High-energy deformation of filaments with internal structure and localized torque-induced melting of DNA

We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a double-stranded DNA oligomer (shorter than its thermal persistence length) whose free ends are linked by a single-stranded DNA chain. This construct, studied by H. Qu and G. Zocchi [Europhys. Lett. 94, 18003 (2011)], displays nonlinear strain softening associated with the local melting of the double-stranded DNA under applied torque and serves as a model system with which to study the nonlinear elasticity of DNA under large energy deformations. We show that one can account quantitatively for the observed bending mechanics using an augmented wormlike chain model, the helix-coil wormlike chain. We also predict that the highly bent and partially molten dsDNA should exhibit particularly large end-to-end fluctuations associated with the fluctuation of the length of the molten region, and propose appropriate experimental tests. We suggest that the augmented wormlike chain model discussed here is a useful analytic approach to the nonlinear mechanics of DNA or other biopolymer systems.