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

NANOPORE DNA ANALYSIS
• Typical system




                   K. Healy et al, 2005
• Field-induced translocation
  – DNA is immersed in electrolyte
  – DNA is attracted to the pore
  – DNA permeates the me...
• 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 ...
Nanopore sequencing
• if a strand of DNA/RNA could be driven
  through a nanopore of suitable diameter
  – the nucleobases...
Other techniques
• Recapture and trapping
  – Improve measurement accuracy




  M. Gershow et al, Nature Nanotechnology, ...
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 ...
Capture Rate
• Capture rate (Rc) -> Sensitivity




                                     M. Wanunu, 2008
• How to improve Rc
  – Increasing voltage
     • Decrease signal duration
  – Decreasing temperature
     • Decrease ion ...
Key Challenge
• To understand and control the motion of DNA
  molecule
  – High speed
     • Ultrafast sequencing but
    ...
Numerical Calculation
• Deformation of DNA chain
  – Stretching
  – Folding
  – Bending
• Translocation process
  – Captur...
• Numerical method for studying many-particle
  systems
  – Quantum theoretical calculation (ab initio)
  – Molecular mech...
B.

METHODOLOGY
MD method
• What can MD do
  – perform hypothetical experiments
    • which is still cannot be carried out
  – perfect com...
Coarse-grained model
• A set of atoms are represented by one
  dynamical unit
  – United atom model
     • A methylene (CH...
Interactions
• Interaction potentials:
  – Excluded volume interactions (bead-bead and
    bead-solvent):
     • Short ran...
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:...
• Pore shape
  – To make region 3 negligible


                          H



                          d1      d2
C.

RESULTS AND ANALYSIS
Simulation setup
• Each bead
  – Correspond to a Kuhn length of a single-stranded DNA
    containing approximately three n...
• Test run
  – Observation of stretching under electric force
Simulation Results
• Snapshots of the chain conformations
  – Outside pore
  – DNA Capture
  – Inside pore
• Center of Mas...
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
D.

DISCUSSIONS
• DNAs initially placed up to tens of nanometers
  from the pore could be captured
• Observation of bending and stretching...
SMA Research Fellow
Ph.D., University of Hong Kong

DR. YAN KUN
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
DNA translocation through a nanopore
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DNA translocation through a nanopore

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DNA translocation through a nanopore

  1. 1. Coarse-Grained Hybrid Molecular Dynamics Simulation of DNA translocation through a nanopore K. Yan, Y. Z. Chen
  2. 2. A. NANOPORE DNA ANALYSIS
  3. 3. • Typical system K. Healy et al, 2005
  4. 4. • Field-induced translocation – DNA is immersed in electrolyte – DNA is attracted to the pore – DNA permeates the membrane through the pore
  5. 5. • Sequencing using ionic current blockage Daniel Branton et al, 2008
  6. 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. 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. 8. Other techniques • Recapture and trapping – Improve measurement accuracy M. Gershow et al, Nature Nanotechnology, 2007
  9. 9. Other techniques • Optical readout – Improve signal contrast Daniel Branton et al, 2008
  10. 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. 11. Capture Rate • Capture rate (Rc) -> Sensitivity M. Wanunu, 2008
  12. 12. • How to improve Rc – Increasing voltage • Decrease signal duration – Decreasing temperature • Decrease ion mobility, degrading the signal
  13. 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. 14. Numerical Calculation • Deformation of DNA chain – Stretching – Folding – Bending • Translocation process – Capture – Escape – Recapture
  15. 15. • Numerical method for studying many-particle systems – Quantum theoretical calculation (ab initio) – Molecular mechanics (MM) – Monte Carlo (MC) – Molecular dynamics (MD)
  16. 16. B. METHODOLOGY
  17. 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. 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. 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. 20. Electric Field • Why not uniform electric field ? Typical Nanopore inner surface. A. V. Sokirko, 1994
  21. 21. Electric Field • Nanopore axial sections A. V. Sokirko, 1994
  22. 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. 23. • Pore shape – To make region 3 negligible H d1 d2
  24. 24. C. RESULTS AND ANALYSIS
  25. 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. 26. • Test run – Observation of stretching under electric force
  27. 27. Simulation Results • Snapshots of the chain conformations – Outside pore – DNA Capture – Inside pore • Center of Mass (CoM) plotted against time
  28. 28. System A • Nanopore geometry: – Inner diameters: d1=2.0nm, d2=2.5nm – Length H=20nm
  29. 29. System A • Electrostatic Field (without DNA)
  30. 30. System A • Snapshots of the chain conformations – Outside pore (every 100 timesteps) – DNA Capture – Inside pore
  31. 31. System A • Snapshots of the chain conformations – Outside pore – DNA Capture (every 100 timesteps) – Inside pore
  32. 32. System A • Snapshots of the chain conformations – Outside pore – DNA Capture – Inside pore (every 1,000 timesteps)
  33. 33. System A • Center of Mass plotted against time
  34. 34. System A • Center of Mass plotted against time
  35. 35. System B • Nanopore geometry: – Inner diameters: d1=4.0nm, d2=5.0nm – Length: H=40nm
  36. 36. System B • Snapshots of the chain conformations – Outside pore (every 100 timesteps) – DNA Capture – Inside pore
  37. 37. System B • Snapshots of the chain conformations – Outside pore – DNA Capture (every 100 timesteps) – Inside pore
  38. 38. System B • Snapshots of the chain conformations – Outside pore – DNA Capture (every 1,000 timesteps) – Inside pore
  39. 39. System B • Snapshots of the chain conformations – Outside pore – DNA Capture – Inside pore (every 10,000 timesteps)
  40. 40. System B • Center of Mass plotted against time
  41. 41. System B • Center of Mass plotted against time
  42. 42. D. DISCUSSIONS
  43. 43. • 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
  44. 44. SMA Research Fellow Ph.D., University of Hong Kong DR. YAN KUN

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