Dielectric response of triplex DNA in ionic solution from simulations

L. Yang, S. Weerasinghe, P. E. Smith, Bernard Pettitt

Research output: Contribution to journalArticle

71 Citations (Scopus)

Abstract

We have analyzed a 1.2-ns molecular dynamics simulation of 51 mM d(CG·G)7 with 21 Na+ counter-ions and 1 M NaCl in water. Via the dipole fluctuations, the dielectric constant for the DNA is found to be around 16, whereas that for the bases and sugars combined is only 3. The dielectric constant for water in this system is 41, which is much smaller than 71 for pure SPC/E water, because of the strong restriction imposed on the motion of water molecules by the DNA and the ions. Also addressed in the present work are several technical issues related to the calculation of the dipole moment of an ionic solution from molecular dynamics simulations using periodic boundary conditions.

Original languageEnglish (US)
Pages (from-to)1519-1527
Number of pages9
JournalBiophysical Journal
Volume69
Issue number4
StatePublished - 1995
Externally publishedYes

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Water
Molecular Dynamics Simulation
Ions
DNA
triplex DNA

ASJC Scopus subject areas

  • Biophysics

Cite this

Yang, L., Weerasinghe, S., Smith, P. E., & Pettitt, B. (1995). Dielectric response of triplex DNA in ionic solution from simulations. Biophysical Journal, 69(4), 1519-1527.

Dielectric response of triplex DNA in ionic solution from simulations. / Yang, L.; Weerasinghe, S.; Smith, P. E.; Pettitt, Bernard.

In: Biophysical Journal, Vol. 69, No. 4, 1995, p. 1519-1527.

Research output: Contribution to journalArticle

Yang, L, Weerasinghe, S, Smith, PE & Pettitt, B 1995, 'Dielectric response of triplex DNA in ionic solution from simulations', Biophysical Journal, vol. 69, no. 4, pp. 1519-1527.
Yang, L. ; Weerasinghe, S. ; Smith, P. E. ; Pettitt, Bernard. / Dielectric response of triplex DNA in ionic solution from simulations. In: Biophysical Journal. 1995 ; Vol. 69, No. 4. pp. 1519-1527.
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