Coarse-grained modelling of DNA: biophysics and nanotechnology
Jueves 20 de marzo a las 12:00
Aula 300
Coarse-grained modelling of DNA: biophysics and nanotechnology
Jonathan P. K. Doye
University of Oxford
Abstract:
I will give an overview of the applications of oxDNA, a coarse-grained model of DNA that we have relatively recently developed in Oxford, to study fundamental DNA biophysics and DNA nanotechnology. The biophysical applications include the dynamics of processes such as hybridization, toehold-mediated strand displacement and hairpin formation, and the response of DNA to mechanical stress, including overstretching under tension, the formation of plectonemes, bubbles and cruciforms under twist, and the nature of extreme bending in DNA, as probed, for example, by cyclization reactions. For nanodevices we have studied the opening and closing of DNA nanotweezers, and the action of a two-footed and a burnt-bridges DNA walker. For nanostructures, we have probed the structure and self-assembly of DNA origami, and a variety of DNA polyhedra.The oxDNA code is freely available from http://dna.physics.ox.ac.uk.