Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage
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1177-Z09-33
Molecular dynamics simulation of ds-DNA on a gold surface at low surface coverage One-Sun Lee and George C. Schatz* Department of Chemistry, Northwestern University 2145 Sheridan Road, Evanston IL 60208-3113
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(CH2)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. Introduction DNA functionalized gold nanoparticles (DNA-Au NPs) have many unique properties including optical, thermodynamic and structural.1 As a result, the DNA-Au NPs have been used in applications to DNA detection, showing the ability to differentiate complementary target ssDNAs from those with single mismatches with high selectivity and sensitivity.2 DNA functionalized gold surfaces have also been used for a wide variety of applications including sequencing,3 drug discovery,4 and biosensing.2 The conformation and other structural properties of the DNAs adsorbed on the nanoparticles or surfaces in these applications significantly affects the properties, however only limited information about these properties is available from experiment. In this paper we use molecular dynamics (MD) simulations to study these properties at the atomistic level. Recently, we developed a model of DNA-Au NPs for the study of ss-DNA chemically adsorbed on a gold particle.5 A truncated octahedron structure composed of 201 gold atoms (diameter ~1.8 nm) is used for the structure of the nanoparticle, and four ss-DNAs are attached to the [111] faces of the particle. From our 8 ns MD simulations, it is found that the attached ssDNAs are well separated from each other and perpendicular to the surface of gold nanoparticle. Even though the expected radius of the DNA-Au NP 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 also found that the sodium ion concentration within 30 Å of the gold particle is about 20% higher than the bulk concentration. In another study, we examined the conformation of ds-DNAs and their interaction with the neighboring ds-DNAs on a [111] gold surface using MD simulations.6 The interaxis distance between the ds-DNAs was initialized at 27 Å in these studies to simulate high packing conditions, and a flexible linker with the surface was included to allow the DNAs to readjust positions and conformations.. We performed a 20 ns MD simulation in water with high salt concentration
([Na+] = 0.62 M), and found th
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