Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage

One Sun Lee, George C Schatz

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Molecular dynamics methods have been used to study the conformation of ds-DNA on a gold surface for low surface coverage at the atomistic level. Each ds-DNA strand, which is attached to the [111] surface of gold with a -S(CH 2)6- linker, is found to be nearly perpendicular to the surface and maintaining the Watson-Crick B-DNA conformation. The tilt angle between the ds-DNA and an axis normal to the gold surface is 7.3 ± 2.2°. The concentration of counterions around the ds-DNA is increased by a factor of 1.8 relative to the bulk, which is significantly lower than in our previous simulations of ds-DNA at high surface coverage.

Original languageEnglish
Title of host publicationMaterials Research Society Symposium Proceedings
Pages55-61
Number of pages7
Volume1177
Publication statusPublished - 2009
Event2009 MRS Spring Meeting - San Francisco, CA, United States
Duration: Apr 13 2009Apr 17 2009

Other

Other2009 MRS Spring Meeting
CountryUnited States
CitySan Francisco, CA
Period4/13/094/17/09

Fingerprint

Gold
Molecular dynamics
DNA
deoxyribonucleic acid
gold
molecular dynamics
Computer simulation
simulation
Conformations
B-Form DNA
strands
methylidyne

ASJC Scopus subject areas

  • Materials Science(all)
  • Condensed Matter Physics
  • Mechanical Engineering
  • Mechanics of Materials

Cite this

Lee, O. S., & Schatz, G. C. (2009). Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage. In Materials Research Society Symposium Proceedings (Vol. 1177, pp. 55-61)

Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage. / Lee, One Sun; Schatz, George C.

Materials Research Society Symposium Proceedings. Vol. 1177 2009. p. 55-61.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Lee, OS & Schatz, GC 2009, Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage. in Materials Research Society Symposium Proceedings. vol. 1177, pp. 55-61, 2009 MRS Spring Meeting, San Francisco, CA, United States, 4/13/09.
Lee OS, Schatz GC. Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage. In Materials Research Society Symposium Proceedings. Vol. 1177. 2009. p. 55-61
Lee, One Sun ; Schatz, George C. / Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage. Materials Research Society Symposium Proceedings. Vol. 1177 2009. pp. 55-61
@inproceedings{3d93e0fb070142a3909b807ec3f05559,
title = "Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage",
abstract = "Molecular dynamics methods have been used to study the conformation of ds-DNA on a gold surface for low surface coverage at the atomistic level. Each ds-DNA strand, which is attached to the [111] surface of gold with a -S(CH 2)6- linker, is found to be nearly perpendicular to the surface and maintaining the Watson-Crick B-DNA conformation. The tilt angle between the ds-DNA and an axis normal to the gold surface is 7.3 ± 2.2°. The concentration of counterions around the ds-DNA is increased by a factor of 1.8 relative to the bulk, which is significantly lower than in our previous simulations of ds-DNA at high surface coverage.",
author = "Lee, {One Sun} and Schatz, {George C}",
year = "2009",
language = "English",
isbn = "9781617383960",
volume = "1177",
pages = "55--61",
booktitle = "Materials Research Society Symposium Proceedings",

}

TY - GEN

T1 - Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage

AU - Lee, One Sun

AU - Schatz, George C

PY - 2009

Y1 - 2009

N2 - Molecular dynamics methods have been used to study the conformation of ds-DNA on a gold surface for low surface coverage at the atomistic level. Each ds-DNA strand, which is attached to the [111] surface of gold with a -S(CH 2)6- linker, is found to be nearly perpendicular to the surface and maintaining the Watson-Crick B-DNA conformation. The tilt angle between the ds-DNA and an axis normal to the gold surface is 7.3 ± 2.2°. The concentration of counterions around the ds-DNA is increased by a factor of 1.8 relative to the bulk, which is significantly lower than in our previous simulations of ds-DNA at high surface coverage.

AB - Molecular dynamics methods have been used to study the conformation of ds-DNA on a gold surface for low surface coverage at the atomistic level. Each ds-DNA strand, which is attached to the [111] surface of gold with a -S(CH 2)6- linker, is found to be nearly perpendicular to the surface and maintaining the Watson-Crick B-DNA conformation. The tilt angle between the ds-DNA and an axis normal to the gold surface is 7.3 ± 2.2°. The concentration of counterions around the ds-DNA is increased by a factor of 1.8 relative to the bulk, which is significantly lower than in our previous simulations of ds-DNA at high surface coverage.

UR - http://www.scopus.com/inward/record.url?scp=77954256261&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77954256261&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:77954256261

SN - 9781617383960

VL - 1177

SP - 55

EP - 61

BT - Materials Research Society Symposium Proceedings

ER -