Bioengineering Research Seminar

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 structure 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 sequence dependent melting temperatures of short oligonucleotides.  The model allows for calculation of free energy profiles of various DNA systems as well as study of dynamics and has been successfully used to study basic DNA biophysics as well as DNA nanotechnology devices such as DNA motors and kissing hairpins. In particular it has been used to help to explain the experimentally observed rates of toehold-mediated strand displacement reaction for different toehold lengths and toehold sequences.  We will present a recent study of DNA hybridization with the coarse-grained model, a process still not fully understood despite its importance. We will further give examples of application of the model to studying properties of single-stranded DNA, kissing hairpins and burnt-bridges DNA motor. Our coarse-graining techniques have recently been extended to RNA as well, with application to study of systems such as kissing RNA hairpins, toehold-mediated strand displacement of RNA molecules  and unzipping of RNA hairpins by pulling. Our simulation code, called oxDNA, is freely available for download at http://dna.physics.ox.ac.uk .