2 research outputs found
Distinguishing Single DNA Nucleotides Based on Their Times of Flight Through Nanoslits: A Molecular Dynamics Simulation Study
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
Electrophoretic Transport of Single DNA Nucleotides through Nanoslits: A Molecular Dynamics Simulation Study
There is potential for flight time
based DNA sequencing involving
disassembly into individual nucleotides which would pass through a
nanochannel with two or more detectors. We performed molecular dynamics
simulations of electrophoretic motion of single DNA nucleotides through
3 nm wide hydrophobic slits with both smooth and rough walls. The
electric field (<i>E</i>) varied from 0.0 to 0.6 V/nm. The
nucleotides adsorb and desorb from walls multiple times during their
transit through the slit. The nucleotide–wall interactions
differed due to nucleotide hydrophobicities and wall roughness which
determined duration and frequency of nucleotide adsorptions and their
velocities while adsorbed. Transient association of nucleotides with
one, two, or three sodium ions occurred, but the mean association
numbers (ANs) were weak functions of nucleotide type. Nucleotide–wall
interactions contributed more to separation of nucleotide flight time
distributions than ion association and thus indicate that nucleotide–wall
interactions play a defining role in successfully discriminating between
nucleotides on the basis of their flight times through nanochannels/slits.
With smooth walls, smaller nucleotides moved faster, but with rough
walls larger nucleotides moved faster due to fewer favorable wall
adsorption sites. This indicates that roughness, or surface patterning,
might be exploited to achieve better time-of-flight based discrimination
between nucleotides