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