Characterizing the DNA binding modes of a topoisomerasei-poisoning terbenzimidazole: Evidence for both intercalative and minor groove binding properties

Daniel S. Pilch, Zhitao Xu, Qun Sun, Edmond J. Lavoie, Leroy-Fong Liu, Nicholas E. Geacintov, Kenneth J. Breslauer

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23 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)115-133
Number of pages19
JournalDrug Design and Discovery
Issue number3-4
Publication statusPublished - 1996
Externally publishedYes



  • DNA base-drug resonance energy transfer
  • Flow linear dichroism
  • Fluorescence quenching
  • Förster critical distance
  • Mixed mode DNA binding

ASJC Scopus subject areas

  • Molecular Medicine
  • Drug Discovery

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