Structure of Homopolymer DNA-CNT Hybrids Suresh Manohar, Tian Tang University

Structure of Homopolymer DNA-CNT Hybrids Suresh Manohar, Tian Tang University www.phwiki.com

Structure of Homopolymer DNA-CNT Hybrids Suresh Manohar, Tian Tang University

Smith, Robert, Features Editor has reference to this Academic Journal, PHwiki organized this Journal Structure of Homopolymer DNA-CNT Hybrids Suresh Manohar, Tian Tang University of Alberta (Canada) What governs the structure of DNA-CNT Is there an optimal wrapping geometry Contributing Terms in the as long as mation of hybrid: Adhesion Entropy loss of DNA backbone Electrostatics Bending in addition to torsion of DNA backbone De as long as mation of CNT Base-Base Stacking Hydrogen bonding + (ns) Contributions to the Binding Energy

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Nucleotide base adsorption on inorganic surfaces (graphite in particular) Edelwirth et al. Surface Science 1998 Sowerby et al. Biosystems 2001 Sowerby et al. PNAS (2001) Vdw stacking interactions Hydrophobic interactions Interfacially enhanced hydrogen bonding DNA on the nanotube: strong binding Contribution due to nanotube de as long as mability can be neglected as long as small-diameter tubes Bending/Twisting ssDNA Bustamante, Bryant, Smith Nature, 421 423 (2003) Very small ‘null’ Kuhn length Large effective Kuhn length at low ionic strength: long range electrostatic repulsion Enthalpic effects

Entropy Loss Due to Backbone Confinement Order of kbT per nm ( in addition to 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 Line of Charges Interacting Through the Debye-Huckel Potential Account as long as nonlinearity using Manning Condensation 100 mM monovalent salt (T = 300K), 1.8 – 3.8 per nm

Contributions to the Binding Energy Molecular Dynamics (MD) Simulation MD was done using CHARMM program in addition to as long as cefield. 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 Pitch = 17.7 nm Minimized Equilibrated at 300K

Phosphate Group Solvated Location of P atoms ( as long as 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 Stacked Base Unstacked 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 W = Adhesion energy as long as single base WAdenine = -7.8 kcal/mol WThymine = -6.3 kcal/mol A > T = Adhesion energy of base in chain Adenine = -2.4 kcal/mol Thymine = -3.3 kcal/mol Poly-dT > Poly-dA 35o stacked base > 35o unstacked base Lateral Mobility of Base Projection of nearest CNT carbon atom onto base plane Mean bond length as long as T base ~ 1.39 Ao Energy Barrier ~ 2 kBT Kuhn Length lk, Kuhn length = 5 nm as long as poly-dT on CNT surface

Analytical Model At low ionic strengths, the competition between electrostatics in addition to effective adhesion lead to an optimal wrapping geometry. 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. Electrostatics is h in addition to led using counterion condenstaion theory. Pitch = 2c a = 9 Ao, d = 2 Ao, = 7 Ao 1 = 80, 2 = 1 Q = -1.609 e-19 C 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 in addition to an analytical model were used to study the hybrid. At low limit of ionic strengths, competition between electrostatics in addition to adhesion leads to optimum wrapped geometry. Poly-dT adheres better than poly-dA even though A>T as long as 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 comm in addition to in CHARMM. Initial structure was minimized as long as 500 steps using Newton Raphson. Two stage heating in addition to equilibration done in NPT ensemble. 400 ps production phase done in NVT ensemble. This procedure was followed as long as structures with varying helical pitches. Gold coated AFM tip Do Force Measurements on samples with Graphite or CNT in water Attach thiolated ssDNA to the tip Extract pull-off as long as ce in addition to adhesion energy Get Force-Deflection plot Scheme as long as AFM experiment

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Force plot as long as (DNA + 2-mercaptoethanol) tip on graphite in water Force plot as long as Au tip on graphite in water CNT Sample in water Graphite in water Ongoing Work AFM experiments. Molecular simulations to estimate the binding free energy between Graphite/CNT in addition to single DNA base (A,T,C,G) using Thermodynamic Integration in addition to Density of States method.

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