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

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

2009-03-10

arxiv.org/abs/0903.1826v1

Biophysical Journal 96 4464-4469 (2009)

Physics

Condensed Matter

Statistical Mechanics

To appear in Biophys. J. 8 pages, supplementary information included (7 pages)

Scientific paper

10.1016/j.bpj.2009.03.035

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.

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