Complexes between osmium tetraoxide bispyridine and DNA: a molecular mechanics study

This study analyzes changes in conformation of five double-stranded DNA fragments related to binding of the single-strand selective probe osmium tetraoxide bispyridine (Os, py) to a thymine. Molecular mechanics was used to investigate four B-DNA and one A-DNA fragments including two structures containing a G.T mispair. The reactivity of a particular thymine was estimated by the difference in energies between interactions in a refined DNA fragment and the corresponding interactions in the transformed fragment with Os, py. Both calculations with and without counterions were performed and the results were in qualitative agreement with experiments. The energetically relaxed fragments with Os, py showed relatively minor global structural changes in comparison to the relaxed fragments without Os, py probe. The computed structures of fragments with Watson-Crick pairing that enable binding of Os, py had similar structural characteristics to geometries found in X-ray studies of single-base mismatches. The possible role of ions in binding Os, py to mispairs is also discussed.