the effects of base-stacking on ssDNA elasticity. We find that base-stacking in poly(dA) significantly enhances the rigidity of the polymer as evidenced by the low-force elasticity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than predictions from mean-field models. Further, we provide a model-independent estimate of the free energy difference between stacked and unstacked nucleic acids, finding it to be roughly -0.25 kT/base and nearly constant over three orders of magnitude in salt concentration.