Petr Sulc
Biodesign Institute and School of Molecular Sciences
Arizona State University
Tempe, AZ

Monday, October 10, 2022
3:00 pm (CT)
Hybrid webinar recording

Abstract

DNA and RNA nanotechnology use designed nucleic acid strands to self- assemble large-scale nanostructures and devices. Computer simulations can provide valuable insights into their function but modeling such systems faces several challenges: The nucleic acid nanostructure assembly and function consists of rare events such as creation and breaking of base pairs, and their sizes are typically up to few thousands of nucleotides. We present a top-down coarse-grained model, oxDNA, which was specifically designed for simulations of DNA nanotechnology systems, and present examples where it has been used to help design and understand function of DNA, RNA and protein-DNA hybrid nanostructures and processes. In particular, we will show the model's use to study of DNA origami tetrastack lattice design (a multicomponent nanostructure consisting of a million of nucleotides, with promising applications to metamaterial design), DNA and RNA strand displacement reaction (a fundamental mechanism in nucleic acid computing) and simulations of ATP-powered DNA leaf-spring engine. We will also present our online browser-based tools for design of DNA and protein-DNA/RNA hybrid nanostructures and provide interactive in-browser simulations to help users design structures with desired function.