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

TL;DR

This study explains the anomalous elasticity of DNA observed in 2D AFM experiments by modeling how small denaturation bubbles affect DNA flexibility, revealing that 2D confinement enhances these effects compared to 3D.

Contribution

The paper introduces a coupled model of DNA bending and denaturation that accurately fits experimental 2D AFM data and clarifies the difference between 2D and 3D DNA elasticity.

Findings

Small denaturation bubbles cause significant flexibility anomalies in 2D

The model fits experimental AFM data very well

3D DNA elasticity anomalies are too weak to detect in experiments

Abstract

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.