271243 Twisting Coarse-Grained DNA

Thursday, November 1, 2012: 9:17 AM
411 (Convention Center )
Margaret C. Linak and Kevin D. Dorfman, Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN

DNA can exhibit a wealth of complex shapes and functions in both in vitro and in vivo systems depending on its sequence, environmental conditions, and the forces acting upon the molecule.  These complex configurations are thought to act as beacons and recognition sites for proteins involved in transcription, regulation, and repair along the length of DNA.  However, in order to be able to capture such diverse features, a suitable model must be developed.  Using an experimentally validated, coarse grained model of DNA, we examined the effect of twisting on nucleic acid systems that cannot be captured with other coarse grained models either because they lack the non-canonical interactions needed for advanced structures or because they are parameterized, and thus biased, for double-stranded B-form DNA.  Including features such as Hoogsteen bonding and a smooth transition between single-, double-, and triple-stranded systems allows P-DNA (duplex with bases on the outside) and H-DNA (triplex formed from cruciform structure) systems to be captured.

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