Placement and orientation of individual DNA shapes on lithographically patterned surfaces

Artificial DNA nanostructures(1,2) show promise for the organization of functional materials(3,4) to create nanoelectronic(5) or nano-optical devices. DNA origami, in which a long single strand of DNA is folded into a shape using shorter 'staple strands'(6), can display 6-nm-resolution patterns of binding sites, in principle allowing complex arrangements of carbon nanotubes, silicon nanowires, or quantum dots. However, DNA origami are synthesized in solution and uncontrolled deposition results in random arrangements; this makes it difficult to measure the properties of attached nanodevices or to integrate them with conventionally fabricated microcircuitry. Here we describe the use of electron-beam lithography and dry oxidative etching to create DNA origami-shaped binding sites on technologically useful materials, such as SiO2 and diamond-like carbon. In buffer with similar to 100 mM MgCl2, DNA origami bind with high selectivity and good orientation: 70-95% of sites have individual origami aligned with an angular dispersion (+/- 1 s.d.) as low as +/- 10 degrees (on diamond-like carbon) or +/- 20 degrees (on SiO2).