Sequence-dependent modelling of local DNA bending phenomena: curvature prediction and vibrational analysis

Bending is a local conformational micropolymorphism of DNA in which the ori ginal B-DNA structure is only distorted but not extensively modified. Bendi ng can be predicted by simple static geometry models as well as by a recent ly developed elastic model that incorporate sequence dependent anisotropic bendability (SDAB). The SDAB model qualitatively explains phenomena includi ng affinity of protein binding, kinking, as well as sequence-dependent vibr ational properties of DNA. The vibrational properties of DNA segments can b e studied by finite element analysis of a model subjected to an initial ben ding moment. The frequency spectrum is obtained by applying Fourier analysi s to the displacement values in the time domain. This analysis shows that t he spectrum of the bending vibrations quite sensitively depends on the sequ ence, for example the spectrum of a curved sequence is characteristically d ifferent from the spectrum of straight sequence motifs of identical basepai r composition. Curvature distributions are genome-specific, and pronounced differences are found between protein-coding and regulatory regions, respec tively, that is, sites of extreme curvature and/or bendability are less fre quent in protein-coding regions. A WWW server is set up for the prediction of curvature and generation of 3D models from DNA sequences (http://www.icg eb.trieste.it/dna).