Molecular dynamics simulation of DNA-functionalized gold nanoparticles

One Sun Lee; George C. Schatz

doi:10.1021/jp8094165

Molecular dynamics simulation of DNA-functionalized gold nanoparticles

One Sun Lee, George C. Schatz

Chemistry

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

78 Scopus citations

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 language	English (US)
Pages (from-to)	2316-2321
Number of pages	6
Journal	Journal of Physical Chemistry C
Volume	113
Issue number	6
DOIs	https://doi.org/10.1021/jp8094165
State	Published - Feb 12 2009

Funding

Special thanks are due to many sponsoring agencies. This work was supported in part by a Sloan Research Fellowship (N.B. Abraham), a research grant from the National Foundation (N.B. Abraham), a research contract from the Army Research Office (N.B. Abraham, L.M. Narducci), a United States-Italy NSF Cooperative Research Grant (N.B. Abraham), a NATO Collaborative Research Grant (N.B. Abraham, L.M. Narducci and P. Mandel), the Fonds National de la Recherche Scientifique (P. Mandel) and the European Commission (P. Mandel). N.B. Abraham wishes to thank the director and staff of the Istituto Nazionale di Ottica for their hospitality and support during the early years of the preparation of this manuscript, and N.B. Abraham and L.M. Narducci are grateful for the pleasant working environment and hospitality offered by the Department of Physics of Jilin University,

ASJC Scopus subject areas

Electronic, Optical and Magnetic Materials
General Energy
Physical and Theoretical Chemistry
Surfaces, Coatings and Films

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10.1021/jp8094165

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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 = "Lee, {One Sun} and Schatz, {George C.}",

note = "Funding Information: Special thanks are due to many sponsoring agencies. This work was supported in part by a Sloan Research Fellowship (N.B. Abraham), a research grant from the National Foundation (N.B. Abraham), a research contract from the Army Research Office (N.B. Abraham, L.M. Narducci), a United States-Italy NSF Cooperative Research Grant (N.B. Abraham), a NATO Collaborative Research Grant (N.B. Abraham, L.M. Narducci and P. Mandel), the Fonds National de la Recherche Scientifique (P. Mandel) and the European Commission (P. Mandel). N.B. Abraham wishes to thank the director and staff of the Istituto Nazionale di Ottica for their hospitality and support during the early years of the preparation of this manuscript, and N.B. Abraham and L.M. Narducci are grateful for the pleasant working environment and hospitality offered by the Department of Physics of Jilin University,",

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PY - 2009/2/12

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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.

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Molecular dynamics simulation of DNA-functionalized gold nanoparticles

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