Dielectric response of triplex DNA in ionic solution from simulations

L. Yang; S. Weerasinghe; P. E. Smith; B. M. Pettitt

doi:10.1016/S0006-3495(95)80022-6

Dielectric response of triplex DNA in ionic solution from simulations

L. Yang, S. Weerasinghe, P. E. Smith, B. M. Pettitt

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71 Scopus citations

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 language	English (US)
Pages (from-to)	1519-1527
Number of pages	9
Journal	Biophysical journal
Volume	69
Issue number	4
DOIs	https://doi.org/10.1016/S0006-3495(95)80022-6
State	Published - 1995
Externally published	Yes

ASJC Scopus subject areas

Biophysics

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10.1016/S0006-3495(95)80022-6

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title = "Dielectric response of triplex DNA in ionic solution from simulations",

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.",

author = "L. Yang and S. Weerasinghe and Smith, {P. E.} and Pettitt, {B. M.}",

note = "Funding Information: The authors thank Jason Cheng and John Perkyns for valuable discussions. We are grateful to the Robert A. Welch Foundation, the National Institutes of Health, and the National Science Foundation for partial support of this work. The SDSC and NSF are thanked for computational support.",

year = "1995",

doi = "10.1016/S0006-3495(95)80022-6",

language = "English (US)",

volume = "69",

pages = "1519--1527",

journal = "Biophysical journal",

issn = "0006-3495",

publisher = "Biophysical Society",

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TY - JOUR

T1 - Dielectric response of triplex DNA in ionic solution from simulations

AU - Yang, L.

AU - Weerasinghe, S.

AU - Smith, P. E.

AU - Pettitt, B. M.

N1 - Funding Information: The authors thank Jason Cheng and John Perkyns for valuable discussions. We are grateful to the Robert A. Welch Foundation, the National Institutes of Health, and the National Science Foundation for partial support of this work. The SDSC and NSF are thanked for computational support.

PY - 1995

Y1 - 1995

N2 - 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.

AB - 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.

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DO - 10.1016/S0006-3495(95)80022-6

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SP - 1519

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JO - Biophysical journal

JF - Biophysical journal

IS - 4

ER -

Dielectric response of triplex DNA in ionic solution from simulations

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