Characterizing the DNA binding modes of a topoisomerase I-poisoning terbenzimidazole: evidence for both intercalative and minor groove binding properties

Drug Des Discov. 1996 Apr;13(3-4):115-33.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Benzimidazoles / chemistry
  • Benzimidazoles / metabolism*
  • Binding Sites
  • Binding, Competitive
  • Circular Dichroism
  • Netropsin / metabolism
  • Poly dA-dT / metabolism
  • Protein Binding
  • Spectrometry, Fluorescence
  • Spectrophotometry, Ultraviolet
  • Topoisomerase I Inhibitors*
  • Viscosity


  • 5-phenyl-2-(2'-(benzimidazol-5''-yl)benzimidazol-5'-yl)benzimidazole
  • Benzimidazoles
  • Topoisomerase I Inhibitors
  • Poly dA-dT
  • Netropsin