dna translocation through a nanopore

Download DNA translocation through a nanopore

Post on 14-Jul-2015

1.096 views

Category:

Technology

2 download

Embed Size (px)

TRANSCRIPT

  • 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

Recommended

View more >