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Issue 26, 2016
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Flexibility of short DNA helices under mechanical stretching

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Abstract

The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces is obtained by computing the average bending angles between adjacent base pairs along the molecular axis. The ensemble averages are performed over a room temperature equilibrium distribution of base pair separations and bending fluctuations. The analysis of the end-to-end distances and persistence lengths shows that even short sequences with less than 100 base pairs maintain a significant bendability ascribed to thermal fluctuational effects and kinks with large bending angles. The discrepancies between the outcomes of the discrete model and those of the worm-like-chain model are examined pointing out the inadequacy of the latter on short length scales.

Graphical abstract: Flexibility of short DNA helices under mechanical stretching

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Article information


Submitted
04 May 2016
Accepted
03 Jun 2016
First published
03 Jun 2016

Phys. Chem. Chem. Phys., 2016,18, 17666-17677
Article type
Paper

Flexibility of short DNA helices under mechanical stretching

M. Zoli, Phys. Chem. Chem. Phys., 2016, 18, 17666
DOI: 10.1039/C6CP02981G

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