Distinguishing Single DNA Nucleotides Based on Their
Times of Flight Through Nanoslits: A Molecular Dynamics Simulation
Study
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Abstract
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′-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 μm, and the minimum analysis
time per dNMP is about 10 μs. These are determined by the nature
of the nucleotide–wall 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