Modeling DNA deformations

Recent developments have been made in modeling double-helical DNA at four l evels of three-dimensional structure: the all-atom level, whereby an oligon ucleotide duplex is surrounded by a shroud of solvent molecules; the base-p air level, with explicit backbone atoms; the mesoscopic level, that is, a f ew hundred base pairs, with the local duplex conformation described by know ledge-based harmonic energy functions; and the scale of several thousand nu cleotides, with the duplex described as an ideal elastic rod. Predictions o f the sequence-dependent bending end twisting of the double helix, as well as solvent- and force-induced B-->A and over-stretching conformational tran sitions, are compared with experimental data. These subtle conformational c hanges are critical to the functioning of the double helix, including its p ackaging in the close confines of the cell, the mutual fit of DNA and prote in in nucleoprotein complexes, and the effective recognition of base pairs in recombination and transcription.