Sequence-dependent DNA structure: a database of octamer structural parameters.

摘要: We have constructed the potential energy surfaces for all unique tetramers, hexamers and octamers in double helical DNA, as a function of two principal degrees freedom, slide shift at central step. From these maps, we calculated database structural flexibility properties each sequences. These include: values six step parameters (twist roll, tilt, rise, shift), sequence; measures both decrease increase property value from minimum conformation step; deviation path hypothetical straight octamer. In an analysis change sequence length, observe that almost DNA tends to B-DNA becomes less flexible. A more detailed octamer has allowed us determine preferences particular elements. GGC GCC sequences tend confer bistability, low stability predisposition A-form whereas AA steps strongly prefer inhibit A-structures. There is no correlation between intrinsic curvature, but bent stable than straight. The most difficult deformation undertwisting. TA stands out flexible element with respect decreasing twist increasing roll. However, properties, this behavior highly context-dependent some are very