Stability of DNA double helix under sharp bending

Sharp DNA bending is essential in DNA structure and function inside the cell, and small DNA minicircles with <100 base pairs (bp) have been employed to mimic sharply bent DNA molecules. In this presentation, we report extensive molecular dynamics (MD) simulations of double-stranded DNA (dsDNA) minicircles with lengths between 64 and 106 bp, investigating the stability of the DNA double helix under various extents of DNA bending. We developed a quantitative definition of the kink, which is the local structural disruption, based on the lifetime of base-pair opening, and presents a diagram for kink formation in the parameter space of curvature and superhelical density, representing the extents of DNA bending and twisting, respectively. Our simulation results show that the DNA double helix endures sharp bending up to the curvature of 0.26 nm^-1 (corresponding to the length of 76 bp) and the stability is sensitive to torsional stress by small over- and under-twisting under sharp DNA bending. The kink formation occurred only at the DNA minor groove facing inward, suggesting the role of the twist-bend coupling in stabilizing sharply bent DNA.