title: A DNA conformational alteration induced by a neighboring oligopurine tract on GAATTA enables nicking by EcoRI.
abstract: The pseudo EcoRI site GAATTA in the U3 region of the long terminal repeat of human immunodeficiency virus, which is flanked by a 26-base pair oligopurine tract, is readily nicked by either EcoRI or RsrI. The strand-specific nick occurs predominantly between the G and A residues and is independent of negative supercoiling. Other GAATTA sites surrounded by random (non-oligopurine) sequences are not nicked by these restriction endonucleases. However, other types and lengths of oligopurine tracts are effective in inducing the nicking in neighboring GAATTA sites. Hence, we propose that the flanking oligopurine tracts induce an altered DNA conformation on the GAATTA target site which may be similar to the transition state induced by EcoRI when binding to its canonical recognition site. Gel retardation analyses on restriction fragments containing the oligopurine-GAATTA-oligopurine sequences suggest the presence of helical axis distortions which are consistent with this interpretation.
authors.affiliation: Department of Biochemistry, School of Medicine, University of Alabama, Birmingham 35294.
authors.forename: S
authors.initials: S
authors.lastname: Venditti
authors.forename: R D
authors.initials: RD
authors.lastname: Wells
mesh_terms: D001483:Base Sequence; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D016325:HIV Long Terminal Repeat; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D013379:Substrate Specificity
chemical_list: D004279:DNA, Viral; D009838:Oligodeoxyribonucleotides; D015246:Deoxyribonuclease EcoRI