title: Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts.
abstract: 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 that 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 comparison with 25 other representative crystal structures from the NDB containing at least four consecutive A or T bases. On average, more local bending occurs at the disruptive T-A step (8.21 degrees ) than at an A-T step (5.71 degrees ). In addition, A-tracts containing an A-T step are more bent than are pure A-tracts, 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 display negative roll and bend slightly towards the minor groove. This illustrates how inherent negative and positive roll are, respectively, at A-T and 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 A, and 15.90 degrees, versus 2.28 degrees, 0.21 A, and 2.99 degrees for A-T steps. Packing constraints determine which local values of these helical parameters an individual T-A step will adopt. For instance, with CCTTTAAAGG and three isomorphous structures, CGATTAATCG, CGATATATCG, and CGATCGATCG, crystal packing forces lead to a series of correlated changes: widened minor groove, large slide, low twist, and large rise. The difference in helical parameters between A-T steps lying within A-tracts, versus A-T steps within alternating AT sequences, demonstrates the importance of neighboring steps on the conformation of a given dinucleotide step.
authors.affiliation: Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
authors.forename: D R
authors.initials: DR
authors.lastname: Mack
authors.forename: T K
authors.initials: TK
authors.lastname: Chiu
authors.forename: R E
authors.initials: RE
authors.lastname: Dickerson
mesh_terms: D020856:AT Rich Sequence / Q000235:genetics; D001483:Base Sequence; D002412:Cations / Q000378:metabolism; D003460:Crystallization; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D002412:Cations; D014867:Water; D004247:DNA