Molecular dynamics study of oligonucleotides containing difluorotoluene

Extended molecular dynamics (MD) and thermodynamic integration (MD-TI) calculations have been used to determine the structural and energetic changes in DNA that accompany the replacement of thymine (T) by the nonnatural isostere difluorotoluene (F). In a duplex DNA oligonucleotide, it is found that the T-->F mutation leads to only small changes in the average structure, but to important alterations in flexibility, hydration, and recognition properties. The T-->F mutation in the Watson-Crick or Hoogsteen position of a pyrimidine purine pyrimidine type DNA tripler does not lead to dramatic changes in the general structure of the tripler, but again, detailed analysis shows some alterations in flexibility, hydration, and recognition properties. MD-TI calculations on the T-->F mutation in duplex DNA reproduce the experimentally determined free energy differences with good accuracy, and detailed analyses of the trajectories have enabled us to rationalize these. Finally, 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 will reduce stability, being most unfavorable in the Watson-Crick strand.