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Abstract
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 A resolution. 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 pairs 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.
