title: The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex.
abstract: While the self-assembly of different types of DNA origami into well-defined complexes could produce nanostructures on which thousands of locations can be independently functionalized with nanometer-scale precision, current assembly processes have low yields. Biomolecular complex formation requires relatively strong interactions and reversible assembly pathways that prevent kinetic trapping. To characterize how these issues control origami complex yields, the equilibrium constants for each possible reaction for the assembly of a heterotetrameric ring, the unit cell of a rectangular lattice, were measured using fluorescence colocalization microscopy. We found that origami interface structure controlled reaction free energies. Cooperativity, measured for the first time for a DNA nanostructure assembly reaction, was weak. Simulations of assembly kinetics suggest assembly occurs via parallel pathways with the primary mechanism of assembly being hierarchical: two dimers form that then bind to one another to complete the ring.
authors.affiliation: Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.
authors.forename: Joshua
authors.initials: J
authors.lastname: Fern
authors.affiliation: Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Lu
authors.affiliation: Chemical and Biomolecular Engineering, Johns Hopkins University , Baltimore, Maryland 21218, United States.|Computer Science, Johns Hopkins University , Baltimore, Maryland 21218, United States.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Schulman
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure*; D004867:Equipment Design; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure*; D036103:Nanotechnology; D013816:Thermodynamics
chemical_list: D004247:DNA
keywords: DNA nanotechnology; DNA origami; equilibrium thermodynamics; reaction pathway analysis; self-assembly