Use of electric linear dichroism and competition experiments with intercalating drugs to investigate the mode of binding of Hoechst 33258, berenil and DAPI to GC sequences

J Biomol Struct Dyn. 1995 Oct;13(2):351-66. doi: 10.1080/07391102.1995.10508845.


The drugs Hoechst 33258, berenil and DAPI bind preferentially to the minor groove of AT sequences in DNA. Despite a strong selectivity for AT sites, they can interact with GC sequences by a mechanism which remains so far controversial. The 2-amino group of guanosine represents a steric hindrance to the entry of the drugs in the minor groove of GC sequences. Intercalation and major groove binding to GC sites of GC-rich DNA and polynucleotides have been proposed for these drugs. To investigate further the mode of binding of Hoechst 33258, berenil and DAPI to GC sequences, we studied by electric linear dichroism the mutual interference in the DNA binding reaction between these compounds and a classical intercalator, proflavine, or a DNA-threading intercalating drug, the amsacrine-4-carboxamide derivative SN16713. The results of the competition experiments show that the two acridine intercalators markedly affect the binding of Hoechst 33258, berenil and DAPI to GC polynucleotides but not to DNA containing AT/GC mixed sequences such as calf thymus DNA. Proflavine and SN16713 exert dissimilar effects on the binding of Hoechst 33258, berenil and DAPI to GC sites. The structural changes in DNA induced upon intercalation of the acridine drugs into GC sites are not identically perceived by the test compounds. The electric linear dichroism data support the hypothesis that Hoechst 33258, berenil and DAPI interact with GC sites via a non-classical intercalation process.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding, Competitive
  • Bisbenzimidazole / chemistry
  • Diminazene / analogs & derivatives
  • Diminazene / chemistry
  • Indoles / chemistry
  • Intercalating Agents / chemistry*
  • Molecular Sequence Data
  • Molecular Structure
  • Poly dA-dT / chemistry
  • Polydeoxyribonucleotides / chemistry*
  • Spectrum Analysis / methods*


  • Indoles
  • Intercalating Agents
  • Polydeoxyribonucleotides
  • Poly dA-dT
  • poly(dC-dG)
  • DAPI
  • diminazene aceturate
  • Bisbenzimidazole
  • Diminazene