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Why DNA chains are "kinked" when observed on surfaces

DNA elastic properties on surfaces differ from ones in solution.

par Manoel Manghi, Nicolas Destainville - 17 mars 2009

Atomic Force Microscopy (AFM) is widely used to observe double-stranded DNA adsorbed on surfaces. In recent experiments by Wiggins et al., « anomalies » have been detected in the distribution of bending angles along DNA (which measures its flexibility) : an over-abundance of large angles were found which are not predicted by the traditional statistical model of DNA chains, the Worm-Like Chain model (see figure). N. Destainville, M. Manghi and J. Palmeri of the statistical group of the laboratory explained these anomalies by the presence of small denaturation bubbles (or kinks) facilitated by the presence of the substrate which modifies interactions between DNA base-pairs. They predict that these anomalies exist in 3D but are too weak to be detected and reconcile the apparent discrepency between observed 2D and 3D elastic properties. Hence, conclusions about 3D properties of DNA (and its companion proteins and enzymes) do not directly follow from 2D experiments by AFM.

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Figure : Snapshot of a DNA observed by AFM. The experimental bending angle distribution (symbols) is plotted for three different values of the distance along the chain. It shows a deviation from the Worm Like Chain model (parabola) for large angles which is well fitted by the theory (solid line). A sketch of DNA adsorbed on a 2D charged mica surface and dried in air is shown, highlightening the substantial modification of DNA base-pair states by the experimetal setup compared to 3D in solution.

Reference : Microscopic mechanism for experimentally observed anomalous elasticity of DNA in 2D by N. Destainville, M. Manghi and J. Palmeri, to appear in Biophysical Journal (2009). abstract arxiv0903.1826

Contact : Manoel Manghi