Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: A comparative analysis of T-A and A-T steps within A-tracts

Introduction of a T-A or pyrimidine-purine step into a straight and rigid A -tract can cause a positive roll deformation that kinks the DNA helix at th at step. In CCTTTAAAGG, the central T-A step has an 8.6 degrees bend toward the major groove. We report the structural analysis of CCTTTAAAGG and a co mparison with 25 other representative crystal structures from the NDB conta ining at least four consecutive A or T bases. On average, more local bendin g occurs at the disruptive T-A step ') than at an A-T step (5.71). In addit ion, A-tracts containing an A(8.2l T step are more bent than are pure A-tra cts, and hence A-A and A-T steps are not equivalent. All T-A steps examined exhibit positive roll, bending towards the major groove, while A-T steps d isplay negative roll and bend slightly towards the minor groove. This illus trates how inherent negative and positive roll are, respectively, at A-T an d T-A steps within A-tracts. T-A steps are more deformable, showing larger and more variable deformations of minor groove width, rise, cup, twist, and buckle. Standard deviations of twist, rise, and cup for T-A steps are 6.66 degrees, 0.55 Angstrom, and 15.90 degrees, versus 2.28 degrees, 0.21 Angst rom, and 2.99 degrees for A-T steps. Packing constraints determine which lo cal values of these helical parameters an individual T-A step will adopt. F or instance, with CCTTTAAAGG and three isomorphous structures, CGATTAATCG, CGATATATCG, and CGATCGATCG, crystal packing forces lead to a series of corr elated changes: widened minor groove, large slide, low twist, and large ris e. The difference in helical parameters between A-T steps lying within A-tr acts, versus A-T steps within alternating AT sequences, demonstrates the im portance of neighboring steps on the conformation of a given dinucleotide s tep. (C) 2001 Academic Press.