Ion and solvent density distributions around canonical B-DNA from integral equations

Jesse J. Howard, Gillian C. Lynch, Bernard Pettitt

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

We calculate the water and ion spatial distributions around charged oligonucleotides using a renormalized three-dimensional reference interaction site theory coupled with the HNC closure. Our goal is to understand the balance between inter-DNA strand forces and solvation forces as a function of oligonucleotide length in the short strand limit. The DNA is considered in aqueous electrolyte solutions of 1 M KCl, 0.1 M KCl, or 0.1 M NaCl. The current theoretical results are compared to molecular dynamics (MD) simulations and experiments. It is found that the integral equation (IE) theory replicates the MD and the experimental results for the base-specific hydration patterns in both the major and the minor grooves. We are also able to discern characteristic structural pattern differences between Na+ and K+ ions. When compared to Poisson-Boltzmann methods, the IE theory, like simulation, predicts a richly structured ion environment, which is better described as multilayer rather than double layer.

Original languageEnglish (US)
Pages (from-to)547-556
Number of pages10
JournalJournal of Physical Chemistry B
Volume115
Issue number3
DOIs
StatePublished - Jan 27 2011
Externally publishedYes

Fingerprint

B-Form DNA
Integral equations
density distribution
integral equations
DNA
deoxyribonucleic acid
oligonucleotides
Oligonucleotides
Ions
strands
Molecular dynamics
molecular dynamics
ions
Solvation
Hydration
grooves
Spatial distribution
Electrolytes
closures
solvation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Ion and solvent density distributions around canonical B-DNA from integral equations. / Howard, Jesse J.; Lynch, Gillian C.; Pettitt, Bernard.

In: Journal of Physical Chemistry B, Vol. 115, No. 3, 27.01.2011, p. 547-556.

Research output: Contribution to journalArticle

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