title: Optimized assembly and covalent coupling of single-molecule DNA origami nanoarrays.
abstract: Artificial DNA nanostructures, such as DNA origami, have great potential as templates for the bottom-up fabrication of both biological and nonbiological nanodevices at a resolution unachievable by conventional top-down approaches. However, because origami are synthesized in solution, origami-templated devices cannot easily be studied or integrated into larger on-chip architectures. Electrostatic self-assembly of origami onto lithographically defined binding sites on Si/SiO2 substrates has been achieved, but conditions for optimal assembly have not been characterized, and the method requires high Mg2+ concentrations at which most devices aggregate. We present a quantitative study of parameters affecting origami placement, reproducibly achieving single-origami binding at 94±4% of sites, with 90% of these origami having an orientation within ±10° of their target orientation. Further, we introduce two techniques for converting electrostatic DNA-surface bonds to covalent bonds, allowing origami arrays to be used under a wide variety of Mg2+-free solution conditions.
authors.affiliation: Departments of †Bioengineering, ‡Computer Science, and §Computation & Neural Systems, California Institute of Technology , Pasadena, California 91125, United States.
authors.forename: Ashwin
authors.initials: A
authors.lastname: Gopinath
authors.forename: Paul W K
authors.initials: PW
authors.lastname: Rothemund
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D012825:Silicon / Q000737:chemistry; D012822:Silicon Dioxide / Q000737:chemistry
chemical_list: D012822:Silicon Dioxide; D004247:DNA; D008274:Magnesium; D012825:Silicon
keywords: DNA nanotechnology; directed self-assembly; nanoarray; single molecule; surface diffusion