Molecular dynamics simulation of DNA duplex, analog of PPT (polypurine tract), its conformation and hydration: a theoretical study

Author:

Yadav Ramesh Kumar,Yadava Umesh

Publisher

Springer Science and Business Media LLC

Subject

Organic Chemistry,General Pharmacology, Toxicology and Pharmaceutics

Reference20 articles.

1. Alexeev DG, Lipanov AA, Skuratovskii IY (1987) The structure of poly(dA)·poly(dT) as revealed by an X-ray fibre diffraction. J Biomol Struct Dyn 4:989–1012

2. Beveridge DL, Swaminathan S, Ravishanker G, Withka JM, Srinivasan J, Prevost C, Louise-May S, Lanley DR, Dicapua FM, Bolton PH (1993) In: Westhof E (ed) Water and biological macromolecules. CRC Press, Boca Raton

3. Case D, Pearlman DA, Caldwell JW, Cheathum TE, Ross WS, Simmerling C, Darden T, Merz KM, Stanton RV, Cheng A, Vincent JJ, Crowley M, Ferguson BM, Radmen R, Seibel GL, Singh UC, Weiner P, Kollman P (1997) AMBER 5.0. University of California, San Francisco

4. Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA (1995) Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 117:4193–4194

5. Compos JL, Subirana JA (1987) The complex of poly(dG)·poly(dC) with arginine: stabilization of the B form and transition to multistranded structures. J Biomol Struct Dyn 5:15–19

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