title: Conformational properties of the TATA-box binding sequence of DNA.
abstract: Nanosecond scale molecular dynamics simulations in water demonstrate that the DNA oligomer, GCGTATATAAAACGC, which contains a target site for the TATA-box binding protein (TBP), has an intrinsic preference to adopt an A-like conformation in the region of the TATA-box and undergoes bending related to that seen within in the TBP complex. This result is obtained from two independent simulations using different starting structures. In line with earlier suggestions of Guzikevich-Guerstein and Shakked, these simulations imply that an A-DNA conformation may be an important intermediate step in forming the strongly distorted DNA observed within the crystallographically determined complex with TBP. These results also support modeling studies by Lebrun et al. which suggest that the TBP binding mechanism can be broken down into a backbone transition to an A-like form coupled with a mechanical distortion which locally stretches and unwinds the DNA.
authors.affiliation: Laboratoire de Biochimie Théorique, CNRS URA77, Institut de Biologie Physico-Chimique, Paris, France.
authors.forename: D
authors.initials: D
authors.lastname: Flatters
authors.forename: M
authors.initials: M
authors.lastname: Young
authors.forename: D L
authors.initials: DL
authors.lastname: Beveridge
authors.forename: R
authors.initials: R
authors.lastname: Lavery
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism; D009690:Nucleic Acid Conformation; D016385:TATA Box; D035181:TATA-Box Binding Protein; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D035181:TATA-Box Binding Protein; D014157:Transcription Factors; D004247:DNA