Recent progress on the mechanics of sharply bent DNA

Abstract

Despite extensive studies on the mechanics of DNA under external constrains, such as tension, torsion, and bending, several important aspects have remained poorly understood. One biologically important example is the mechanics of DNA under sharp bending conditions, which has been debated for a decade without thorough comprehension. The debate is about the interesting phenomenon raised from a series of different experiments: sharply bent DNA has a surprisingly high apparent bending flexibility that deviates from the canonical bending elasticity of DNA. This finding has motivated various theoretical models, which mainly incorporate the excitation of mechanical defects inside severely bent DNA molecules. Here, we review the recent progress on the understanding of the mechanics of sharply bent DNA and provide our view on this important question by interrogating the theoretical foundation of these experimental measurements.DNA mechanics, DNA elasticity, DNA nicks, molecular dynamics simulation PACS number(s):

A polymer model of bacterial supercoiled DNA including structural transitions of the double helix

“…In effect, our 2sRLC model bridges "kinkable" worm-like chain models and self-avoiding rod like chain models, which have been developed to respectively address the high flexibility of sharply bent DNA [53] and the superstructuring properties of supercoiled B-DNA molecules [15,20]. By doing so, it opens novel perspectives in the field of supercoiled DNA, not only to better rationalize magnetic tweezers experiments but also to predict behaviors of bacterial genomes in vivo.…”

“…In this work, we aim at filling these gaps by extending the sRLC model so that it includes the possibility to have multiple DNA forms. To this end, we follow an approach initially proposed to tackle the problem of the large flexibility of small DNA molecules [53]. Namely, as proposed in [54,55,56], the softening of sharply bent DNA can be rationalized by considering a structural degree of freedom allowing the appearance of alternative forms more flexible than B-DNA, with a free energy cost reflecting the destabilization of the double helix.…”