Microscopic Mechanism for Experimentally Observed Anomalous Elasticity of DNA in Two Dimensions

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2009 Jun 3

PMID 19486670

Citations 6

Authors

Nicolas Destainville

Manoel Manghi

John Palmeri

Affiliations

Soon will be listed here.

Abstract

By exploring a recent model in which DNA bending elasticity, described by the wormlike chain model, is coupled to basepair 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 experiments. 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 atomic-force microscopy.

Citing Articles

Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.

Saran R, Wang Y, Li I Sensors (Basel). 2020; 20(24).

PMID: 33302459 PMC: 7764255. DOI: 10.3390/s20247019.

Revisiting the Anomalous Bending Elasticity of Sharply Bent DNA.

Cong P, Dai L, Chen H, van der Maarel J, Doyle P, Yan J Biophys J. 2015; 109(11):2338-51.

PMID: 26636945 PMC: 4675846. DOI: 10.1016/j.bpj.2015.10.016.

Probing a label-free local bend in DNA by single molecule tethered particle motion.

Brunet A, Chevalier S, Destainville N, Manghi M, Rousseau P, Salhi M Nucleic Acids Res. 2015; 43(11):e72.

PMID: 25765645 PMC: 4477641. DOI: 10.1093/nar/gkv201.

Atomic force microscopy study of DNA flexibility on short length scales: smooth bending versus kinking.

Mazur A, Maaloum M Nucleic Acids Res. 2014; 42(22):14006-12.

PMID: 25414337 PMC: 4267637. DOI: 10.1093/nar/gku1192.

Probing the elasticity of DNA on short length scales by modeling supercoiling under tension.

Schopflin R, Brutzer H, Muller O, Seidel R, Wedemann G Biophys J. 2012; 103(2):323-30.

PMID: 22853910 PMC: 3400772. DOI: 10.1016/j.bpj.2012.05.050.

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