title: Direct Simulation of the Self-Assembly of a Small DNA Origami.
abstract: By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies.
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom.
authors.forename: Benedict E K
authors.initials: BE
authors.lastname: Snodin
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom.
authors.forename: Flavio
authors.initials: F
authors.lastname: Romano
authors.affiliation: Faculty of Physics, University of Vienna , Boltzmanngasse 5, A-1090 Vienna, Austria.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Rovigatti
authors.affiliation: Department of Mathematics, Imperial College , 180 Queen's Gate, London SW7 2AZ, United Kingdom.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ouldridge
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford, OX1 3NP, United Kingdom.
authors.forename: Ard A
authors.initials: AA
authors.lastname: Louis
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom.
authors.forename: Jonathan P K
authors.initials: JP
authors.lastname: Doye
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D006358:Hot Temperature; D056004:Molecular Dynamics Simulation; D036103:Nanotechnology / Q000379:methods*
chemical_list: D004247:DNA
keywords: DNA nanotechnology; DNA origami; coarse-grained modeling; self-assembly; simulation