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