title: Characterizing the DNA binding modes of a topoisomerase I-poisoning terbenzimidazole: evidence for both intercalative and minor groove binding properties.
abstract: We have used a broad range of spectroscopic and viscometric techniques to demonstrate that the complexation of a cytotoxic, topoisomerase I-poisoning terbenzimidazole (5PTB) with the poly(dA).poly(dT) duplex exhibits properties characteristic of both intercalation and minor groove binding. Our results reveal the following features: (i) Optical melting profiles reveal that 5PTB binding enhances the thermal stability of the poly(dA).poly(dT) duplex; (ii) Fluorescence-detected 5PTB binding to the poly(dA).poly(dT) duplex reveals four apparent "site sizes," ranging from 1 to 13 base pairs (bp) per bound drug; (iii) Flow linear dichroism data suggest conformational heterogeneity among the poly(dA).poly(dT)-bound 5PTB molecules, with substantial contributions from drug molecules bound in the minor groove; (iv) Fluorescence resonance energy transfer data reveal properties characteristic of a significant contribution from an intercalative mode of binding; (v) Viscometric, fluorescence quenching, and netropsin competition data are consistent with 5PTB binding to poly(dA).poly(dT) by "mixed" modes, which are operationally defined as single or multiple binding populations that individually and/or collectively express both intercalative and minor groove binding properties. We comment on a potential correlation between drugs that exhibit such "mixed" mode binding motifs and those that express antineoplastic activity through inhibition of topoisomerase I.
authors.affiliation: Department of Chemistry, Rutgers-State University of New Jersey, New Brunswick 08903, USA.
authors.forename: D S
authors.initials: DS
authors.lastname: Pilch
authors.forename: Z
authors.initials: Z
authors.lastname: Xu
authors.forename: Q
authors.initials: Q
authors.lastname: Sun
authors.forename: E J
authors.initials: EJ
authors.lastname: Lavoie
authors.forename: L F
authors.initials: LF
authors.lastname: Liu
authors.forename: N E
authors.initials: NE
authors.lastname: Geacintov
authors.forename: K J
authors.initials: KJ
authors.lastname: Breslauer
mesh_terms: D001562:Benzimidazoles / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D001667:Binding, Competitive; D002942:Circular Dichroism; D009429:Netropsin / Q000378:metabolism; D011067:Poly dA-dT / Q000378:metabolism; D011485:Protein Binding; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D059004:Topoisomerase I Inhibitors; D014783:Viscosity
chemical_list: C103388:5-phenyl-2-(2'-(benzimidazol-5''-yl)benzimidazol-5'-yl)benzimidazole; D001562:Benzimidazoles; D059004:Topoisomerase I Inhibitors; D011067:Poly dA-dT; D009429:Netropsin