1. Binding Energy between a Nucleotide and Graphite: Single Molecule Force Microscopy (SMFM) – AFM Approach

2. Introduction ssDNA wraps around CNT to form the hybrid. Purpose:
Dispersion, sorting and patterned placement of CNTs.
Transportation of DNA into cells
Thermal ablation to kill cancer cells
Zheng, M. et. al., Nat. Mat. 2003,2,
Motivation:
Binding strength decides stability, dispersion and sorting ability of the hybrid
Interaction of DNA with hydrophobic surfaces

3. Single Base Binding Energy G,A,T,C (kBT)
Reference
23.55, 18.91, 18.91, 18.91
(with graphite)
Gowtham, S. et. Al. Phys Rev B 2007, 76,
25.09, 23.16, 21.23, 18.53
(with CNT)
Johnson, R. R. et. Al. Nano Lett 2008, 8, 1,
50, 45, 43, 40
Shi, X. et. Al. Acta Mech Sinica 2005, 21,
12.1, 13, 10.5, 10.8
Manohar, S. et. Al. J Phys Chem C 2007, 111,
18.9 for Thymine
Manohar, S. et. Al. ACS Nano (submitted)
8 for Adenine (base only)
(with graphite)
Sowerby, S. J. Astrobiology 2001, 1, 4,
11.5 for Thymidine (SMFM)
Manohar, S. et. Al. ACS Nano (submitted)
Current Work

4. Experimental Scheme –
MHA
MHA – Mercaptohexanoic acid ssDNA – 5’-T50-3’-O-(CH2)3-SH

5. Main Results Control Experiments: No tip adhesion
Gold tip with poly-(dT)50 and MHA:
Desorption forces show plateau force jumps.

6. Main Results (contd …) Force jump was independent of:
Location on the graphite surface
Rate of peeling or AFM tip velocity
AFM tip used
Ionic Strength of buffer used. Electrostatic contribution to binding energy is negligible.
Mean value of force jump = 84.2 ± 8.4 pN
Analytical model to relate the measured plateau forces to the binding energy of DNA bases. This gave single base binding energy for Thymidine to be 11.5 ± 0.6 kBT.
MD: Estimated single base pull off from graphite surface for thymine is 18.9 kBT.

7. Results from the Model: PfgT ensemble
Dimensionless free energy of adhesion
Dimensionless Force
Partition Function
Free Energy
Average Number of Desorbed links
Fpeel = 85 pN, b = 1.6 nm, T = 300 K, N = 18
Condition for Desorption
Average end-to-end distance of desorbed chain

8. Results from MD:
Thermodynamic Integration Method
where <F>h is the average force to hold the base at a distance, h from the graphite surface