Synergy between protein positioning and dna elasticity: Energy minimization of protein-decorated dna minicircles

Nicolas Clauvelin, Wilma K. Olson

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

The binding of proteins onto DNA contributes to the shaping and packaging of the genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation of DNA involved in such processes, we developed a new method to minimize the elastic energy of DNA fragments at the mesoscale level. Our method makes it possible to obtain the optimal pathways of protein-decorated DNA molecules for which the terminal base pairs are spatially constrained. We focus in this work on the deformations induced by selected architectural proteins on circular DNA. We report the energy landscapes of DNA minicircles subjected to different levels of torsional stress and containing one or two proteins as functions of the chain length and spacing between the proteins. Our results reveal cooperation between the elasticity of the double helix and the structural distortions of DNA induced by bound proteins. We find that the imposed mechanical stress influences the placement of proteins on DNA and that the proteins, in turn, modulate the mechanical stress and thereby broadcast their presence along DNA.

Original languageEnglish (US)
Pages (from-to)2277-2287
Number of pages11
JournalJournal of Physical Chemistry B
Volume125
Issue number9
DOIs
StatePublished - Mar 11 2021

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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