Molecular Modeling-Based Energy Analysis of Dimeric Binding of Ligands to the Minor DNA Groove

Molecular-modeling methods have been used to perform energy analysis of dimeric complex formation between lexitropsins and double-stranded DNA. Stabilization of dimeric complexes by hydrophobic and van der Waals interactions has been demonstrated. Electrostatic interactions and the contributions of hydrogen bonds and changes in the number of degrees of freedom had a destabilizing influence. The energy of monomeric and dimeric binding has been compared.