Abstract
The factors affecting the binding of the minor-groove binding drug, Hoechst 33258, to the DNA double helix, are investigated in this work. The relative contribution of hydrogen bonding, van der Waals contacts and the electrostatic factor are evaluated. This is done by considering the interaction of the four DNA bases adenine, thymine, guanine and cytosine with two different fragments of Hoechst 33258, one representing only hydrogen bonding forces, while the other fragment, comprising the protonated N-methylpiperazine ring bound to a benzimidazole ring, representing electrostatic forces as well. It is found that it is the electrostatic factor that contributes most to its specificity for AT-rich sites. Of the two bases, adenine and thymine, the latter binds more strongly to the drug.
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