Structure of Homopolymer DNA-CNT Hybrids

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Structure of Homopolymer DNA-CNT Hybrids

• Suresh Manohar, Tian Tang
• University of Alberta (Canada)

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What governs the structure of DNA-CNT?Is there
an optimal wrapping geometry?
(ns)

• Contributing Terms in the formation of hybrid
• Adhesion
• Entropy loss of DNA backbone
• Electrostatics
• Bending and torsion of DNA backbone
• Deformation of CNT
• Base-Base Stacking
• Hydrogen bonding

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Contributions to the Binding Energy
Contributing Term Estimate (kT/nm for a 1-nm tube)
1 Base-CNT Adhesion 13-35 (based on base-graphite adsorption data)
2 Entropic free energy increase due to chain confinement 0.4 1.3
3 Electrostatics 1.8 3.8 (100 mM salt)
4 Enthalpy increase due to DNA/CNT deformation Negligible for DNA and for CNTs lt 1 nm in diameter
5 Base-base stacking Order of base-CNT adhesion, absorbed into it.
6 Hydrogen bonding Potentially very important sequence dependent (upto 28 kT for GC in vacuum). Negligible for cases studied here.
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DNA on the nanotube strong binding

• Nucleotide base adsorption on inorganic surfaces
  (graphite in particular)

Vdw stacking interactions Hydrophobic
interactions Interfacially enhanced hydrogen
bonding

Sowerby et al. PNAS (2001)
Edelwirth et al. Surface Science 1998 Sowerby et
al. Biosystems 2001
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Contribution due to nanotube deformability can
be neglected for small-diameter tubes
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Bending/Twisting ssDNA
Very small null Kuhn length? Large effective
Kuhn length at low ionic strength long range
electrostatic repulsion Enthalpic effects?
Bustamante, Bryant, Smith Nature, 421 423 (2003)
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Entropy Loss Due to Backbone Confinement

• Order of kbT per nm (and smaller at low ionic
  strength)
• Important at high ionic strength
• Negligible at low ionic strength

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Enthalpic terms (stretch, bend, twist)
negligible!
Small null Kuhn length!

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Electrostatics

• Line of Charges Interacting Through the
  Debye-Huckel Potential
• Account for nonlinearity using Manning
  Condensation

100 mM monovalent salt (T 300K), 1.8 3.8
per nm
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Contributions to the Binding Energy
Contributing Term Estimate (kT/nm for a 1-nm tube)
1 Base-CNT Adhesion 13-35 (based on base-graphite adsorption data)
2 Entropic free energy increase due to chain confinement 0.4 1.3
3 Electrostatics 1.8 3.8 (100 mM salt)
4 Enthalpy increase due to DNA/CNT deformation Negligible for DNA and for CNTs lt 1 nm in diameter
5 Base-base stacking Order of base-CNT adhesion, absorbed into it.
6 Hydrogen bonding Potentially very important sequence dependent (upto 28 kT for GC in vacuum). Negligible for cases studied here.
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Molecular Dynamics (MD) Simulation

• MD was done using CHARMM program and forcefield.
• Systematic study of poly(T) with 12 bases around
  (10,0) CNT.
• CNT interacts with other atoms through vdw
  interactions only.
• PME Method was used.

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Equilibration


Minimized
Equilibrated at 300K
Pitch 17.7 nm
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Phosphate Group Solvated

Location of P atoms (for DNA with helical pitch
of 61.5 nm). Yellow Starting loactions Red
Final locations P distance 9.8 0.5 Å from CNT
axis
Solvated P atoms. Blue P atoms
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Several Bases Un-Stack

Unstacked BAse
Stacked Base
Stacked Base is at a distance of 3.45 Å from CNT
surface Water envelope starts at a distance of
6.8 0.5 Å from CNT axis
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Unstacking of Bases
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Reduction of Effective Adhesion Energy
a 35o stacked base a gt 35o unstacked base
W Adhesion energy for single base WAdenine
-7.8 kcal/mol WThymine -6.3 kcal/mol A gt T
? Adhesion energy of base in chain ?Adenine
-2.4 kcal/mol ?Thymine -3.3 kcal/mol Poly-dT gt
Poly-dA
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Lateral Mobility of Base



Mean bond length for T base 1.39 Ao Energy
Barrier 2 kBT
Projection of nearest CNT carbon atom onto base
plane
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Kuhn Length

lk, Kuhn length 5 nm for poly-dT on CNT surface
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Analytical Model
Pitch 2pc a 9 Ao, d 2 Ao, d 7 Ao e1 80,
e2 1 Q -1.609 e-19 C

1. At low ionic strengths, the competition between
   electrostatics and effective adhesion lead to an
   optimal wrapping geometry.
2. Free energy due to adhesion, Gad -l?, where l
   is the arc length of DNA per unit length of CNT,
   ? is the adhesion energy per unit arc length of
   DNA.
3. Electrostatics is handled using counterion
   condenstaion theory.

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Sum charge-charge interactions on a HelixApply
counterion-condensation theory
g gad gel
Free energy of hybrid,
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For low-ionic strength, competition between
electrostatics adhesion gives an optimal
helical wrap
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Summary

• Scaling analysis, molecular dynamics and an
  analytical model were used to study the hybrid.
• At low limit of ionic strengths, competition
  between electrostatics and adhesion leads to
  optimum wrapped geometry.
• Poly-dT adheres better than poly-dA even though
  AgtT for single bases.

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Methodology

• Starting structure was created in Materials
  StudioTM (MS).
• Sodium ions placed at a distance of 3.5 Å from P
  atoms.
• A pre-equilibrated water box of dimension
  102x39x33 Å3 was used.
• The solute (DNACNTions) was placed at the
  center of water box.
• Periodic boundary conditions were employed using
  CRYSTAL command in CHARMM.
• Initial structure was minimized for 500 steps
  using Newton Raphson.
• Two stage heating and equilibration done in NPT
  ensemble.
• 400 ps production phase done in NVT ensemble.
• This procedure was followed for structures with
  varying helical pitches.

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Scheme for AFM experiment
Gold coated AFM tip
Attach thiolated ssDNA to the tip
Do Force Measurements on samples with Graphite or
CNT in water
Get Force-Deflection plot
Extract pull-off force and adhesion energy
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CNT Sample in water
Graphite in water
Force plot for Au tip on graphite in water
Force plot for (DNA 2-mercaptoethanol) tip on
graphite in water
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• Ongoing Work
• AFM experiments.
• Molecular simulations to estimate the binding
  free energy between Graphite/CNT and single DNA
  base (A,T,C,G) using Thermodynamic Integration
  and Density of States method.