Structure of rhodamine 6G-DNA complexes from molecular dynamics simulations

Chromophore-DNA complexes are useful for understanding charge transport along pi-stacks once their structural properties have been clarified. We studied two rhodamine 6G semicapping complexes with 15-mer B-DNA duplexes to determine the preferred orientation of the dye with respect to the neighboring base pair. For each of these systems, two distinct chromophore alignments were identified and quantified in terms of base-step parameters. The obtained geometries agree well with those derived from an NMR structure refinement of similar complexes. Cross-correlation analysis of the base-step parameters shows that slide and twist are highly interdependent during the structural transition from one conformation to the other.