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Center for Nonlinear Studies |
We present a recently developed coarse-grained model for DNA. It captures basic structural, mechanical and thermodynamic properties of both single and double-stranded DNA. Its structural properties agree well with known properties of DNA and its thermodynamic properties are in quantitative agreement with available experimental data. The model reproduces duplex formation from single strands, hairpin formation and melting temperatures of short oligonucleotides. The persistence length and force-extension properties of single strands and double strands in the model are in satisfactory agreement with experiments. Our model allows for calculation of free energy profiles of various DNA systems as well as study of dynamics on long timescales. The model has been successfully used to study DNA biophysics as well as DNA nanotechnology devices. In particular, we will show its applications to the study of toehold-mediated strand displacement reaction, which is an essential component of many DNA nanotechnology systems such as DNA computing, and to the study of DNA hybridization, a process which is still not fully understood despite its importance.
Our coarse-graining techniques have recently been extended to RNA as well. Our simulation code, called oxDNA, is freely available for download at dna.physics.ox.ac.uk
Host: Gnana Gnanakaran