A molecular simulation picture of DNA hydration around A- and B-DNA

Michael Feig, Bernard Pettitt

Research output: Contribution to journalArticle

81 Citations (Scopus)

Abstract

Recent results from molecular dynamics (MD) simulations on hydration of DNA with respect to conformation are reviewed and compared with experimental data. MD simulations of explicit solvent around DNA can now give a detailed model of DNA that not only matches well with the experimental data but provides additional insight beyond current experimental limitations. Such simulation results are analyzed with a focus on differential hydration properties between A- and B-DNA and between C/G and A/T base pairs. The extent of hydration is determined from the number of waters in the primary shell and compared to experimental numbers from different measurements. High- resolution hydration patterns around the whole DNA are shown and correlated with the conformations. The role of ions associating with DNA is discussed with respect to changes in the hydration structure correlating with DNA conformation. (C) 2000 John Wiley and Sons, Inc.

Original languageEnglish (US)
Pages (from-to)199-209
Number of pages11
JournalBiopolymers
Volume48
Issue number4
DOIs
StatePublished - 1998
Externally publishedYes

Fingerprint

B-Form DNA
Hydration
DNA
Conformations
Molecular Dynamics Simulation
Molecular dynamics
Nucleic Acid Conformation
Base Pairing
Computer simulation
Ions
Water

Keywords

  • Conformation
  • DNA hydration
  • Molecular dynamics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics

Cite this

A molecular simulation picture of DNA hydration around A- and B-DNA. / Feig, Michael; Pettitt, Bernard.

In: Biopolymers, Vol. 48, No. 4, 1998, p. 199-209.

Research output: Contribution to journalArticle

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