dna translocation through a nanopore
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Coarse-Grained Hybrid Molecular Dynamics Simulation of DNA
translocation through a nanopore
K. Yan, Y. Z. Chen
NANOPORE DNA ANALYSISA.
• Typical system
K. Healy et al, 2005
• Field-induced translocation
– DNA is immersed in electrolyte
– DNA is attracted to the pore
– DNA permeates the membrane through the pore
• Sequencing using ionic current blockage
Daniel Branton et al, 2008
• Why nanopore sequencing?
– Determine the order in which nucleotides occur on a strand of DNA (with minimal sample preparation)
• How it works ?
– Electrophoresis might attract DNA towards nanopore
– DNA might eventually pass through nanopore as a long string, one base at a time
– Each nucleotide obstructs nanopore to a different, characteristic degree
Nanopore sequencing
• if a strand of DNA/RNA could be driven through a nanopore of suitable diameter
– the nucleobases would modulate the ionic current through the nanopore.
• if each nucleotide produced a characteristic modulation of the ionic current
– the sequence of current modulations could reflect the sequence of bases in the polymer.
Other techniques
• Recapture and trapping
– Improve measurement accuracy
M. Gershow et al, Nature Nanotechnology, 2007
Other techniques
• Optical readout
– Improve signal contrast
Daniel Branton et al, 2008
Other techniques
• Reverse DNA translocation
– DNA is pulled mechanically by a magnetic bead
– Parallel manipulations of DNAs in multiple nanopores.
H. Peng et al, Nanotechnology, 2009
Capture Rate
• Capture rate (Rc) -> Sensitivity
M. Wanunu, 2008
• How to improve Rc
– Increasing voltage
• Decrease signal duration
– Decreasing temperature
• Decrease ion mobility, degrading the signal
Key Challenge
• To understand and control the motion of DNA molecule
– High speed
• Ultrafast sequencing but
• Unattainable measurements of very small currents
– Stochastic motion
• increase signal noise
• reduce the potential for single-base resolution
Numerical Calculation
• Deformation of DNA chain
– Stretching
– Folding
– Bending
• Translocation process
– Capture
– Escape
– Recapture
• Numerical method for studying many-particle systems
– Quantum theoretical calculation (ab initio)
– Molecular mechanics (MM)
– Monte Carlo (MC)
– Molecular dynamics (MD)
METHODOLOGYB.
MD method
• What can MD do
– perform hypothetical experiments
• which is still cannot be carried out
– perfect computer experiments
• if the multi-body interactions employed are appropriate
• and can lead to a reasonable description of specific system properties
Coarse-grained model
• A set of atoms are represented by one dynamical unit
– United atom model
• A methylene (CH2) unit is represented by single mass point
– Gay-Berne potential model
• a rigid part of molecule is represented by single ellipsoid
– Bead-spring model
• Several monomer units are represented by single bead (mass point)
Interactions
• Interaction potentials:
– Excluded volume interactions (bead-bead and bead-solvent):
• Short range repulsive LJ potential
– Connectivity between neighboring monomers (bead-bead)
• Finite Extension Nonlinear Elastic (FENE) spring
Electric Field
• Why not uniform electric field ?
Typical Nanopore inner surface. A. V. Sokirko, 1994
Electric Field
• Nanopore axial sections
A. V. Sokirko, 1994
Theoretical model
• Region 1: Inside pore
– Between the inner surface and the ellipsoidal boundary
• Inner surface: a hyperboloid of rotation
• Oblate ellipsoidal coordinate system
• Region 2: Outside pore
– Over the semispherical boundary
• Spherical coordinate system
• Region 3: Area between region 1 and 2
– Between the ellipsoidal and the semispherical boundary
• Contribution can be neglected
• Pore shape
– To make region 3 negligible
d1 d2
H
RESULTS AND ANALYSISC.
Simulation setup
• Each bead
– Correspond to a Kuhn length of a single-stranded DNA containing approximately three nucleotide bases
• Parameters
– Length unit: 1.5 nm
– Mass unit: 936 amu
– Energy unit: 3.39E-21 J
– Time scale: 32.1ps
– force scale: 2.3pN
• Test run
– Observation of stretching under electric force
Simulation Results
• Snapshots of the chain conformations
– Outside pore
– DNA Capture
– Inside pore
• Center of Mass (CoM) plotted against time
System A
• Nanopore geometry:
– Inner diameters: d1=2.0nm, d2=2.5nm
– Length H=20nm
System A
• Electrostatic Field (without DNA)
System A
• Snapshots of the chain conformations
– Outside pore (every 100 timesteps)
– DNA Capture
– Inside pore
System A
• Snapshots of the chain conformations
– Outside pore
– DNA Capture (every 100 timesteps)
– Inside pore
System A
• Snapshots of the chain conformations
– Outside pore
– DNA Capture
– Inside pore (every 1,000 timesteps)
System A
• Center of Mass plotted against time
System A
• Center of Mass plotted against time
System B
• Nanopore geometry:
– Inner diameters: d1=4.0nm, d2=5.0nm
– Length: H=40nm
System B
• Snapshots of the chain conformations
– Outside pore (every 100 timesteps)
– DNA Capture
– Inside pore
System B
• Snapshots of the chain conformations
– Outside pore
– DNA Capture (every 100 timesteps)
– Inside pore
System B
• Snapshots of the chain conformations
– Outside pore
– DNA Capture (every 1,000 timesteps)
– Inside pore
System B
• Snapshots of the chain conformations
– Outside pore
– DNA Capture
– Inside pore (every 10,000 timesteps)
System B
• Center of Mass plotted against time
System B
• Center of Mass plotted against time
DISCUSSIONSD.
• DNAs initially placed up to tens of nanometers from the pore could be captured
• Observation of bending and stretching that accompanies translocation of DNA
• DNA translocation can be slowed down, or even be stopped, before DNA arrived the narrowest part of the pores
DR. YAN KUN
SMA Research Fellow
Ph.D., University of Hong Kong
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