title: Effect of bending anisotropy on the 3D conformation of short DNA loops.
abstract: The equilibrium three dimensional shape of relatively short loops of DNA is studied using an elastic model that takes into account anisotropy in bending rigidities. Using a reasonable estimate for the anisotropy, it is found that cyclized DNA with lengths that are not integer multiples of the pitch take on nontrivial shapes that involve bending out of planes and formation of kinks. The effect of sequence inhomogeneity on the shape of DNA is addressed, and shown to enhance the geometrical features. These findings could shed some light on the role of DNA conformation in protein-DNA interactions.
authors.affiliation: Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45195, Iran.
authors.forename: Davood
authors.initials: D
authors.lastname: Norouzi
authors.forename: Farshid
authors.initials: F
authors.lastname: Mohammad-Rafiee
authors.forename: Ramin
authors.initials: R
authors.lastname: Golestanian
mesh_terms: D000465:Algorithms; D016880:Anisotropy; D004247:DNA / Q000737:chemistry*; D004548:Elasticity; D008958:Models, Molecular; D015233:Models, Statistical; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA