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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Phys. | doi: 10.3389/fphy.2019.00195

Strongly bent double-stranded DNA: reconciling theory and experiment

  • 1Virginia Tech, United States

The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending deformation increases beyond a certain (polymer-specific) point, the change in the convexity properties of the effective bending energy of the polymer makes the harmonic deformation energetically unfavorable: in this strong bending regime the energy of the polymer varies linearly with the average bending angle as the system follows the convex hull of the deformation energy function.
For double-stranded DNA, the effective bending deformation energy becomes non-convex for bends greater than ∼ 2◦ per base-pair, equivalent to the curvature of a closed circular loop of ∼ 160 base pairs. A simple equation is derived for the polymer loop energy that covers both the weak and strong bending regimes. The theory shows quantitative agreement with recent DNA cyclization experiments on short DNA fragments, while maintaining the expected agreement with experiment in the weak bending regime. Counter-intuitively, cyclization probability (j-factor) o f very short DNA loops is predicted to increase with decreasing loop length; the j-factor reaches its minimum for loops of ≃ 45 base pairs. Atomistic simulations reveal that the attractive component of the short-range Lennard-Jones interaction between the backbone atoms can explain the underlying non-convexity of the DNA effective bending energy, leading to the linear bending regime. Applicability of the theory to protein-DNA complexes, including the nucleosome, is discussed.

Keywords: polymer bending, Convex hull, J-factor, DNA cyclization, deformation, Nucleosome

Received: 30 Jun 2019; Accepted: 06 Nov 2019.

Copyright: © 2019 Onufriev, Drozdetski and Mukhopadhyay. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Alexey V. Onufriev, Virginia Tech, Blacksburg, United States, alexey@cs.vt.edu