Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Challenges and opportunities for structural DNA nanotechnology

Abstract

DNA molecules have been used to build a variety of nanoscale structures and devices over the past 30 years, and potential applications have begun to emerge. But the development of more advanced structures and applications will require a number of issues to be addressed, the most significant of which are the high cost of DNA and the high error rate of self-assembly. Here we examine the technical challenges in the field of structural DNA nanotechnology and outline some of the promising applications that could be developed if these hurdles can be overcome. In particular, we highlight the potential use of DNA nanostructures in molecular and cellular biophysics, as biomimetic systems, in energy transfer and photonics, and in diagnostics and therapeutics for human health.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Examples of structural DNA nanotechnology.
Figure 2: Challenges for DNA nanostructures.
Figure 3: DNA nanotechnology for biophysical studies.
Figure 4: DNA nanostructures as biomimetic and in vivo active systems.
Figure 5: DNA nanotechnology for energy transfer and photonics.
Figure 6: Structural DNA nanotheranostics.

References

  1. Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982). This paper laid out the proposal of using branched DNA junctions to make lattices, which set the foundation for structural DNA nanotechnology.

    CAS  Google Scholar 

  2. Seeman, N. C. Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87 (2010).

    CAS  Google Scholar 

  3. Aldaye, F. A., Palmer, A. L. & Sleiman, H. F. Assembling materials with DNA as the guide. Science 321, 1795–1799 (2008).

    CAS  Article  Google Scholar 

  4. Kuzuya, A. & Komiyama, M. DNA origami: fold, stick and beyond. Nanoscale 2, 310–322 (2010).

    CAS  Google Scholar 

  5. Shih, W. M. & Lin, C. Knitting complex weaves with DNA origami. Curr. Opin. Struct. Biol. 20, 276–282 (2010).

    CAS  Google Scholar 

  6. Nangreave, J., Han, D., Liu, Y. & Yan, H. DNA origami: a history and current perspective. Curr. Opin. Chem. Biol. 14, 608–615 (2010).

    CAS  Google Scholar 

  7. Tørring, T., Voigt, N. V., Nangreave, J., Yan, H. & Gothelf, K. V. DNA origami: a quantum leap for self-assembly of complex structures. Chem. Soc. Rev. http://dx.doi.org/10.1039/C1CS15057J (2011).

  8. Kallenbach, N. R., Ma, R. I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829–831 (1983). The first experimental demonstration of an immobile DNA junction.

    CAS  Google Scholar 

  9. Seeman, N. C. et al. Synthetic DNA knots and catenanes. New J. Chem. 17, 739–755 (1993).

    CAS  Google Scholar 

  10. Chen, J. & Seeman, N. C. Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633 (1991). The first example of synthetic 3D DNA nanostructures with the connectivity of a cube.

    CAS  Article  Google Scholar 

  11. Zhang, Y. & Seeman, N. C. Construction of a DNA-truncated octahedron. J. Am. Chem. Soc. 116, 1661–1669 (1994).

    CAS  Google Scholar 

  12. Goodman, R. P., Berry, R. M. & Turberfield, A. J. The single-step synthesis of a DNA tetrahedron. Chem. Commun. 1372–1373 (2004).

  13. Goodman, R. P. et al. Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310, 1661–1665 (2005).

    CAS  Google Scholar 

  14. Erben, C. M., Goodman, R. P. & Turberfield, A. J. A self-assembled DNA bipyramid. J. Am. Chem. Soc. 129, 6992–6993 (2007).

    CAS  Google Scholar 

  15. Aldaye, F. A. & Sleiman, H. F. Modular access to structurally switchable 3D discrete DNA assemblies. J. Am. Chem. Soc. 129, 13376–13377 (2007).

    CAS  Google Scholar 

  16. Yang, H. et al. Metal–nucleic acid cages. Nature Chem. 1, 390–396 (2009).

    CAS  Google Scholar 

  17. Fu, T. J. & Seeman, N. C. DNA double-crossover molecules. Biochemistry 32, 3211–3220 (1993). The construction of DNA double-crossover molecules laid the foundation for many DNA nanostructures, including scaffolded DNA origami, to become realistic.

    CAS  Google Scholar 

  18. Li, X., Yang, X., Qi, J. & Seeman, N. C. Antiparallel DNA double crossover molecules as components for nanoconstruction. J. Am. Chem. Soc. 118, 6131–6140 (1996).

    CAS  Google Scholar 

  19. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998). The first successful example of building 2D periodic lattices using DNA nanostructures.

    CAS  Google Scholar 

  20. Schulman, R. & Winfree, E. Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc. Natl Acad. Sci. USA 104, 15236–15241 (2007).

    CAS  Google Scholar 

  21. LaBean, T. H. et al. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000).

    CAS  Google Scholar 

  22. Yan, H. et al. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882–1884 (2003).

    CAS  Google Scholar 

  23. Mathieu, F. et al. Six-helix bundles designed from DNA. Nano Lett. 5, 661–665 (2005).

    CAS  Google Scholar 

  24. He, Y. et al. Self-assembly of hexagonal DNA two-dimensional (2D) arrays. J. Am. Chem. Soc. 127, 12202–12203 (2005).

    CAS  Google Scholar 

  25. He, Y., Tian, Y., Ribbe, A. E. & Mao, C. Highly connected two-dimensional crystals of DNA six-point-stars. J. Am. Chem. Soc. 128, 15978–15979 (2006).

    CAS  Google Scholar 

  26. Sun, X. et al. Surface-mediated DNA self-assembly. J. Am. Chem. Soc. 131, 13248–13249 (2009).

    CAS  Google Scholar 

  27. Malo, J., Mitchell, J. C. & Turberfield, A. J. A two-dimensional DNA array: the three-layer logpile. J. Am. Chem. Soc. 131, 13574–13575 (2009).

    CAS  Google Scholar 

  28. Liu, Y., Ke, Y. & Yan, H. Self-assembly of symmetric finite-size DNA nanoarrays. J. Am. Chem. Soc. 127, 17140–17141 (2005).

    CAS  Google Scholar 

  29. Park, S. H. et al. Finite-size, fully addressable DNA tile lattices formed by hierarchical assembly procedures. Angew. Chem. Int. Ed. 45, 735–739 (2006).

    CAS  Google Scholar 

  30. Rothemund, P. W. K., Papadakis, K. & Winfree, E. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, e424 (2004). The first experimental demonstration of algorithmic DNA self-assembly to create 2D aperiodic patterns.

    Google Scholar 

  31. Liu, D., Park, S. H., Reif, J. H. & LaBean, T. H. DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires. Proc. Natl Acad. Sci. USA 101, 717–722 (2004).

    CAS  Google Scholar 

  32. Rothemund, P. W. K. et al. Design and characterization of programmable DNA nanotubes. J. Am. Chem. Soc. 126, 16344–16352 (2004).

    CAS  Google Scholar 

  33. Mitchell, J. C. et al. Self-assembly of chiral DNA nanotubes. J. Am. Chem. Soc. 126, 16342–16343 (2004).

    CAS  Google Scholar 

  34. Ke, Y., Liu, Y., Zhang, J. & Yan, H. A study of DNA tube formationmechanisms using 4-, 8-, and 12-helix DNA nanostructures. J. Am. Chem. Soc. 128, 4414–4421 (2006).

    CAS  Google Scholar 

  35. Liu, H. et al. Approaching the limit: can one DNA oligonucleotide assemble into large nanostructures? Angew. Chem. Int. Ed. 45, 1942–1945 (2006).

    CAS  Google Scholar 

  36. Yin, P. et al. Programming DNA tube circumferences. Science 321, 824–826 (2008).

    CAS  Google Scholar 

  37. Aldaye, F. A. et al. Modular construction of DNA nanotubes of tunable geometry and single- or double-stranded character. Nature Nanotech. 4, 349–352 (2009).

    CAS  Google Scholar 

  38. Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009). The first successful experiment to create self-assembling 3D crystals through sticky-ended associations using DNA tiles.

    CAS  Google Scholar 

  39. Liu, D. et al. Tensegrity: construction of rigid DNA triangles with flexible four-arm DNA junctions. J. Am. Chem. Soc. 126, 2324–2325 (2004).

    CAS  Google Scholar 

  40. Yan, H., LaBean, T. H., Feng, L. & Reif, J. H. Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices. Proc. Natl Acad. Sci. USA 100, 8103–8108 (2003).

    CAS  Google Scholar 

  41. Shih, W. M., Quispe, J. D. & Joyce, G. F. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618–621 (2004).

    CAS  Google Scholar 

  42. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 279–302 (2006). The first experimental demonstration of spatially addressable 2D patterns using scaffolded DNA origami.

    Google Scholar 

  43. Andersen, E. S. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–76 (2009).

    CAS  Google Scholar 

  44. Ke, Y. et al. Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano Lett. 9, 2445–2447 (2009).

    CAS  Google Scholar 

  45. Kuzuya, A. & Komiyama, M. Design and construction of a box-shaped 3D-DNA origami. Chem. Commun. 4182–4184 (2009).

  46. Endo, M. et al. DNA prism structures constructed by folding of multiple rectangular arms. J. Am. Chem. Soc. 131, 15570–15571 (2009).

    CAS  Google Scholar 

  47. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009). This study extended DNA origami to solid 3D shapes as stacked layers of DNA double helices.

    CAS  Google Scholar 

  48. Ke, Y. et al. Multilayer DNA origami packed on a square lattice. J. Am. Chem. Soc. 131, 15903–15908 (2009).

    CAS  Google Scholar 

  49. Dietz, H., Douglas, S. M. & Shih, W. M. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730 (2009).

    CAS  Google Scholar 

  50. Han, D. et al. DNA origami with complex curvatures in three dimensional space. Science 332, 342–346 (2011).

    CAS  Google Scholar 

  51. Park, S. H. et al. Programmable DNA self-assemblies for nanoscale organization of ligands and proteins. Nano Lett. 5, 729–733 (2005).

    CAS  Google Scholar 

  52. Lund, K., Liu, Y., Lindsay, S. & Yan, H. Self-assembling a molecular pegboard. J. Am. Chem. Soc. 127, 17606–17607 (2005).

    CAS  Google Scholar 

  53. Liu, Y., Lin, C., Li, H. & Yan, H. Aptamer-directed self-assembly of protein arrays on a DNA nanostructure. Angew. Chem. Int. Ed. 44, 4333–4338 (2005).

    CAS  Google Scholar 

  54. Li, H., LaBean, T. H. & Kenan, D. J. Single-chain antibodies against DNA aptamers for use as adapter molecules on DNA tile arrays in nanoscale materials organization. Org. Biomol. Chem. 4, 3420–3426 (2006).

    CAS  Google Scholar 

  55. Erben, C. M., Goodman, R. P. & Turberfield, A. J. Single-molecule protein encapsulation in a rigid DNA cage. Angew. Chem. Int. Ed. 45, 7417–7417 (2006).

    Google Scholar 

  56. Chhabra, R. et al. Spatially addressable multiprotein nanoarrays template by aptamer-tagged DNA nanoarchitectures. J. Am. Chem. Soc. 129, 10304–10305 (2007).

    CAS  Google Scholar 

  57. Saccà, B. et al. Orthogonal protein decoration of DNA origami. Angew. Chem. Int. Ed. 49, 9378–9383 (2010).

    Google Scholar 

  58. Williams, B. A. R. et al. Self-assembled peptide nanoarrays: an approach to studying protein-protein interactions. Angew. Chem. Int. Ed. 46, 3051–3054 (2007).

    CAS  Google Scholar 

  59. Stephanopoulos, N. et al. Immobilization and one-dimensional arrangement of virus capsids with nanoscale precision using DNA origami. Nano Lett. 10, 2714–2720 (2010).

    CAS  Google Scholar 

  60. Mirkin, C. A., Letsinger, R. L., Mucic, R. C. & Storhoff, J. J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382, 607–609 (1996).

    CAS  Google Scholar 

  61. Alivisatos. et al. Organization of 'nanocrystal molecules' using DNA. Nature 382, 609–611 (1996).

    CAS  Google Scholar 

  62. Le, J. D. et al. DNA-templated self-assembly of metallic nanocomponent arrays on a surface. Nano Lett. 4, 2343–2347 (2004).

    CAS  Google Scholar 

  63. Aldaye, F. A. & Sleiman, H. F. Sequential self-assembly of a DNA hexagon as a template for the organization of gold nanoparticles. Angew. Chem. Int. Ed. 45, 2204–2209 (2006).

    CAS  Google Scholar 

  64. Zhang, J., Liu, Y., Ke, J. & Yan, H. Periodic square-like gold nanoparticle arrays templated by self-assembled 2D DNA nanogrids on a surface. Nano Lett. 6, 248–251 (2006).

    CAS  Google Scholar 

  65. Sharma, J., Chhabra, R., Liu, Y., Ke, Y. & Yan, H. DNA-templated self-assembly of two-dimensional and periodical gold nanoparticle arrays. Angew. Chem. Int. Ed. 45, 730–735 (2006).

    CAS  Google Scholar 

  66. Zheng, J. et al. Two-dimensional nanoparticle arrays show the organizational power of robust DNA motifs. Nano Lett. 6, 1502–1504 (2006).

    CAS  Google Scholar 

  67. Sharma, J. et al. DNA-tile-directed self-assembly of quantum dots into two-dimensional nanopatterns. Angew. Chem. Int. Ed. 47, 5157–5159 (2008).

    CAS  Google Scholar 

  68. Sharma, J. et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112–116 (2009).

    CAS  Google Scholar 

  69. Ding, B. et al. Gold nanoparticle self-similar chain structure organized by DNA origami. J. Am. Chem. Soc. 132, 3248–3249 (2010).

    CAS  Google Scholar 

  70. Pal, S. et al. DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. Angew. Chem. Int. Ed. 49, 1–5 (2010).

    Google Scholar 

  71. Bui, H. et al. Programmable periodicity of quantum dot arrays with DNA origami nanotubes. Nano Lett. 10, 3367–3372 (2010).

    CAS  Google Scholar 

  72. Zhao, Z., Lacovetty, E. L., Liu, Y. & Yan, H. Encapsulation of gold nanoparticles in a DNA origami cage. Angew. Chem. Int. Ed. 50, 2041–2044 (2011).

    CAS  Google Scholar 

  73. Nykypanchuk, D., Maye, M. M., Lelie, D. & Gang, O. DNA-guided crystallization of colloidal nanoparticles. Nature 451, 549–552 (2008).

    CAS  Google Scholar 

  74. Tikhomirov, T. et al. DNA-based programming of quantum dot valency, self-assembly and luminescence. Nature Nanotech. 6, 485–490 (2011).

    CAS  Google Scholar 

  75. Maune, H. T. et al. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nature Nanotech. 5, 61–66 (2010).

    CAS  Google Scholar 

  76. Wilner, O. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nature Nanotech. 4, 249–254 (2009).

    CAS  Google Scholar 

  77. Niemeyer, C. M., Koehler, J. & Wuerdemann, C. DNA-directed assembly of bienzymic complexes from in vivo biotinylated NAD(P)H:FMN oxidoreductase and luciferase. ChemBioChem 3, 242–245 (2002).

    CAS  Google Scholar 

  78. Sonnichsen, C., Reinhard, B. M., Liphardt, J. & Alivisatos, A. P. A molecular ruler based on plasmon coupling of single gold and silver nanoparticles. Nature Biotechnol. 23, 741–745 (2005).

    Google Scholar 

  79. Maye, M. M. et al. Stepwise surface encoding for high-throughput assembly of nanoclusters. Nature Mater. 8, 388–391 (2009).

    CAS  Google Scholar 

  80. Cheng, W. et al. Free-standing nanoparticle superlattice sheets controlled by DNA. Nature Mater. 8, 519–525 (2009).

    CAS  Google Scholar 

  81. Tian, J., Ma, K. & Saaem, I. Advancing high-throughput gene synthesis technology. Mol. Biosyst. 5, 714–722 (2009).

    CAS  Google Scholar 

  82. Kosuri, S. et al. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nature Nanotech. 28, 1295–1299 (2010).

    CAS  Google Scholar 

  83. Li, Z. et al. Molecular behavior of DNA origami in higher-order self-assembly. J. Am. Chem. Soc. 132, 13545–13552 (2010).

    CAS  Google Scholar 

  84. Liu, W., Zhong, H., Wang, R. & Seeman, N. C. Crystalline two-dimensional DNA-origami arrays. Angew. Chem. Int. Ed. 50, 264–267 (2011).

    CAS  Google Scholar 

  85. Zhao, Z., Yan, H. & Liu, Y. A route to scale up DNA origami using DNA tiles as folding staples. Angew. Chem. Int. Ed. 49, 1414–1417 (2010).

    CAS  Google Scholar 

  86. Endo, M. et al. Two-dimensional DNA origami assemblies using a four-way connector. Chem. Commun. 47, 3213–3215 (2011).

    CAS  Google Scholar 

  87. Rajendran, A. et al. Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces. ACS Nano 5, 665–671 (2011).

    CAS  Google Scholar 

  88. Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nature Chem. 3, 620–627 (2011).

    CAS  Google Scholar 

  89. Zhao, Z., Liu, Y. & Yan, H. Organizing DNA origami tiles into larger structures using pre-formed scaffold frames. Nano Lett. http://dx.doi.org/10.1021/nl201603a (2011).

  90. Hung, A. M., Noh, H. & Cha, J. N. Recent advances in DNA-based directed assembly on surfaces. Nanoscale 2, 2530–2537 (2010).

    CAS  Google Scholar 

  91. Ding, B. et al. Interconnecting gold islands with DNA origami nanotubes. Nano Lett. 10, 5065–5069 (2010).

    CAS  Google Scholar 

  92. Kershner, R. J. et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nature Nanotech. 4, 557–561 (2009).

    CAS  Google Scholar 

  93. Hung, A. M. et al. Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nature Nanotech. 5, 121–126 (2010).

    CAS  Google Scholar 

  94. Saccà, B. et al. High-throughput, real-time monitoring of the self-assembly of DNA nanostructures by FRET spectroscopy. Angew. Chem. Int. Ed. 47, 2135–2137 (2008).

    Google Scholar 

  95. Nangreave, J., Yan, H. & Liu, Y. Studies of thermal stability of multivalent DNA hybridization in a nanostructured system. Biophys. J. 97, 563–571 (2009).

    CAS  Google Scholar 

  96. Nangreave, J., Yan, H. & Liu, Y. DNA nanostructures as models for evaluating the role of enthalpy and entropy in polyvalent binding. J. Am. Chem. Soc. 133, 4490–4497 (2011).

    CAS  Google Scholar 

  97. Chen, Y. X., Triola, G. & Waldmann, H. Bioorthogonal chemistry for site-specific labeling and surface immobilization of proteins. Acc. Chem. Res. 44, 762–773 (2011).

    CAS  Google Scholar 

  98. Singh, Y., Murat, P. & Defrancq, E. Recent developments in oligonucleotide conjugation. Chem. Soc. Rev. 39, 2054–2070 (2010).

    CAS  Google Scholar 

  99. Diederich, F. & Gomes-Lopez, M. Supramolecular fullerene chemistry. Chem. Soc. Rev. 28, 263–277 (1999).

    CAS  Google Scholar 

  100. Richter, J. Metallization of DNA. Physica E 16, 157–173 (2003).

    CAS  Google Scholar 

  101. Samano, E. C. et al. Self-assembling DNA templates for programmed artificial biomineralization. Soft Matt. 7, 3240–3245 (2011).

    CAS  Google Scholar 

  102. Liu, J. et al. Metallization of branched DNA origami for nanoelectronic circuit fabrication. ACS Nano 5, 2240–2247 (2005).

    Google Scholar 

  103. Schreiber, R. et al. DNA origami-templated growth of arbitrarily shaped metal nanoparticles. Small http://dx.doi.org/10.1002/smll.201100465 (2011).

  104. Mao, C., Sun, W., Shen, Z. & Seeman, N. C. A DNA nanomechanical device based on the B–Z transition. Nature 397, 144–146 (1999).

    CAS  Google Scholar 

  105. Gu, H., Chao, J., Xiao, S. J. & Seeman, N. C. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–205 (2010).

    CAS  Google Scholar 

  106. Yurke, B. et al. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).

    CAS  Google Scholar 

  107. Zhang, D. Y. & Seelig, G. Dynamic DNA nanotechnology using strand-displacement reactions. Nature Chem. 3, 103–113 (2011).

    CAS  Google Scholar 

  108. Chen, X. & Ellington, A. D. Shaping up nucleic acid computation. Curr. Opin. Biotechnol. 21, 392–400 (2010).

    CAS  Google Scholar 

  109. Stojanovic, M. N. Some experiments and directions in molecular computing and robotics. Isr. J. Chem. 51, 99–105 (2011).

    CAS  Google Scholar 

  110. Liu, H. & Liu, D. DNA nanomachines and their functional evolution. Chem. Commun. 2625–2639 (2009).

  111. Delius, M. & Leigh, D. A. Walking molecules. Chem. Soc. Rev. 40, 3656–3676 (2011).

    Google Scholar 

  112. Goodman, R. P. et al. Reconfigurable, braced, three-dimensional DNA nanostructure. Nature Nanotech. 3, 93–96 (2008).

    CAS  Google Scholar 

  113. Han, D., Pal, S., Liu, Y., Yan, H. Folding and cutting DNA into reconfigurable topological nanostructures. Nature Nanotech. 5, 712–717 (2010).

    CAS  Google Scholar 

  114. Aldaye, F. A. & Sleiman, H. F. Modular access to structurally switchable 3D discrete DNA assemblies. J. Am. Chem. Soc. 129, 13376–13377 (2007).

    CAS  Google Scholar 

  115. Lo, P. K. et al. Loading and selective release of cargo in DNA nanotubes with longitudinal variation. Nature Chem. 2, 319–328 (2010).

    CAS  Google Scholar 

  116. Dirks, R. M. & Pierce, N. A. Triggered amplification by hybridization chain reaction. Proc. Natl Acad. Sci. USA 101, 15275–15278 (2004).

    CAS  Google Scholar 

  117. Venkataraman, S., Dirks, R. M., Rothemund, P. W. K., Winfree, E. & Pierce, N. A. An autonomous polymerization motor powered by DNA hybridization. Nature Nanotech. 2, 490–494 (2007).

    Google Scholar 

  118. Lin, C. et al. Rolling circle enzymatic replication of a complex multi-crossover DNA nanostructure. J. Am. Chem. Soc. 129, 14475–14481 (2007).

    CAS  Google Scholar 

  119. Lin, C. et al. In vivo cloning of artificial DNA nanostructures. Proc. Natl Acad. Sci. USA 105, 17626–17631 (2008).

    CAS  Google Scholar 

  120. Li, Z. et al. A replicable tetrahedral nanostructure self-assembled from a single DNA strand. J. Am. Chem. Soc. 131, 13093–13098 (2009).

    CAS  Google Scholar 

  121. Guo, P. The emerging field of RNA nanotechnology. Nature Nanotech. 5, 833–842 (2010).

    CAS  Google Scholar 

  122. Delebecque C. J., Lindner, A. B., Silver, P. A. & Aldaye, F. A. Organization of intracellular reactions with rationally designed RNA assemblies. Science http://dx.doi.org/10.1126/science.1206938 (2011).

  123. Ko, S. H. et al. Synergistic self-assembly of RNA and DNA molecules. Nature Chem. 2, 1050–1055 (2010).

    CAS  Google Scholar 

  124. Mei, Q. et al. Stability of DNA origami nanoarrays in cell lysate. Nano Lett. 11, 1477–1482 (2011).

    CAS  Google Scholar 

  125. Castro, C. E. et al. A primer to scaffold DNA origami. Nature Methods 8, 221–229 (2011).

    CAS  Google Scholar 

  126. Marton, S. et al. In vitro and ex vivo selection procedures for identifying potentially therapeutic DNA and RNA molecules. Molecules 15, 4610–4638 (2010).

    CAS  Google Scholar 

  127. Esvelt, K. M., Carlson, J. C. & Liu, D. R. A system for the continuous directed evolution of biomolecules. Nature 472, 499–503 (2011).

    CAS  Google Scholar 

  128. Douglas, S. M., Chou, J. J. & Shih, W. M. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc. Natl Acad. Sci. USA 104, 6644–6648 (2007).

    CAS  Google Scholar 

  129. Berardi, M. J., Shih, W. M., Harrison, S. C. & Chou, J. J. Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature 476, 109–113 (2011).

    CAS  Google Scholar 

  130. Selmi, D. N. et al. DNA-templated protein arrays for single-molecule imaging. Nano Lett. 11, 657–660 (2011).

    CAS  Google Scholar 

  131. Chhabra, C., Sharma, J., Liu, Y. & Yan, H. Addressable molecular tweezers for DNA-templated coupling reactions. Nano Lett. 6, 978–983 (2006).

    CAS  Google Scholar 

  132. Gu, H., Yang, W. & Seeman, N. C. DNA scissors device used to measure MutS binding to DNA mis-pairs. J. Am. Chem. Soc. 132, 4352–4357 (2010).

    CAS  Google Scholar 

  133. Liedl, T. et al. Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nature Nanotech. 5, 520–524 (2010).

    CAS  Google Scholar 

  134. Sannohe, Y. et al. Visualization of dynamic conformational switching of the G-quadruplex in a DNA nanostructure. J. Am. Chem. Soc. 132, 16311–16313 (2010).

    CAS  Google Scholar 

  135. Endo, M., Katsuda, Y., Hidaka, K. & Suguyama, H. Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. J. Am. Chem. Soc. 132, 1592–1597 (2010).

    CAS  Google Scholar 

  136. McConnell, I., Li, G. & Brudvig, G. W. Energy conversion in natural and artificial photosynthesis. Chem. Biol. 17, 434–447 (2010).

    CAS  Google Scholar 

  137. Wasielewski, M. R. Self-assembly strategies for integrating light harvesting and charge separation in artificial photosynthetic systems. Acc. Chem. Res. 42, 1910–1921 (2009).

    CAS  Google Scholar 

  138. Balzani, V., Credi, A. & Venturi, M. Photochemical conversion of solar energy. ChemSusChem 1, 26–58 (2008).

    CAS  Google Scholar 

  139. Giese, B. Long distance charge transport in DNA: the hopping mechanism. Acc. Chem. Res. 33, 631–636 (2000).

    CAS  Google Scholar 

  140. Schuster, G. B. Long-range charge transfer in DNA: transient structural distortions control the distance dependence. Acc. Chem. Res. 33, 253–260 (2000).

    CAS  Google Scholar 

  141. Garcia-Parajó, M. F. et al. Energy transfer in single-molecule photonic wires. ChemPhysChem 6, 819–827 (2005).

    Google Scholar 

  142. Tinnefeld, P., Heilemann, M. & Sauer, M. Design of molecular photonic wires based on multistep electronic excitation transfer. ChemPhysChem 6, 217–222 (2005).

    CAS  Google Scholar 

  143. Su, W. et al. Site-specific assembly of DNA-based photonic wires by using programmable polyamides. Angew. Chem. Int. Ed. 50, 2712–2715 (2011).

    CAS  Google Scholar 

  144. Stein, I. H., Steinhauer, C. & Tinnefeld, P. Single-molecule four-color FRET visualizes energy-transfer paths on DNA origami. J. Am. Chem. Soc. 133, 4193–4195 (2011).

    CAS  Google Scholar 

  145. Tan, S. J., Campolongo, M. J., Luo, D. & Cheng, W. Building plasmonic structures with DNA. Nature Nanotech. 6, 268–276 (2011).

    CAS  Google Scholar 

  146. Yan, R., Gargas, D. & Yang, P. Nanowire photonics. Nature Photon. 3, 569–576 (2009).

    CAS  Google Scholar 

  147. Chrastina, A., Massey, K. A. & Schnitzer, J. E. Overcoming in vivo barriers to targeted nanodelivery. Nanomed. Nanobiotechnol. 3, 421–437 (2011).

    CAS  Google Scholar 

  148. Lammers, T. Theranostics nanomedicines. Acc. Chem. Res. http://dx.doi.org/10.1021/ar200019c (2011).

  149. Venkataraman, S., Dirks, R. M., Ueda, C. T. & Pierce, N. A. Selective cell death mediated by small conditional RNAs. Proc. Natl Acad. Sci. USA 107, 16777–16782 (2010).

    CAS  Google Scholar 

  150. Yin, P., Choi, H. M. T., Calvert, C. R. & Pierce, N. A. Programming biomolecular self-assembly pathways. Nature 451, 318–322 (2008). This study demonstrated programmable dynamic control over isothermal DNA self-assembly using hairpin motifs.

    CAS  Google Scholar 

  151. Aldaye, F. A., Senapedis, W. T., Silver, P. A. & Way, J. C. A structurally tunable DNA-based extracellular matrix. J. Am. Chem. Soc. 132, 14727–14729 (2010).

    CAS  Google Scholar 

Download references

Acknowledgements

We thank K. Gothelf and T. LaBean for discussions. H.Y. acknowledges funding support from the Office of Naval Research (ONR), the Army Research office, the National Science Foundation, the National Institutes of Health (NIH), the Department of Energy, Sloan Research Fellowship and Arizona State University. W.M.S acknowledges funding support from ONR, NIH, Agilent Technologies and the Wyss Institute for Biologically Inspired Engineering. We also thank J. Nangreave for proofreading the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to William M. Shih or Hao Yan.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Pinheiro, A., Han, D., Shih, W. et al. Challenges and opportunities for structural DNA nanotechnology. Nature Nanotech 6, 763–772 (2011). https://doi.org/10.1038/nnano.2011.187

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nnano.2011.187

Further reading

Search

Quick links

Find nanotechnology articles, nanomaterial data and patents all in one place. Visit Nano by Nature Research