The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami

Methods Mol Biol. 2023:2639:93-112. doi: 10.1007/978-1-0716-3028-0_6.

¹ Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK. jonathan.doye@chem.ox.ac.uk.
² Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
³ Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK.
⁴ Dipartimento di Fisica, Sapienza Universitá di Roma, Rome, Italy.
⁵ School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
⁶ Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford, UK.
⁷ Computational and Information Systems Laboratory, National Center for Atmospheric Research (NCAR), Boulder, USA.
⁸ School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
⁹ Department of Philosophy, Future of Humanity Institute, University of Oxford, Oxford, UK.

Abstract

This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.

Keywords: Coarse-grained models; DNA origami; Molecular simulation.