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

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

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.

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

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

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)

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

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

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

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.

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.

Equilibration Minimized Equilibrated at 300K Pitch = 17.7 nm

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

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

Unstacking of Bases

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

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

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

Analytical Model Pitch = 2πc a = 9 Ao, d = 2 Ao, δ = 7 Ao ε1 = 80, ε2 = 1 Q = -1.609 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.

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

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

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.

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.

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

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

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