Sodium and chlorine ions as part of the DNA solvation shell

Michael Feig; B. Montgomery Pettitt

doi:10.1016/S0006-3495(99)77023-2

Sodium and chlorine ions as part of the DNA solvation shell

Michael Feig, B. Montgomery Pettitt

Research output: Contribution to journal › Article › peer-review

189 Scopus citations

Abstract

The distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C₅T₅) · (A₅G₅) in explicit solvent with 0.8 M additional NaCl salt. One simulation was carried out for 10 ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12 ns with the AMBER force field that preferentially stabilizes B-DNA conformations (Feig and Pettitt, 1998, Biophys. J. 75:134-149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and residence times of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the stabilization of A-DNA and B- DNA conformations are discussed.

Original language	English (US)
Pages (from-to)	1769-1781
Number of pages	13
Journal	Biophysical journal
Volume	77
Issue number	4
DOIs	https://doi.org/10.1016/S0006-3495(99)77023-2
State	Published - Oct 1999
Externally published	Yes

ASJC Scopus subject areas

Biophysics

Access to Document

10.1016/S0006-3495(99)77023-2

Cite this

@article{a718cafb9f704a3b9f8e1cb9ed41ce3e,

title = "Sodium and chlorine ions as part of the DNA solvation shell",

abstract = "The distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C5T5) · (A5G5) in explicit solvent with 0.8 M additional NaCl salt. One simulation was carried out for 10 ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12 ns with the AMBER force field that preferentially stabilizes B-DNA conformations (Feig and Pettitt, 1998, Biophys. J. 75:134-149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and residence times of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the stabilization of A-DNA and B- DNA conformations are discussed.",

author = "Michael Feig and Pettitt, {B. Montgomery}",

note = "Funding Information: We thank the Robert A. Welch Foundation, the Texas Coordinating Board, and the National Institutes of Health for partial support of this research and Gillian C. Lynch for valuable discussions and suggestions. The Metacenter is acknowledged for a generous allocation of computer time at Pittsburgh Supercomputing Center. MSI is acknowledged for providing graphics software support.",

year = "1999",

month = oct,

doi = "10.1016/S0006-3495(99)77023-2",

language = "English (US)",

volume = "77",

pages = "1769--1781",

journal = "Biophysical journal",

issn = "0006-3495",

publisher = "Elsevier B.V.",

number = "4",

}

TY - JOUR

T1 - Sodium and chlorine ions as part of the DNA solvation shell

AU - Feig, Michael

AU - Pettitt, B. Montgomery

N1 - Funding Information: We thank the Robert A. Welch Foundation, the Texas Coordinating Board, and the National Institutes of Health for partial support of this research and Gillian C. Lynch for valuable discussions and suggestions. The Metacenter is acknowledged for a generous allocation of computer time at Pittsburgh Supercomputing Center. MSI is acknowledged for providing graphics software support.

PY - 1999/10

Y1 - 1999/10

N2 - The distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C5T5) · (A5G5) in explicit solvent with 0.8 M additional NaCl salt. One simulation was carried out for 10 ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12 ns with the AMBER force field that preferentially stabilizes B-DNA conformations (Feig and Pettitt, 1998, Biophys. J. 75:134-149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and residence times of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the stabilization of A-DNA and B- DNA conformations are discussed.

AB - The distribution of sodium and chlorine ions around DNA is presented from two molecular dynamics simulations of the DNA fragment d(C5T5) · (A5G5) in explicit solvent with 0.8 M additional NaCl salt. One simulation was carried out for 10 ns with the CHARMM force field that keeps the DNA structure close to A-DNA, the other for 12 ns with the AMBER force field that preferentially stabilizes B-DNA conformations (Feig and Pettitt, 1998, Biophys. J. 75:134-149). From radial distributions of sodium and chlorine ions a primary ion shell is defined. The ion counts and residence times of ions within this shell are compared between conformations and with experiment. Ordered sodium ion sites were found in minor and major grooves around both A and B-DNA conformations. Changes in the surrounding hydration structure are analyzed and implications for the stabilization of A-DNA and B- DNA conformations are discussed.

UR - http://www.scopus.com/inward/record.url?scp=0032851951&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0032851951&partnerID=8YFLogxK

U2 - 10.1016/S0006-3495(99)77023-2

DO - 10.1016/S0006-3495(99)77023-2

M3 - Article

C2 - 10512802

AN - SCOPUS:0032851951

SN - 0006-3495

VL - 77

SP - 1769

EP - 1781

JO - Biophysical journal

JF - Biophysical journal

IS - 4

ER -

Sodium and chlorine ions as part of the DNA solvation shell

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this