Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffolds as well as a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75?nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure's surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT. 1. Introduction The design and self-assembly of DNA strands into precisely defined objects on the nanometer scale has emerged as a promising technique in the field of nanotechnology. Stemming from the initial idea of generating periodic lattices from DNA [1], the concurrent exploitation of (i) complimentary base pairing between short strands, (ii) branch-like Holliday junctions, and (iii) the inherent helical twist of double-stranded DNA complexes has allowed for the assembly of small, identical motifs which constitute the repeating unit cells of periodic two-dimensional sheets or three-dimensional crystal structures extending nearly to the millimeter scale [2–5]. The development of techniques to build rigid, three-dimensional DNA-based structures is, however, an important aspect to the future utilization of this methodology in nanofabrication [6–11]. While many attempts to construct simple three-dimensional polyhedra have been fraught with problems of instability, unwanted by-products, low-yield, or overly complex synthesis strategies, the recent utilization of hierarchical assembly schemes [12] and the DNA origami technique [13, 14] has provided a path towards the relatively simple generation of uniform populations. The DNA origami technique is based on the use of a long, usually circular “scaffold” strand, which is folded and clamped into a desired shape by hybridization with hundreds of shorter “staple” oligonucleotides [13]. In contrast to earlier schemes for generating nanostructures from synthesized oligonucleotides, the utilization of a viral
References
[1]
N. C. Seeman, “Nucleic acid junctions and lattices,” Journal of Theoretical Biology, vol. 99, no. 2, pp. 237–247, 1982.
[2]
E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman, “Design and self-assembly of two-dimensional DNA crystals,” Nature, vol. 394, no. 6693, pp. 539–544, 1998.
[3]
J. Malo, J. C. Mitchell, C. Vénien-Bryan et al., “Engineering a 2D protein-DNA crystal,” Angewandte Chemie—International Edition, vol. 44, no. 20, pp. 3057–3061, 2005.
[4]
Y. He, Y. Chen, H. Liu, A. E. Ribbe, and C. Mao, “Self-assembly of hexagonal DNA two-dimensional (2D) arrays,” Journal of the American Chemical Society, vol. 127, no. 35, pp. 12202–12203, 2005.
[5]
J. Zheng, J. J. Birktoft, Y. Chen et al., “From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal,” Nature, vol. 461, no. 7260, pp. 74–77, 2009.
[6]
J. Chen and N. C. Seeman, “Synthesis from DNA of a molecule with the connectivity of a cube,” Nature, vol. 350, no. 6319, pp. 631–633, 1991.
[7]
Y. Zhang and N. C. Seeman, “Construction of a DNA-truncated octahedron,” Journal of the American Chemical Society, vol. 116, no. 5, pp. 1661–1669, 1994.
[8]
W. M. Shih, J. D. Quispe, and G. F. Joyce, “A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron,” Nature, vol. 427, no. 6975, pp. 618–621, 2004.
[9]
J. Zimmermann, M. P. J. Cebulla, S. M?nninghoff, and G. von Kiedrowski, “Self-assembly of a DNA dodecahedron from 20 trisoligonucleotides with C3h linkers,” Angewandte Chemie—International Edition, vol. 47, no. 19, pp. 3626–3630, 2008.
[10]
R. P. Goodman, I. A. T. Schaap, C. F. Tardin et al., “Chemistry: rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication,” Science, vol. 310, no. 5754, pp. 1661–1665, 2005.
[11]
Z. Li, B. Wei, J. Nangreave et al., “A replicable tetrahedral nanostructure self-assembled from a single DNA strand,” Journal of the American Chemical Society, vol. 131, no. 36, pp. 13093–13098, 2009.
[12]
Y. He, T. Ye, M. Su et al., “Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra,” Nature, vol. 452, no. 7184, pp. 198–201, 2008.
[13]
P. W. K. Rothemund, “Folding DNA to create nanoscale shapes and patterns,” Nature, vol. 440, no. 7082, pp. 297–302, 2006.
[14]
S. M. Douglas, H. Dietz, T. Liedl, B. H?gberg, F. Graf, and W. M. Shih, “Self-assembly of DNA into nanoscale three-dimensional shapes,” Nature, vol. 459, no. 7245, pp. 414–418, 2009.
[15]
B. H?gberg, T. Liedl, and W. M. Shih, “Folding DNA origami from a double-stranded source of scaffold,” Journal of the American Chemical Society, vol. 131, no. 26, pp. 9154–9155, 2009.
[16]
E. Pound, J. R. Ashton, H. A. Becerril, and A. T. Woolley, “Polymerase chain reaction based scaffold preparation for the production of thin, branched DNA origami nanostructures of arbitrary sizes,” Nano Letters, vol. 9, no. 12, pp. 4302–4305, 2009.
[17]
S. M. Douglas, J. J. Chou, and W. M. Shih, “DNA-nanotube-induced alignment of membrane proteins for NMR structure determination,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 16, pp. 6644–6648, 2007.
[18]
I. H. Stein, V. Schüller, P. B?hm, P. Tinnefeld, and T. Liedl, “Single-molecule FRET ruler based on rigid DNA origami blocks,” ChemPhysChem, vol. 12, no. 3, pp. 689–695, 2011.
[19]
C. Steinhauer, R. Jungmann, T. L. Sobey, F. C. Simmel, and P. Tinnefeld, “DNA origami as a nanoscopic ruler for superresolution microscopy,” Angewandte Chemie—International Edition, vol. 48, no. 47, pp. 8870–8873, 2009.
[20]
T. Liedl, B. H?gberg, J. Tytell, D. E. Ingber, and W. M. Shih, “Self-assembly of three-dimensional prestressed tensegrity structures from DNA,” Nature Nanotechnology, vol. 5, no. 7, pp. 520–524, 2010.
[21]
H. Dietz, S. M. Douglas, and W. M. Shih, “Folding DNA into twisted and curved nanoscale shapes,” Science, vol. 325, no. 5941, pp. 725–730, 2009.
[22]
B. Huang, M. Bates, and X. Zhuang, “Super-resolution fluorescence microscopy,” Annual Review of Biochemistry, vol. 78, pp. 993–1016, 2009.
[23]
S. W. Hell, “Microscopy and its focal switch,” Nature Methods, vol. 6, no. 1, pp. 24–32, 2009.
[24]
R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F. C. Simmel, “Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami,” Nano Letters, vol. 10, no. 11, pp. 4756–4761, 2010.
[25]
S. M. Douglas, A. H. Marblestone, S. Teerapittayanon, A. Vazquez, G. M. Church, and W. M. Shih, “Rapid prototyping of 3D DNA-origami shapes with caDNAno,” Nucleic Acids Research, vol. 37, no. 15, pp. 5001–5006, 2009.
[26]
R. Jungmann, T. Liedl, T. L. Sobey, W. Shih, and F. C. Simmel, “Isothermal assembly of DNA origami structures using denaturing agents,” Journal of the American Chemical Society, vol. 130, no. 31, pp. 10062–10063, 2008.
[27]
C. E. Castro, F. Kilchherr, D.-N. Kim et al., “A primer to scaffolded DNA origami,” Nature Methods, vol. 8, no. 3, pp. 221–229, 2011.
[28]
A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka, and H. Sugiyama, “Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces,” ACS Nano, vol. 5, no. 1, pp. 665–671, 2011.
[29]
K. N. Kim, K. Sarveswaran, L. Mark, and M. Lieberman, “Comparison of methods for orienting and aligning DNA origami,” Soft Matter, vol. 7, no. 10, pp. 4636–4643, 2011.
[30]
M. Rief, H. Clausen-Schaumann, and H. E. Gaub, “Sequence-dependent mechanics of single DNA molecules,” Nature Structural Biology, vol. 6, no. 4, pp. 346–349, 1999.
[31]
T. Strunz, K. Oroszlan, R. Sch?fer, and H. J. Güntherodt, “Dynamic force spectroscopy of single DNA molecules,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 20, pp. 11277–11282, 1999.
[32]
M. Grandbois, M. Beyer, M. Rief, H. Clausen-Schaumann, and H. E. Gaub, “How strong is a covalent bond?” Science, vol. 283, no. 5408, pp. 1727–1730, 1999.
[33]
C. Steinhauer, C. Forthmann, J. Vogelsang, and P. Tinnefeld, “Superresolution microscopy on the basis of engineered dark states,” Journal of the American Chemical Society, vol. 130, no. 50, pp. 16840–16841, 2008.
[34]
Software for PAINT analysis, http://www.e14.ph.tum.de.
[35]
A.-P. Eskelinen, A. Kuzyk, T. K. Kaltiaisenaho et al., “Assembly of single-walled carbon nanotubes on DNA-origami templates through streptavidin-biotin interaction,” Small, vol. 7, no. 6, pp. 746–750, 2011.
[36]
R. Schreiber, S. Kempter, S. Holler, et al., “DNA origami templated growth of arbitrarily shaped metal nanoparticles,” Small, vol. 7, no. 13, pp. 1795–1799, 2011.
[37]
K. Keren, M. Krueger, R. Gilad, G. Ben-Yoseph, U. Sivan, and E. Braun, “Sequence-specific molecular lithography on single DNA molecules,” Science, vol. 297, no. 5578, pp. 72–75, 2002.
[38]
J. Liu, Y. Geng, E. Pound et al., “Metallization of branched DNA origami for nanoelectronic circuit fabrication,” ACS Nano, vol. 5, no. 3, pp. 2240–2247, 2011.