Molecular dynamics of water-mediated interactions of a linear benzimidazole-biphenyl diamidine with the DNA minor groove

The dynamics of the DB921-DNA (where DB291 has a benzimidazole-biphenyl system with terminal amidines) complex and the utility of water in designing compounds to recognize DNA are studied by using a 100 ns molecular dynamics simulation of the complex. The results have helped in understanding how water has coupled the linear DB291 compound to the minor groove for tight binding, without a large unfavorable contribution to the entropy of binding.