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

Abstract

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.

Nanoscale Pulling of Type IV Pili Reveals Their Flexibility and Adhesion to Surfaces over Extended Lengths of the Pili

“…Instead, the force plateaus can be interpreted as forced desorption or peeling of an extended length of the T4P from the underlying surface ( Fig. 1 a2), as observed using AFM for other semi-flexible polymer chains (33)(34)(35)(36). If the major pilin subunit mediates adherence, the adhesive force between the T4P and the surface should be constant along the length of the pilus, and the peeling force should remain constant over an extended range of tip-sample separations, producing a force plateau in the AFM force-separation curve (Fig.…”

“…We can understand the relationship between the peeling force f and the adhesion energy per unit length ε through the use of an equilibrium statistical model for the peeling of a freely-jointed-chain (FJC, Kuhn length a ¼ 2L p for the relaxed T4P) that is allowed to slide freely on a flat surface (35). A detailed analysis of this model is presented in the Supporting Material.…”

A novel aptasensor based on single-molecule force spectroscopy for highly sensitive detection of mercury ions

“…For the statistical analysis, all data were expressed as means ± standard deviation (SD) for n>80 (n represents the number of data being analyzed). 26,27 When Hg 2+ is added into the system, a more rigid hairpin-shaped duplex DNA structure will form through formation of T-Hg 2+ -T complexes and folding of the aptamer. The strategy for Hg 2+ detection by our SMFS-based aptasensor is illustrated in Fig.…”

DNA Base Dimers Are Stabilized by Hydrogen-Bonding Interactions Including Non-Watson–Crick Pairing Near Graphite Surfaces

“…21 They reported that stacking interactions were favored in water and hydrogen bonded complexes in nonpolar solvents like carbon tetrachloride. Manohar et al 26 and Iliafar et al 27 conducted measurements of the binding strength of DNA homopolymers by atomic force microscopy-based single molecule force spectroscopy. 22 They also observed that hydrogen bonding interactions were mainly stabilized by electrostatic contribution to the free energies while stacking interactions were mainly stabilized by van der Waals interactions.…”