Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution.

@article{pakov2003MolecularDS,
  title={Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution.},
  author={Nad'a {\vS}pa{\vc}kov{\'a} and Thomas E. Cheatham and Filip Ryj{\'a}cek and Filip Lanka{\vs} and Luc Van Meervelt and Pavel Hobza and Jiř{\'i} {\vS}poner},
  journal={Journal of the American Chemical Society},
  year={2003},
  volume={125 7},
  pages={1759-69}
}
An extended set of nanosecond-scale molecular dynamics simulations of DNA duplex sequences in explicit solvent interacting with the minor groove binding drug 4',6-diamidino-2-phenylindole (DAPI) are investigated for four different and sequence specific binding modes. Force fields for DAPI have been parametrized to properly reflect its internal nonplanarity. Sequences investigated include the binding modes observed experimentally, that is, AATT in d(CGCGAATTCGCG)(2) and ATTG in d(GGCCAATTGG)(2… CONTINUE READING

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