1. Structure of Homopolymer DNA-CNT Hybrids
Suresh Manohar, Tian Tang*
*University of Alberta (Canada)

2. Contributing Terms in the formation of hybrid:
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

3. 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 CNT’s < 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.

4. 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

5. Contribution due to nanotube deformability can be neglected for small-diameter tubes

6. 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, (2003)

7. 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

8. Enthalpic terms (stretch, bend, twist) – negligible!
Small ‘null’ Kuhn length!

9. Electrostatics 100 mM monovalent salt (T = 300K), 1.8 – 3.8 per nm
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

10. 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 CNT’s < 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.

11. 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.

12. Equilibration
Minimized
Equilibrated at 300K
Pitch = 17.7 nm

13. 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

14. 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

15. Unstacking of Bases

16. Reduction of Effective Adhesion Energy
α ≤ 35o stacked base
α > 35o unstacked base
W = Adhesion energy for single base
WAdenine = -7.8 kcal/mol
WThymine = -6.3 kcal/mol
A > T
γ = Adhesion energy of base in chain
γAdenine = -2.4 kcal/mol
γThymine = -3.3 kcal/mol
Poly-dT > Poly-dA

17. 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

18. Kuhn Length
lk, Kuhn length = 5 nm for poly-dT on CNT surface

19. Analytical Model
Pitch = 2πc
a = 9 Ao, d = 2 Ao, δ = 7 Ao
ε1 = 80, ε2 = 1
Q = e-19 C
At low ionic strengths, the competition between electrostatics and effective adhesion lead to an optimal wrapping geometry.
Free energy due to adhesion, Gad = -lγ, where l is the arc length of DNA per unit length of CNT, γ is the adhesion energy per unit arc length of DNA.
Electrostatics is handled using counterion condenstaion theory.

20. Sum charge-charge interactions on a Helix Apply counterion-condensation theory
g = gad + gel
Free energy of hybrid,

21. For low-ionic strength, competition between electrostatics & adhesion gives an optimal helical wrap

22. 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 A>T for single bases.

23. 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 (DNA+CNT+ions) 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.

24. 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 24

25. Force plot for Au tip on graphite in water
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 25

26. 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. 26