Molecular dynamics simulation of ions and water around triplex DNA

V. Mohan, Paul E. Smith, Bernard Pettitt

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

We report the results of a 100-ps molecular dynamics simulation study of triple helical DNA with explicit water, counterions, and salt using periodic boundary conditions at 300 K. The simulation involved an antiparallel reverse-Hoogsteen-like homopolymeric CGG 7-mer triple helix, 837 water molecules, 21 Na+ ions, and 1 M NaCl. We have used the Ewald method to compute the electrostatic interactions. Specific ion and water associations as well as relative solvent and ion mobilities are reported. Specific patterns of ion and water molecule associations are found which are novel and may have implications for stability and recognition of triplex-forming oligonucleotides by duplex DNA. Exchanges of ions around neighboring phosphate were found to correspond to a concerted mechanism of displacement. Comparisons are made with available data from related systems.

Original languageEnglish (US)
Pages (from-to)12984-12990
Number of pages7
JournalJournal of Physical Chemistry
Volume97
Issue number49
StatePublished - 1993
Externally publishedYes

Fingerprint

Molecular dynamics
DNA
deoxyribonucleic acid
Ions
molecular dynamics
Water
Computer simulation
water
ions
simulation
Molecules
oligonucleotides
Oligonucleotides
Coulomb interactions
helices
molecules
Ion exchange
phosphates
Phosphates
Salts

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry

Cite this

Molecular dynamics simulation of ions and water around triplex DNA. / Mohan, V.; Smith, Paul E.; Pettitt, Bernard.

In: Journal of Physical Chemistry, Vol. 97, No. 49, 1993, p. 12984-12990.

Research output: Contribution to journalArticle

Mohan, V. ; Smith, Paul E. ; Pettitt, Bernard. / Molecular dynamics simulation of ions and water around triplex DNA. In: Journal of Physical Chemistry. 1993 ; Vol. 97, No. 49. pp. 12984-12990.
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