title: Single-molecule observations of topotecan-mediated TopIB activity at a unique DNA sequence.
abstract: The rate of DNA supercoil removal by human topoisomerase IB (TopIB) is slowed down by the presence of the camptothecin class of antitumor drugs. By preventing religation, these drugs also prolong the lifetime of the covalent TopIB-DNA complex. Here, we use magnetic tweezers to measure the rate of supercoil removal by drug-bound TopIB at a single DNA sequence in real time. This is accomplished by covalently linking camptothecins to a triple helix-forming oligonucleotide that binds at one location on the DNA molecule monitored. Surprisingly, we find that the DNA dynamics with the TopIB-drug interaction restricted to a single DNA sequence are indistinguishable from the dynamics observed when the TopIB-drug interaction takes place at multiple sites. Specifically, the DNA sequence does not affect the instantaneous supercoil removal rate or the degree to which camptothecins increase the lifetime of the covalent complex. Our data suggest that sequence-dependent dynamics need not to be taken into account in efforts to develop novel camptothecins.
authors.affiliation: Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Koster
authors.forename: Fabian
authors.initials: F
authors.lastname: Czerwinski
authors.forename: Ludovic
authors.initials: L
authors.lastname: Halby
authors.forename: Aurélien
authors.initials: A
authors.lastname: Crut
authors.forename: Pierre
authors.initials: P
authors.lastname: Vekhoff
authors.forename: Komaraiah
authors.initials: K
authors.lastname: Palle
authors.forename: Paola B
authors.initials: PB
authors.lastname: Arimondo
authors.forename: Nynke H
authors.initials: NH
authors.lastname: Dekker
mesh_terms: D000970:Antineoplastic Agents / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D001483:Base Sequence; D001696:Biomechanical Phenomena; D004247:DNA / Q000737:chemistry; D004264:DNA Topoisomerases, Type I / Q000737:chemistry / Q000378:metabolism; D004278:DNA, Superhelical / Q000737:chemistry / Q000187:drug effects*; D004791:Enzyme Inhibitors / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D059004:Topoisomerase I Inhibitors; D019772:Topotecan / Q000031:analogs & derivatives* / Q000494:pharmacology
chemical_list: D000970:Antineoplastic Agents; D004278:DNA, Superhelical; D004791:Enzyme Inhibitors; D059004:Topoisomerase I Inhibitors; C051802:triplex DNA; D019772:Topotecan; D004247:DNA; D004264:DNA Topoisomerases, Type I; C528909:TOP1 protein, human