Placement and orientation of individual DNA shapes on lithographically patterned surfaces

Abstract

Artificial DNA nanostructures1,2 show promise for the organization of functional materials3,4 to create nanoelectronic5 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 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° (on diamond-like carbon) or ±20° (on SiO2).

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Figure 1: The problem of random DNA nanostructure deposition and a lithographic scheme for addressing it.
Figure 2: Alignment of DNA origami on SiO2 and diamond-like carbon (DLC) surfaces.
Figure 3: Dynamic binding of DNA origami under atomic force microscopy (AFM).
Figure 4: Placement of triangles onto a variety of shapes.

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Acknowledgements

This work was supported by National Science Foundation grants CCF/NANO/EMT-0622254 and -0829951 and the Focus Center Research Program (FCRP). Center on Functional Engineered Nano Architectonics (FENA) Theme 2. P.W.K.R thanks Microsoft Corporation for support. The authors thank D. Miller for performing XPS measurements, B. Davis for optical lithography, D. Hoffman for sample preparation, and M. Sanchez, M. Hart and F. Houle for helpful discussions.

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All authors contributed significantly to the work presented in this paper.

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Correspondence to Paul W. K. Rothemund or Gregory M. Wallraff.

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Kershner, R., Bozano, L., Micheel, C. et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nature Nanotech 4, 557–561 (2009). https://doi.org/10.1038/nnano.2009.220

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