Molecular mechanics of the interactions of spermine with DNA: DNA bending as a result of ligand binding

We used energy minimization of a molecular mechanical force field to evaluate spermine interactions with B-form DNA oligomers with either alternating purine/pyrimidine or homopolymeric sequences. Four different positions for spermine docking-within, along, and bridging the minor groove and bridging the major groove-were assessed for each sequence. Interaction at the major groove of alternating purine/pyrimidine sequences appears to be the most favorable of all models assessed, and are associated with significant bending of DNA. Interactions at the major groove of homopolymers were less favorable than those of heteropolymers and showed little or no bending. Interactions with the minor groove were most favorable for spermine positioned near the base of the groove, and became less favorable as spermine was moved toward the top of the groove. Association along the phosphate backbone alone was the least favorable of the interactions.