The synergy between protein positioning and DNA elasticity: energy minimization of protein-decorated DNA minicircles

摘要

The binding of proteins onto DNA contributes to the shaping and packaging ofgenome as well as to the expression of specific genetic messages. With a viewto understanding the interplay between the presence of proteins and thedeformation of DNA involved in such processes, we developed a new method tominimize the elastic energy of DNA fragments at the mesoscale level. Our methodmakes it possible to obtain the optimal pathways of protein-decorated DNAmolecules for which the terminal base pairs are spatially constrained. We focusin this work on the deformations induced by selected architectural proteins oncircular DNA. We report the energy landscapes of DNA minicircles subjected todifferent levels of torsional stress and containing one or two proteins asfunctions of the chain length and spacing between the proteins. Our resultsreveal cooperation between the elasticity of the double helix and thestructural distortions of DNA induced by bound proteins. We find that theimposed mechanical stress influences the placement of proteins on DNA and that,the proteins, in turn, modulate the mechanical stress and thereby broadcasttheir presence along DNA.