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DNA Origami Nanostructures

  • Huajie Liu
  • Chunhai Fan
Chapter
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Abstract

The term “DNA origami” was proposed by Paul Rothemund in 2006 to describe his invention of a new type of DNA nanostructures. In that revolutionary work, he showed the ability of controlled folding of a long single-stranded scaffold DNA, with the help of hundreds of short staple strands, into exquisite nanopatterns. After his invention, this technique has been a constant focus in the field of DNA nanotechnology for the past few years. Great efforts have been made to build new 2D and 3D DNA origami structures, improve assembly strategy, study inherent properties, and develop new applications. In this chapter, we will summarize the structural evolution of DNA origami from Rothemund’s first invention to the latest developments in constructing more complex and larger structures, optimizing the assembly, and combining it with top-down techniques.

Keywords

DNA origami DNA nanostructures DNA self-assembly Top-down fabrication Bottom-up self-assembly 
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References

  1. 1.
    Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 99(2):237–247CrossRefGoogle Scholar
  2. 2.
    Seeman NC (2003) DNA in a material world. Nature 421(6921):427–431CrossRefGoogle Scholar
  3. 3.
    Seeman NC (2000) DNA nicks and nodes and nanotechnology. Nano Lett 1(1):22–26CrossRefGoogle Scholar
  4. 4.
    Winfree E, Liu F, Wenzler LA, Seeman NC (1998) Design and self-assembly of two-dimensional DNA crystals. Nature 394(6693):539–544CrossRefGoogle Scholar
  5. 5.
    Liu Y, Ke Y, Yan H (2005) Self-assembly of symmetric finite-size DNA nanoarrays. J Am Chem Soc 127(49):17140–17141CrossRefGoogle Scholar
  6. 6.
    Goodman RP, Schaap IAT, Tardin CF, Erben CM, Berry RM, Schmidt CF, Turberfield AJ (2005) Rapid chiral assembly of rigid DNA building blocks for molecular nanofabrication. Science 310(5754):1661–1665CrossRefGoogle Scholar
  7. 7.
    Zheng J, Birktoft JJ, Chen Y, Wang T, Sha R, Constantinou PE, Ginell SL, Mao C, Seeman NC (2009) From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461(7260):74–77CrossRefGoogle Scholar
  8. 8.
    Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440(7082):297–302CrossRefGoogle Scholar
  9. 9.
    Sanderson K (2010) What to make with DNA origami. Nature 464:158–189CrossRefGoogle Scholar
  10. 10.
    Zhang DY, Seelig G (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem 3(2):103–113CrossRefGoogle Scholar
  11. 11.
    Steitz TA (2008) A structural understanding of the dynamic ribosome machine. Nat Rev Mol Cell Biol 9(3):242–253CrossRefGoogle Scholar
  12. 12.
    Qian L, Wang Y, Zhang Z, Zhao J, Pan D, Zhang Y, Liu Q, Fan C, Hu J, He L (2006) Analogic China map constructed by DNA. Chin Sci Bull 51(24):2973–2976CrossRefGoogle Scholar
  13. 13.
    Andersen ES, Dong M, Nielsen MM, Jahn K, Lind-Thomsen A, Mamdouh W, Gothelf KV, Besenbacher F, Kjems J (2008) DNA origami design of dolphin-shaped structures with flexible tails. ACS Nano 2(6):1213–1218CrossRefGoogle Scholar
  14. 14.
    Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R, Mamdouh W, Golas MM, Sander B, Stark H, Oliveira CL, Pedersen JS, Birkedal V, Besenbacher F, Gothelf KV, Kjems J (2009) Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459(7243):73–76CrossRefGoogle Scholar
  15. 15.
    Kuzuya A, Komiyama M (2009) Design and construction of a box-shaped 3D-DNA origami. Chem Commun 28:4182–4184CrossRefGoogle Scholar
  16. 16.
    Endo M, Hidaka K, Kato T, Namba K, Sugiyama H (2009) DNA prism structures constructed by folding of multiple rectangular arms. J Am Chem Soc 131(43):15570–15571CrossRefGoogle Scholar
  17. 17.
    Ke Y, Sharma J, Liu M, Jahn K, Liu Y, Yan H (2009) Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano Lett 9(6):2445–2447CrossRefGoogle Scholar
  18. 18.
    Douglas S, Dietz H, Liedl T, Hogberg B, Graf F, Shih W (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245):414–418CrossRefGoogle Scholar
  19. 19.
    Douglas SM, Marblestone AH, Teerapittayanon S, Vazquez A, Church GM, Shih WM (2009) Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res 37(15):5001–5006CrossRefGoogle Scholar
  20. 20.
    Dietz H, Douglas SM, Shih WM (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325(5941):725–730CrossRefGoogle Scholar
  21. 21.
    Ke Y, Douglas SM, Liu M, Sharma J, Cheng A, Leung A, Liu Y, Shih WM, Yan H (2009) Multilayer DNA origami packed on a square lattice. J Am Chem Soc 131(43):15903–15908CrossRefGoogle Scholar
  22. 22.
    Han D, Pal S, Liu Y, Yan H (2010) Folding and cutting DNA into reconfigurable topological nanostructures. Nat Nanotechnol 5(10):712–717CrossRefGoogle Scholar
  23. 23.
    Han D, Pal S, Nangreave J, Deng Z, Liu Y, Yan H (2011) DNA origami with complex curvatures in three-dimensional space. Science 332(6027):342–346CrossRefGoogle Scholar
  24. 24.
    Liedl T, Hogberg B, Tytell J, Ingber DE, Shih WM (2010) Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat Nanotechnol 5(7):520–524CrossRefGoogle Scholar
  25. 25.
    Jungmann R, Liedl T, Sobey TL, Shih W, Simmel FC (2008) Isothermal assembly of DNA origami structures using denaturing agents. J Am Chem Soc 130(31):10062–10063CrossRefGoogle Scholar
  26. 26.
    Hogberg B, Liedl T, Shih WM (2009) Folding DNA origami from a double-stranded source of scaffold. J Am Chem Soc 131(26):9154–9155CrossRefGoogle Scholar
  27. 27.
    Pound E, Ashton JR, Becerril HA, Woolley AT (2009) Polymerase chain reaction based scaffold preparation for the production of thin, branched DNA origami nanostructures of arbitrary sizes. Nano Lett 9(12):4302–4305CrossRefGoogle Scholar
  28. 28.
    Ke Y, Bellot G, Voigt NV, Fradkov E, Shih WM (2012) Two design strategies for enhancement of multilayer-DNA-origami folding: underwinding for specific intercalator rescue and staple-break positioning. Chem Sci 3(8):2587–2597CrossRefGoogle Scholar
  29. 29.
    Bellot G, McClintock MA, Lin C, Shih WM (2011) Recovery of intact DNA nanostructures after agarose gel-based separation. Nat Methods 8(3):192–194CrossRefGoogle Scholar
  30. 30.
    Jungmann R, Scheible M, Simmel FC (2012) Nanoscale imaging in DNA nanotechnology. WIREs Nanomed Nanobiotechnol 4(1):66–81CrossRefGoogle Scholar
  31. 31.
    Alloyeau D, Ding B, Ramasse Q, Kisielowski C, Lee Z, Jeon K-J (2011) Direct imaging and chemical analysis of unstained DNA origami performed with a transmission electron microscope. Chem Commun 47(33):9375–9377CrossRefGoogle Scholar
  32. 32.
    Kuzyk A, Yurke B, Toppari JJ, Linko V, Törmä P (2008) Dielectrophoretic trapping of DNA origami. Small 4(4):447–450CrossRefGoogle Scholar
  33. 33.
    Linko V, Paasonen S-T, Kuzyk A, Törmä P, Toppari JJ (2009) Characterization of the conductance mechanisms of DNA origami by AC impedance spectroscopy. Small 5(21):2382–2386CrossRefGoogle Scholar
  34. 34.
    Edson PB, Bobadilla AD, Rangel NL, Zhong H, Norton ML, Sinitskii A, Seminario JM (2009) Current-voltage-temperature characteristics of DNA origami. Nanotechnology 20(17):175102CrossRefGoogle Scholar
  35. 35.
    Alfredo DB, Edson PB, Norma LR, Hong Z, Michael LN, Alexander S, Jorge MS (2009) DNA origami impedance measurement at room temperature. J Chem Phys 130(17):171101CrossRefGoogle Scholar
  36. 36.
    Song J, Arbona J-M, Zhang Z, Liu L, Xie E, Elezgaray J, Aime J-P, Gothelf KV, Besenbacher F, Dong M (2012) Direct visualization of transient thermal response of a DNA origami. J Am Chem Soc 134(24):9844–9847CrossRefGoogle Scholar
  37. 37.
    Rajendran A, Endo M, Katsuda Y, Hidaka K, Sugiyama H (2011) Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly. J Am Chem Soc 133(37):14488–14491CrossRefGoogle Scholar
  38. 38.
    Kauert DJ, Kurth T, Liedl T, Seidel R (2011) Direct mechanical measurements reveal the material properties of three-dimensional DNA origami. Nano Lett 11(12):5558–5563CrossRefGoogle Scholar
  39. 39.
    Ke Y, Nangreave J, Yan H, Lindsay S, Liu Y (2008) Developing DNA tiles for oligonucleotide hybridization assay with higher accuracy and efficiency. Chem Commun 43:5622–5624CrossRefGoogle Scholar
  40. 40.
    Ke Y, Lindsay S, Chang Y, Liu Y, Yan H (2008) Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319(5860):180–183CrossRefGoogle Scholar
  41. 41.
    Mei Q, Wei X, Su F, Liu Y, Youngbull C, Johnson R, Lindsay S, Yan H, Meldrum D (2011) Stability of DNA origami nanoarrays in cell lysate. Nano Lett 11(4):1477–1482CrossRefGoogle Scholar
  42. 42.
    Li Z, Wang L, Yan H, Liu Y (2012) Effect of DNA hairpin loops on the twist of planar DNA origami tiles. Langmuir 28(4):1959–1965CrossRefGoogle Scholar
  43. 43.
    Zhang H, Chao J, Pan D, Liu H, Huang Q, Fan C (2012) Folding super-sized DNA origami with scaffold strands from long-range PCR. Chem Commun 48(51):6405–6407CrossRefGoogle Scholar
  44. 44.
    Yang Y, Han D, Nangreave J, Liu Y, Yan H (2012) DNA origami with double-stranded DNA as a unified scaffold. ACS Nano 6(9):8209–8215CrossRefGoogle Scholar
  45. 45.
    Douglas SM, Chou JJ, Shih WM (2007) DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc Natl Acad Sci U S A 104(16):6644–6648CrossRefGoogle Scholar
  46. 46.
    Jungmann R, Steinhauer C, Scheible M, Kuzyk A, Tinnefeld P, Simmel FC (2010) Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett 10(11):4756–4761CrossRefGoogle Scholar
  47. 47.
    Jungmann R, Scheible M, Kuzyk A, Pardatscher G, Carlos EC, Simmel FC (2011) DNA origami-based nanoribbons: assembly, length distribution, and twist. Nanotechnology 22(27):275301CrossRefGoogle Scholar
  48. 48.
    Kim KN, Sarveswaran K, Mark L, Lieberman M (2011) Comparison of methods for orienting and aligning DNA origami. Soft Matter 7(10):4636–4643CrossRefGoogle Scholar
  49. 49.
    Li Z, Liu M, Wang L, Nangreave J, Yan H, Liu Y (2010) Molecular behavior of DNA origami in higher-order self-assembly. J Am Chem Soc 132(38):13545–13552CrossRefGoogle Scholar
  50. 50.
    Endo M, Sugita T, Katsuda Y, Hidaka K, Sugiyama H (2010) Programmed-assembly system using DNA jigsaw pieces. Chem Eur J 16(18):5362–5368CrossRefGoogle Scholar
  51. 51.
    Rajendran A, Endo M, Katsuda Y, Hidaka K, Sugiyama H (2011) Programmed two-dimensional self-assembly of multiple DNA origami jigsaw pieces. ACS Nano 5(1):665–671CrossRefGoogle Scholar
  52. 52.
    Liu W, Zhong H, Wang R, Seeman NC (2010) Crystalline two-dimensional DNA-origami arrays. Angew Chem Int Ed 50(1):264–267CrossRefGoogle Scholar
  53. 53.
    Endo M, Sugita T, Rajendran A, Katsuda Y, Emura T, Hidaka K, Sugiyama H (2011) Two-dimensional DNA origami assemblies using a four-way connector. Chem Commun 47(11):3213–3215CrossRefGoogle Scholar
  54. 54.
    Zhao Z, Yan H, Liu Y (2010) A route to scale up DNA origami using DNA tiles as folding staples. Angew Chem Int Ed 49(8):1414–1417CrossRefGoogle Scholar
  55. 55.
    Zhao Z, Liu Y, Yan H (2011) Organizing DNA origami tiles into larger structures using preformed scaffold frames. Nano Lett 11(7):2997–3002CrossRefGoogle Scholar
  56. 56.
    Woo S, Rothemund PWK (2011) Programmable molecular recognition based on the geometry of DNA nanostructures. Nat Chem 3(8):620–627CrossRefGoogle Scholar
  57. 57.
    Kuzyk A, Kimmo TL, Torma P (2009) DNA origami as a nanoscale template for protein assembly. Nanotechnology 20(23):235305CrossRefGoogle Scholar
  58. 58.
    Saccà B, Meyer R, Erkelenz M, Kiko K, Arndt A, Schroeder H, Rabe KS, Niemeyer CM (2010) Orthogonal protein decoration of DNA origami. Angew Chem Int Ed 49(49):9378–9383CrossRefGoogle Scholar
  59. 59.
    Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T (2012) Zinc-finger proteins for site-specific protein positioning on DNA-origami structures. Angew Chem Int Ed 51(10):2421–2424CrossRefGoogle Scholar
  60. 60.
    Numajiri K, Yamazaki T, Kimura M, Kuzuya A, Komiyama M (2010) Discrete and active enzyme nanoarrays on DNA origami scaffolds purified by affinity tag separation. J Am Chem Soc 132(29):9937–9939CrossRefGoogle Scholar
  61. 61.
    Sharma J, Chhabra R, Andersen CS, Gothelf KV, Yan H, Liu Y (2008) Toward reliable gold nanoparticle patterning on self-assembled DNA nanoscaffold. J Am Chem Soc 130(25):7820–7821CrossRefGoogle Scholar
  62. 62.
    Pal S, Deng Z, Ding B, Yan H, Liu Y (2010) DNA-origami-directed self-assembly of discrete silver-nanoparticle architectures. Angew Chem Int Ed 49(15):2700–2704CrossRefGoogle Scholar
  63. 63.
    Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller E-M, Hogele A, Simmel FC, Govorov AO, Liedl T (2012) DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483(7389):311–314CrossRefGoogle Scholar
  64. 64.
    Liu H, Torring T, Dong M, Rosen CB, Besenbacher F, Gothelf KV (2010) DNA-templated covalent coupling of G4 PAMAM dendrimers. J Am Chem Soc 132(51):18054–18056CrossRefGoogle Scholar
  65. 65.
    Maune HT, S-p H, Barish RD, Bockrath M, Goddard IIA, RothemundPaul WK, Winfree E (2010) Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat Nanotechnol 5(1):61–66CrossRefGoogle Scholar
  66. 66.
    Eskelinen A-P, Kuzyk A, Kaltiaisenaho TK, Timmermans MY, Nasibulin AG, Kauppinen EI, Törmä P (2011) Assembly of single-walled carbon nanotubes on DNA-origami templates through streptavidin–biotin interaction. Small 7(6):746–750CrossRefGoogle Scholar
  67. 67.
    Gerdon AE, Oh SS, Hsieh K, Ke Y, Yan H, Soh HT (2009) Controlled delivery of DNA origami on patterned surfaces. Small 5(17):1942–1946CrossRefGoogle Scholar
  68. 68.
    Gao B, Sarveswaran K, Bernstein GH, Lieberman M (2010) Guided deposition of individual DNA nanostructures on silicon substrates. Langmuir 26(15):12680–12683CrossRefGoogle Scholar
  69. 69.
    Yun JM, Kim KN, Kim JY, Shin DO, Lee WJ, Lee SH, Lieberman M, Kim SO (2012) DNA origami nanopatterning on chemically modified graphene. Angew Chem Int Ed 51(4):912–915CrossRefGoogle Scholar
  70. 70.
    Kershner RJ, Bozano LD, Micheel CM, Hung AM, Fornof AR, Cha JN, Rettner CT, Bersani M, Frommer J, Rothemund PWK, Wallraff GM (2009) Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nat Nanotechnol 4(9):557–561CrossRefGoogle Scholar
  71. 71.
    Hung AM, Micheel CM, Bozano LD, Osterbur LW, Wallraff GM, Cha JN (2010) Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat Nanotechnol 5(2):121–126CrossRefGoogle Scholar
  72. 72.
    Ding B, Wu H, Xu W, Zhao Z, Liu Y, Yu H, Yan H (2010) Interconnecting gold islands with DNA origami nanotubes. Nano Lett 10(12):5065–5069CrossRefGoogle Scholar
  73. 73.
    Pearson AC, Pound E, Woolley AT, Linford MR, Harb JN, Davis RC (2011) Chemical alignment of DNA origami to block copolymer patterned arrays of 5 nm gold nanoparticles. Nano Lett 11(5):1981–1987CrossRefGoogle Scholar

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© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Laboratory of Physical BiologyShanghai Institute of Applied Physics, Chinese Academy of SciencesShanghaiChina

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