Quantifying Interactions between DNA Oligomers and Graphite Surface Using Single Molecule Force Spectroscopy

In single molecule force spectroscopy experiments, force probes chemically modified with synthetic, single-stranded DNA oligomers produced characteristic steady-state forces connected by abrupt steps between plateaus, as the probes moved away from a graphite substrate. The force plateaus represent peeling of a small number of polymer molecules from the flat surface. The final force jump in the retraction region of the force-distance curves can be attributed to a single DNA molecule detaching from the graphite surface. Previously, Manohar et al. (Nano Lett. 2008, 8, 4365) reported the peeling forces of the pyrimidine oligomers as 85.3 +/- 4.7 and 60.8 +/- 5.5 pN for polythymine and polycytosine, respectively. We measured the force-distance curves for purine oligomers on a graphite surface and found the peeling forces to be 76.6 +/- 3.0 and 66.4 +/- 1.4 pN for polyadenine and polyguanine, respectively. Using a refined model for peeling a single freely jointed polymer chain from a frictionless substrate, we determined a ranking of the effective average binding energy per nucleotide for all four bases as T >= A > G >= C (11.3 +/- 0.8, 9.9 +/- 0.5, 8.3 +/- 0.2, and 7.5 +/- 0.8 k(B)T, respectively). The binding energy determined from the peeling force data did not scale with the size of the base. The distribution of peeling forces of polyguanine from the graphite surface was unusually broad in comparison to the other homopolymers, and often with inconsistent chain extensions, possibly indicating the presence of secondary structures (intra- or intermolecular) for this sequence.