Book of Abstracts: Albany 2005
Sequence-dependent Cyclization of Short DNA Sequences
A new non-canonical Monte Carlo sampling methodology is applied to approximate the conformational properties of DNA in a discrete elastic base-pair step model. This technique can be used to investigate arbitrary-length DNA with greatly enhanced sampling sizes (N=1016) and elucidate sequence-dependent features which are expected to contribute greatly to the dynamics of DNA at short lengths. Electrostatic repulsion between base-pair steps is also considered. DNA is modeled as either intrinsically straight or with local sequence-dependent bending, twisting, and shearing, both with or without anisotropic bending and more deformable base-pair steps. These models are intended to fit data from cyclization experiments of short DNA sequences by Cloutier and Widom, which suggest possible faults in current theories of DNA elasticity, and to address the need for further modeling and sampling techniques.
Department of Chemistry & Chemical Biology