Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles

François Sicard, Nicolas Destainville, Philippe Rousseau, Catherine Tardin, and Manoel Manghi
Phys. Rev. E 101, 012403 – Published 8 January 2020

Abstract

We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.

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  • Received 4 August 2019

DOI:https://doi.org/10.1103/PhysRevE.101.012403

©2020 American Physical Society

Physics Subject Headings (PhySH)

  1. Physical Systems
Polymers & Soft Matter

Authors & Affiliations

François Sicard1,*, Nicolas Destainville2, Philippe Rousseau3, Catherine Tardin4, and Manoel Manghi2

  • 1Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
  • 2Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, France
  • 3Laboratoire de Microbiologie et Génetique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
  • 4Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, France

  • *Corresponding author: francois.sicard@free.fr

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Vol. 101, Iss. 1 — January 2020

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