Equilibrium Bending Fluctuations of Short DNA

Abstract

Short-lengthscale double-stranded DNA (dsDNA) bending elasticity plays an important role in many biological contexts. We measured dsDNA bending fluctuations using small-angle X-ray scattering from bulk solutions of two gold nanoparticles covalently linked by a 42-94 basepair dsDNA chain, freely fluctuating and not subject to external forces or surface interactions. This method reports on the equilibrium ensemble of bending fluctuations, not just an average value (as in ensemble FRET) or an extreme value (as in cyclization). Through Monte Carlo sampling of coarse-grained models, we find these experiments are consistent with a wormlike chain model of dsDNA, with a persistence length of ∼50nm, in agreement with single-molecule force-extension experiments on much longer chains, but in contrast to recent suggestions of enhanced flexibility at these shorter lengthscales. These findings are plausible because even our shortest dsDNA chain still greatly exceeds the lengthscale of correlated microscopic fluctuations (roughly half a turn, 5 base pairs), and our observable is dominated by (high probability) mild fluctuations and thus insensitive to extremely rare fluctuations. Reproducing experiments required more detailed modeling at the DNA-gold interface, emphasizing the need for care in choosing the appropriate coarse-graining level for complex biomolecular systems.View Large Image | View Hi-Res Image | Download PowerPoint Slide