Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.

@article{Dixit2005MolecularDS,
  title={Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.},
  author={Surjit B. Dixit and David L. Beveridge and David A Case and Thomas E. Cheatham and Elisabetta Giudice and Filip Lanka{\vs} and Richard Lavery and John H Maddocks and Roman Osman and Heinz Sklenar and Kelly M. Thayer and P{\'e}ter V{\'a}rnai},
  journal={Biophysical journal},
  year={2005},
  volume={89 6},
  pages={
          3721-40
        }
}
Molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide basepair steps are reported. The objective is to obtain the calculated dynamical structure for at least two copies of each case, use the results to examine issues with regard to convergence and dynamical stability of MD on DNA, and determine the significance of sequence context effects on all unique dinucleotide steps. This information is essential to understand… CONTINUE READING

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