13 research outputs found
Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores
The
integration of local heat sources with solid-state nanopores
offers new means for controlling the transmembrane transport of charged
biomacromolecules. In the case of electrophoretic transport of DNA,
recent experimental studies revealed unexpected temperature dependences
of the DNA capture rate, the DNA translocation velocity, and the ionic
current blockades produced by the presence of DNA in the nanopore.
Here, we report the results of all-atom molecular dynamics simulations
that elucidated the effect of temperature on the key microscopic processes
governing electric field-driven transport of DNA through nanopores.
Mimicking the experimental setup, we simulated the capture and subsequent
translocation of short DNA duplexes through a locally heated nanopore
at several temperatures and electrolyte conditions. The temperature
dependence of ion mobility at the DNA surface was found to cause the
dependence of the relative conductance blockades on temperature. To
the first order, the effective force on DNA in the nanopore was found
to be independent of temperature, despite a considerable reduction
of solution viscosity. The temperature dependence of the solution
viscosity was found to make DNA translocations faster for a uniformly
heated system but not in the case of local heating that does not affect
viscosity of solution surrounding the untranslocated part of the molecule.
Increasing solution temperature was also found to reduce the lifetime
of bonds formed between cations and DNA. Using a flow suppression
algorithm, we were able to separate the effects of electro-osmotic
flow and direct ion binding, finding the reduced durations of DNA–ion
bonds to increase, albeit weakly, the effective force experienced
by DNA in an electric field. Unexpectedly, our simulations revealed
a considerable temperature dependence of solvent velocity at the DNA
surfaceî—¸slip velocity, an effect that can alter hydrodynamic
coupling between the motion of DNA and the surrounding fluid
Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores
Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated <i>via</i> a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA
Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores
Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated <i>via</i> a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA
Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores
Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated <i>via</i> a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA
Assessing Graphene Nanopores for Sequencing DNA
Using all-atom molecular dynamics and atomic-resolution
Brownian
dynamics, we simulate the translocation of single-stranded DNA through
graphene nanopores and characterize the ionic current blockades produced
by DNA nucleotides. We find that transport of single DNA strands through
graphene nanopores may occur in single nucleotide steps. For certain
pore geometries, hydrophobic interactions with the graphene membrane
lead to a dramatic reduction in the conformational fluctuations of
the nucleotides in the nanopores. Furthermore, we show that ionic
current blockades produced by different DNA nucleotides are, in general,
indicative of the nucleotide type, but very sensitive to the orientation
of the nucleotides in the nanopore. Taken together, our simulations
suggest that strand sequencing of DNA by measuring the ionic current
blockades in graphene nanopores may be possible, given that the conformation
of DNA nucleotides in the nanopore can be controlled through precise
engineering of the nanopore surface
Assessing Graphene Nanopores for Sequencing DNA
Using all-atom molecular dynamics and atomic-resolution
Brownian
dynamics, we simulate the translocation of single-stranded DNA through
graphene nanopores and characterize the ionic current blockades produced
by DNA nucleotides. We find that transport of single DNA strands through
graphene nanopores may occur in single nucleotide steps. For certain
pore geometries, hydrophobic interactions with the graphene membrane
lead to a dramatic reduction in the conformational fluctuations of
the nucleotides in the nanopores. Furthermore, we show that ionic
current blockades produced by different DNA nucleotides are, in general,
indicative of the nucleotide type, but very sensitive to the orientation
of the nucleotides in the nanopore. Taken together, our simulations
suggest that strand sequencing of DNA by measuring the ionic current
blockades in graphene nanopores may be possible, given that the conformation
of DNA nucleotides in the nanopore can be controlled through precise
engineering of the nanopore surface
Assessing Graphene Nanopores for Sequencing DNA
Using all-atom molecular dynamics and atomic-resolution
Brownian
dynamics, we simulate the translocation of single-stranded DNA through
graphene nanopores and characterize the ionic current blockades produced
by DNA nucleotides. We find that transport of single DNA strands through
graphene nanopores may occur in single nucleotide steps. For certain
pore geometries, hydrophobic interactions with the graphene membrane
lead to a dramatic reduction in the conformational fluctuations of
the nucleotides in the nanopores. Furthermore, we show that ionic
current blockades produced by different DNA nucleotides are, in general,
indicative of the nucleotide type, but very sensitive to the orientation
of the nucleotides in the nanopore. Taken together, our simulations
suggest that strand sequencing of DNA by measuring the ionic current
blockades in graphene nanopores may be possible, given that the conformation
of DNA nucleotides in the nanopore can be controlled through precise
engineering of the nanopore surface
Assessing Graphene Nanopores for Sequencing DNA
Using all-atom molecular dynamics and atomic-resolution
Brownian
dynamics, we simulate the translocation of single-stranded DNA through
graphene nanopores and characterize the ionic current blockades produced
by DNA nucleotides. We find that transport of single DNA strands through
graphene nanopores may occur in single nucleotide steps. For certain
pore geometries, hydrophobic interactions with the graphene membrane
lead to a dramatic reduction in the conformational fluctuations of
the nucleotides in the nanopores. Furthermore, we show that ionic
current blockades produced by different DNA nucleotides are, in general,
indicative of the nucleotide type, but very sensitive to the orientation
of the nucleotides in the nanopore. Taken together, our simulations
suggest that strand sequencing of DNA by measuring the ionic current
blockades in graphene nanopores may be possible, given that the conformation
of DNA nucleotides in the nanopore can be controlled through precise
engineering of the nanopore surface
Assessing Graphene Nanopores for Sequencing DNA
Using all-atom molecular dynamics and atomic-resolution
Brownian
dynamics, we simulate the translocation of single-stranded DNA through
graphene nanopores and characterize the ionic current blockades produced
by DNA nucleotides. We find that transport of single DNA strands through
graphene nanopores may occur in single nucleotide steps. For certain
pore geometries, hydrophobic interactions with the graphene membrane
lead to a dramatic reduction in the conformational fluctuations of
the nucleotides in the nanopores. Furthermore, we show that ionic
current blockades produced by different DNA nucleotides are, in general,
indicative of the nucleotide type, but very sensitive to the orientation
of the nucleotides in the nanopore. Taken together, our simulations
suggest that strand sequencing of DNA by measuring the ionic current
blockades in graphene nanopores may be possible, given that the conformation
of DNA nucleotides in the nanopore can be controlled through precise
engineering of the nanopore surface
Stretching and Controlled Motion of Single-Stranded DNA in Locally Heated Solid-State Nanopores
Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated <i>via</i> a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4–8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA