The molecular structure of the complex of hoechst 33258 and the DNA dodecamer d(CGCGAATTCGCG)

Mai Kun Teng, Nassim Usman, Christin A. Frederick, Andrew H.J. Wang

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343 Citations (Scopus)


The crystal structure of the complex between the dodecamer d(CGCGAATTCGCG) and a synthetic dye molecule Hoechst 33258 was solved by X-ray diffraction analysis and refined to an R-factor of 15.7% at 2.25 9 Åresolution The crescent-shaped Hoechst compound is found to bind to the central four AATT base pairs in the narrow minor groove of the B-DNA double helix. The piperazine ring of the drug has its flat face almost parallel to the aromatic bisbenzimidazole ring and lies sideways in the minor groove. No evidence of disordered structure of the drug is seen in the complex. The binding of Hoechst to DNA is stabilized by a combination of hydrogen bonding, van der Waals interaction and electrostatic interactions. The binding preference for AT base pairs by the drug is the result of the close contact between the Hoechst molecule and the C2 hydrogen atoms of adenine. The nature of these contacts precludes the binding of the drug to G-C base airs due to the presence of N2 amino groups of guanines. The present crystal structural information agrees well with the data obtained from chemical footprinting experiments.

Original languageEnglish
Pages (from-to)2671-2690
Number of pages20
JournalNucleic Acids Research
Issue number6
Publication statusPublished - Mar 25 1988
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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