Optimized assembly and covalent coupling of single-molecule DNA origami nanoarrays

ACS Nano. 2014 Dec 23;8(12):12030-40. doi: 10.1021/nn506014s. Epub 2014 Dec 9.


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.

Keywords: DNA nanotechnology; directed self-assembly; nanoarray; single molecule; surface diffusion.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • DNA / chemistry*
  • Magnesium / chemistry
  • Nanostructures / chemistry*
  • Nucleic Acid Conformation*
  • Silicon / chemistry
  • Silicon Dioxide / chemistry


  • Silicon Dioxide
  • DNA
  • Magnesium
  • Silicon