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Thermodynamics of force-induced B-DNA melting: single-strand discreteness matters

Research paper by Nikos Theodorakopoulos

Indexed on: 15 Feb '19Published on: 15 Feb '19Published in: arXiv - Physics - Biological Physics



Abstract

Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induced melting have been correctly described by Rouzina and Bloomfield \cite{RouzinaBloomfield2001a}, neither force threshold has been exactly calculated by theory. In this work, a detailed analysis of the force-extension curve is presented, based on a description of single-stranded DNA in terms of the discrete Kratky-Porod model, consistent with (i) the contour length expected from the crystallographically determined monomer distance, and (ii) a high value of the elastic stretch modulus arising from covalent bonding. The value estimated for the ss-DNA persistence length, $\lambda = 1.0 $ nm, is at the low end of currently known estimates and reflects the intrinsic stiffness of the partially, or fully stretched state, where electrostatic repulsion effects are expected to be minimal. A detailed analysis of single- and double-stranded DNA free energies provides estimates of the overstretching force thresholds. In the unconstrained geometry, the predicted threshold is 64 pN. In the constrained geometry, after allowing for the entropic penalty of the plectonemic topology of the molten state, the predicted threshold is 111 pN.