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By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville.2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described bythe wormlike chain model, is coupled to base-pair denaturation, we demonstratethat small denaturation bubbles lead to anomalies in the flexibility of DNA atthe nanometric scale, when confined in two dimensions (2D), as reported inatomic force microscopy (AFM) experiments [Wiggins, P. A., et al. 2006. NatureNanotech. 1:137-141]. Our model yields very good fits to experimental data andquantitative predictions that can be tested experimentally. Although suchanomalies exist when DNA fluctuates freely in three dimensions (3D), they aretoo weak to be detected. Interactions between bases in the helicaldouble-stranded DNA are modified by electrostatic adsorption on a 2D substrate,which facilitates local denaturation. This work reconciles the apparentdiscrepancy between observed 2D and 3D DNA elastic properties and points outthat conclusions about the 3D properties of DNA (and its companion proteins andenzymes) do not directly follow from 2D experiments by AFM.

Microscopic mechanism for experimentally observed anomalous elasticity of DNA in 2D