DNA nanomechanics in the nucleosome.
The sequence-dependent mechanics of DNA-histone binding are essential for nucleosome positioning and mobility. Here we reanalyze nucleosome crystal structures in terms of the well-characterized base-pair scale DNA elasticity, extracting the forces and torques acting on all bound DNA base pairs. We find that the strongest forces follow a characteristic repeating pattern that recovers the 12 known DNA backbone-histone contact sites. DNA twist defects and histone point mutations modify this pattern in interpretable ways. Additional, irregular forces between contact sites reveal histone tail-DNA interactions, whereas requiring the absence of external forces leads to a structural refinement of linker DNA. Based on these observations, we propose a simple, structure-based mechanical model of the nucleosome that is able to explain the placement of DNA twist defects in 146 base-pair nucleosomes and allows an estimate of the elastic energy spectrum of nucleosome twist defect states.
Laboratoire de Physique de l'Ecole Normale Supérieure, Université de Lyon, France. nils.becker@ens-lyon.fr
Nils B
NB
Becker
Ralf
R
Everaers
D020029:Base Pairing; D001483:Base Sequence; D001696:Biomechanical Phenomena; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004548:Elasticity; D006657:Histones / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017354:Point Mutation
D006657:Histones; D009707:Nucleosomes; D004247:DNA