Dresden 2009 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 20: DNA, RNA and Chromatin

BP 20.5: Vortrag

Donnerstag, 26. März 2009, 15:15–15:30, HÜL 186

overstretching of DNA duplexes studied with steered molecular dynamics simulations — •hui li and thomas gisler — Universität Konstanz, Fachbereich Physik, 78457 Konstanz, Germany

Single-molecule experiments on long-chain DNA show that the molecule can be overstretched at nearly constant force (65-110 pN) to 60% beyond its relaxed contour length. The origin of this plateau in the force-extension curve is still under debate. Molecular dynamics (MD) simulations of a short DNA duplex with 12 base pairs suggest that it is caused by a transition to a new conformation ("S-DNA") with inclined base pairs; competing scenarios based on MD simulations of 12-basepair DNA duplexes and thermodynamic considerations suggest the force plateau to arise from a continuous loss of base pairing under external force.

In this contribution we present results from steered MD simulations of a 30-basepair DNA duplex for which a force plateau was recently observed experimentally. We analyzed the pairing between complementary bases and the tilt angles during the stretching. Structure at the force plateau show a coexistence of "S-DNA" segments with "B-DNA" segment which are separated by denatured bases, which has not been seen in stretching simulations of shorter oligomers. In addition, we study the effect of a mismatched base or a gap in backbone on the force plateau and stretched structure. A mismatched base has little effect on the force curves, but the neighbor segments are unwound at the force plateau. A gap in backbone causes the "nicked" region denatured and stretched more than other parts.