Molecular dynamics simulation of DNA-functionalized gold nanoparticles

One-Sun Lee, George C. Schatz

Research output: Contribution to journalArticle

62 Citations (Scopus)

Abstract

Molecular dynamics methods have been used to study a 2 nm gold nanoparticle that is functionalized with four single stranded DNAs at the atomistic level. The DNA strands, which are attached to the [111] faces of a 201 atom truncated octahedral gold particle with a -S(CH 2) 6- linker, are found to be perpendicular to the surface of the particle, with the alkane chain lying on the surface. There are no significant hydrogen bonding interactions between the adsorbed ss-DNAs during the simulation. Even though the expected radius would be 49 Å (3.4 Å per base) for a Watson-Crick DNA structure, the simulation with 0.5 M salt shows a radius of about 29 Å (2.2 Å per base), which is a result that is consistent with recent experimental reports. It is alsofound that the sodium concentration within 30 Å of the gold particle is about 20% higher than the bulk concentration. This is consistent with an observed increase in the melting temperature of DNA when many functionalized gold particles are hybridized together.

Original languageEnglish
Pages (from-to)2316-2321
Number of pages6
JournalJournal of Physical Chemistry C
Volume113
Issue number6
DOIs
Publication statusPublished - 12 Feb 2009
Externally publishedYes

Fingerprint

Gold
Molecular dynamics
DNA
deoxyribonucleic acid
gold
molecular dynamics
Nanoparticles
nanoparticles
Computer simulation
simulation
Alkanes
Single-Stranded DNA
radii
Melting point
Hydrogen bonds
Salts
strands
Sodium
Paraffins
alkanes

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Electronic, Optical and Magnetic Materials
  • Surfaces, Coatings and Films
  • Energy(all)

Cite this

Molecular dynamics simulation of DNA-functionalized gold nanoparticles. / Lee, One-Sun; Schatz, George C.

In: Journal of Physical Chemistry C, Vol. 113, No. 6, 12.02.2009, p. 2316-2321.

Research output: Contribution to journalArticle

@article{42e90bcee4c64c0d94437068502e80a5,
title = "Molecular dynamics simulation of DNA-functionalized gold nanoparticles",
abstract = "Molecular dynamics methods have been used to study a 2 nm gold nanoparticle that is functionalized with four single stranded DNAs at the atomistic level. The DNA strands, which are attached to the [111] faces of a 201 atom truncated octahedral gold particle with a -S(CH 2) 6- linker, are found to be perpendicular to the surface of the particle, with the alkane chain lying on the surface. There are no significant hydrogen bonding interactions between the adsorbed ss-DNAs during the simulation. Even though the expected radius would be 49 {\AA} (3.4 {\AA} per base) for a Watson-Crick DNA structure, the simulation with 0.5 M salt shows a radius of about 29 {\AA} (2.2 {\AA} per base), which is a result that is consistent with recent experimental reports. It is alsofound that the sodium concentration within 30 {\AA} of the gold particle is about 20{\%} higher than the bulk concentration. This is consistent with an observed increase in the melting temperature of DNA when many functionalized gold particles are hybridized together.",
author = "One-Sun Lee and Schatz, {George C.}",
year = "2009",
month = "2",
day = "12",
doi = "10.1021/jp8094165",
language = "English",
volume = "113",
pages = "2316--2321",
journal = "Journal of Physical Chemistry C",
issn = "1932-7447",
publisher = "American Chemical Society",
number = "6",

}

TY - JOUR

T1 - Molecular dynamics simulation of DNA-functionalized gold nanoparticles

AU - Lee, One-Sun

AU - Schatz, George C.

PY - 2009/2/12

Y1 - 2009/2/12

N2 - Molecular dynamics methods have been used to study a 2 nm gold nanoparticle that is functionalized with four single stranded DNAs at the atomistic level. The DNA strands, which are attached to the [111] faces of a 201 atom truncated octahedral gold particle with a -S(CH 2) 6- linker, are found to be perpendicular to the surface of the particle, with the alkane chain lying on the surface. There are no significant hydrogen bonding interactions between the adsorbed ss-DNAs during the simulation. Even though the expected radius would be 49 Å (3.4 Å per base) for a Watson-Crick DNA structure, the simulation with 0.5 M salt shows a radius of about 29 Å (2.2 Å per base), which is a result that is consistent with recent experimental reports. It is alsofound that the sodium concentration within 30 Å of the gold particle is about 20% higher than the bulk concentration. This is consistent with an observed increase in the melting temperature of DNA when many functionalized gold particles are hybridized together.

AB - Molecular dynamics methods have been used to study a 2 nm gold nanoparticle that is functionalized with four single stranded DNAs at the atomistic level. The DNA strands, which are attached to the [111] faces of a 201 atom truncated octahedral gold particle with a -S(CH 2) 6- linker, are found to be perpendicular to the surface of the particle, with the alkane chain lying on the surface. There are no significant hydrogen bonding interactions between the adsorbed ss-DNAs during the simulation. Even though the expected radius would be 49 Å (3.4 Å per base) for a Watson-Crick DNA structure, the simulation with 0.5 M salt shows a radius of about 29 Å (2.2 Å per base), which is a result that is consistent with recent experimental reports. It is alsofound that the sodium concentration within 30 Å of the gold particle is about 20% higher than the bulk concentration. This is consistent with an observed increase in the melting temperature of DNA when many functionalized gold particles are hybridized together.

UR - http://www.scopus.com/inward/record.url?scp=65249155473&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=65249155473&partnerID=8YFLogxK

U2 - 10.1021/jp8094165

DO - 10.1021/jp8094165

M3 - Article

VL - 113

SP - 2316

EP - 2321

JO - Journal of Physical Chemistry C

JF - Journal of Physical Chemistry C

SN - 1932-7447

IS - 6

ER -