Characterizing the DNA binding modes of a topoisomerase I-poisoning terbenzimidazole: evidence for both intercalative and minor groove binding properties.
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.
Pilch
D S
DS
Department of Chemistry, Rutgers-State University of New Jersey, New Brunswick 08903, USA.
Xu
Z
Z
Sun
Q
Q
Lavoie
E J
EJ
Liu
L F
LF
Geacintov
N E
NE
Breslauer
K J
KJ
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
C103388:5-phenyl-2-(2'-(benzimidazol-5''-yl)benzimidazol-5'-yl)benzimidazole; D001562:Benzimidazoles; D059004:Topoisomerase I Inhibitors; D011067:Poly dA-dT; D009429:Netropsin