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Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation

Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation

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LI, Hui, Thomas GISLER, 2009. Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation. In: European physical journal / E. 30(3), pp. 325-332

@article{Li2009Overs-4786, title={Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation}, year={2009}, doi={10.1140/epje/i2009-10524-5}, number={3}, volume={30}, journal={European physical journal / E}, pages={325--332}, author={Li, Hui and Gisler, Thomas} }

2009 Gisler, Thomas Overstretching of a 30 bp DNA duplex studied with steered molecular dynamics simulation: Effects of structural defects on structure and force-extension relation Li, Hui eng 2011-03-24T14:50:19Z Single-molecule experiments on polymeric DNA show that the molecule can be overstretched at nearly constant force by about 70% beyond its relaxed contour length. In this publication we use steered molecular dynamics (MD) simulation to study the effect of structural defects on force-extension curves and structures at high elongation in a 30 base pair duplex pulled by its torsionally unconstrained 5'-5' ends.<br />The defect-free duplex shows a plateau in the force-extension curve at 120 pN in which large segments with inclined and paired bases ( S-DNA ) near both ends of the duplex coexist with a central B-type segment separated from the former by small denaturation bubbles. In the presence of a base mismatch or a nick, force-extension curves are very similar to the ones of the defect-free duplex. For the duplex with a base mismatch, S-type segments with highly inclined base pairs are not observed; rather, the overstretched duplex consists of B-type segments separated by denaturation bubbles. The nicked duplex evolves, via a two-step transition, into a two-domain structure characterized by a large S-type segment coexisting with several short S-type segments which are separated by short denaturation bubbles. Our results suggest that in the presence of nicks the force-extension curve of highly elongated duplex DNA might reflect locally highly inhomogeneous stretching. Li, Hui 2011-03-24T14:50:19Z deposit-license First publ. in: European physical journal / E, 30 (2009), 3, pp. 325-332 application/pdf Gisler, Thomas

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