title: De novo reconstruction of DNA origami structures through atomistic molecular dynamics simulation.
abstract: The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures.
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, IL 61801, USA Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, IL 61801, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Maffeo
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, IL 61801, USA Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, IL 61801, USA.
authors.forename: Jejoong
authors.initials: J
authors.lastname: Yoo
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, IL 61801, USA Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, IL 61801, USA Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, USA aksiment@illinois.edu.
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
mesh_terms: D020285:Cryoelectron Microscopy; D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA