1. Coarse-Grained Hybrid Molecular
Dynamics Simulation of DNA
translocation through a nanopore
K. Yan, Y. Z. Chen

2. A.
NANOPORE DNA ANALYSIS

3. • Typical system
K. Healy et al, 2005

4. • Field-induced translocation
– DNA is immersed in electrolyte
– DNA is attracted to the pore
– DNA permeates the membrane through the pore

5. • Sequencing using ionic current blockage
Daniel Branton et al, 2008

6. • 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

7. 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.

8. Other techniques
• Recapture and trapping
– Improve measurement accuracy
M. Gershow et al, Nature Nanotechnology, 2007

9. Other techniques
• Optical readout
– Improve signal contrast
Daniel Branton et al, 2008

10. 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

11. Capture Rate
• Capture rate (Rc) -> Sensitivity
M. Wanunu, 2008

12. • How to improve Rc
– Increasing voltage
• Decrease signal duration
– Decreasing temperature
• Decrease ion mobility, degrading the signal

13. 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

14. Numerical Calculation
• Deformation of DNA chain
– Stretching
– Folding
– Bending
• Translocation process
– Capture
– Escape
– Recapture

15. • Numerical method for studying many-particle
systems
– Quantum theoretical calculation (ab initio)
– Molecular mechanics (MM)
– Monte Carlo (MC)
– Molecular dynamics (MD)

16. B.
METHODOLOGY

17. 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

18. 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)

19. 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

20. Electric Field
• Why not uniform electric field ?
Typical Nanopore inner surface. A. V. Sokirko, 1994

21. Electric Field
• Nanopore axial sections
A. V. Sokirko, 1994

22. 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

23. • Pore shape
– To make region 3 negligible
H
d1 d2

24. C.
RESULTS AND ANALYSIS

25. 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

26. • Test run
– Observation of stretching under electric force

41. Simulation Results
• Snapshots of the chain conformations
– Outside pore
– DNA Capture
– Inside pore
• Center of Mass (CoM) plotted against time

42. System A
• Nanopore geometry:
– Inner diameters: d1=2.0nm, d2=2.5nm
– Length H=20nm

43. System A
• Electrostatic Field (without DNA)

44. System A
• Snapshots of the chain conformations
– Outside pore (every 100 timesteps)
– DNA Capture
– Inside pore

45. System A
• Snapshots of the chain conformations
– Outside pore
– DNA Capture (every 100 timesteps)
– Inside pore

46. System A
• Snapshots of the chain conformations
– Outside pore
– DNA Capture
– Inside pore (every 1,000 timesteps)

47. System A
• Center of Mass plotted against time

48. System A
• Center of Mass plotted against time

49. System B
• Nanopore geometry:
– Inner diameters: d1=4.0nm, d2=5.0nm
– Length: H=40nm

50. System B
• Snapshots of the chain conformations
– Outside pore (every 100 timesteps)
– DNA Capture
– Inside pore

51. System B
• Snapshots of the chain conformations
– Outside pore
– DNA Capture (every 100 timesteps)
– Inside pore

52. System B
• Snapshots of the chain conformations
– Outside pore
– DNA Capture (every 1,000 timesteps)
– Inside pore

53. System B
• Snapshots of the chain conformations
– Outside pore
– DNA Capture
– Inside pore (every 10,000 timesteps)

54. System B
• Center of Mass plotted against time

55. System B
• Center of Mass plotted against time

56. D.
DISCUSSIONS

57. • 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

58. SMA Research Fellow
Ph.D., University of Hong Kong
DR. YAN KUN