Molecular dynamics study of oligonucleotides containing difluorotoluene

Extended molecular dynamics (MD) and thermodynamic integration (MD-TI) calc ulations have been used to determine the structural and energetic changes i n DNA that accompany the replacement of thymine (T) by the nonnatural isost ere difluorotoluene (F). In a duplex DNA oligonucleotide, it is found that the T-->F mutation leads to only small changes in the average structure, bu t to important alterations in flexibility, hydration, and recognition prope rties. The T-->F mutation in the Watson-Crick or Hoogsteen position of a py rimidine purine pyrimidine type DNA tripler does not lead to dramatic chang es in the general structure of the tripler, but again, detailed analysis sh ows some alterations in flexibility, hydration, and recognition properties. MD-TI calculations on the T-->F mutation in duplex DNA reproduce the exper imentally determined free energy differences with good accuracy, and detail ed analyses of the trajectories have enabled us to rationalize these. Final ly, MD-TI simulations have been used to predict the changes in stability of a tripler due to a T-->F mutation in either the Watson-Crick or Hoogsteen- binding pyrimidine strands. We predict that in either case the mutation wil l reduce stability, being most unfavorable in the Watson-Crick strand.