title: Effect of phosphorothioate substitutions on DNA cleavage by Escherichia coli DNA topoisomerase I.
abstract: To evaluate the structural influence of the DNA phosphate backbone on the activity of Escherichia coli DNA topoisomerase I, modified forms of oligonucleotide dA(7) were synthesized with a chiral phosphorothioate replacing the non-bridging oxygens at each position along the backbone. A deoxy-iodo-uracil replaced the 5'-base to crosslink the oligonucleotides by ultraviolet (UV) and assess binding affinity. At the scissile phosphate there was little effect on the cleavage rate. At the +1 phosphate, the rectus phosphorus (Rp)-thio-substitution reduced the rate of cleavage by a factor of 10. At the +3 and -2 positions from the scissile bond, the Rp-isomer was cleaved at a faster rate than the sinister phosphorus (Sp)-isomer. The results demonstrate the importance of backbone contacts between DNA substrate and E. coli topoisomerase I.
authors.affiliation: Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
authors.forename: C J
authors.initials: CJ
authors.lastname: Roche
authors.forename: Y C
authors.initials: YC
authors.lastname: Tse-Dinh
mesh_terms: D001665:Binding Sites; D020134:Catalytic Domain; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004264:DNA Topoisomerases, Type I / Q000378:metabolism*; D004305:Dose-Response Relationship, Drug; D004926:Escherichia coli / Q000201:enzymology*; D008956:Models, Chemical; D009841:Oligonucleotides / Q000737:chemistry*; D010100:Oxygen / Q000378:metabolism; D010710:Phosphates / Q000737:chemistry; D011485:Protein Binding; D013997:Time Factors
chemical_list: D009841:Oligonucleotides; D010710:Phosphates; D004247:DNA; D004264:DNA Topoisomerases, Type I; D010100:Oxygen