Distinguishing Single DNA Nucleotides Based on Their Times of Flight Through Nanoslits: A Molecular Dynamics Simulation Study

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• 作者：Brian R. Novak ; Dorel Moldovan ; Dimitris E. Nikitopoulos ; Steven A. Soper
• 刊名：The Journal of Physical Chemistry B
• 出版年：2013
• 出版时间：March 28, 2013
• 年：2013
• 卷：117
• 期：12
• 页码：3271-3279
• 全文大小：420K
• 年卷期：v.117,no.12(March 28, 2013)
• ISSN：1520-5207

文摘

Transport of single molecules in nanochannels or nanoslits might be used to identify them via their transit (flight) times. In this paper, we present molecular dynamics simulations of transport of single deoxynucleotide 5鈥?monophoshates (dNMP) in aqueous solution under pressure-driven flow, to average velocities between 0.4 and 1.0 m/s, in 3 nm wide slits with hydrophobic walls. The simulation results show that, while moving along the slit, the mononucleotides are adsorbed and desorbed from the walls multiple times. For the simulations, the estimated minimum slit length required for separation of the dNMP flight time distributions is about 5.9 渭m, and the minimum analysis time per dNMP is about 10 渭s. These are determined by the nature of the nucleotide鈥搘all interactions, channel width, and by the flow characteristics. A simple analysis using realistic dNMP velocities shows that, in order to reduce the effects of diffusional broadening and keep the analysis time per dNMP reasonably small, the nucleotide velocity should be relatively high. Tailored surface chemistry could lead to further reduction of the analysis time toward its minimum value for a given driving force.