1932

Abstract

Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson–Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-bioeng-062117-120904
2018-06-04
2024-05-28
Loading full text...

Full text loading...

/deliver/fulltext/bioeng/20/1/annurev-bioeng-062117-120904.html?itemId=/content/journals/10.1146/annurev-bioeng-062117-120904&mimeType=html&fmt=ahah

Literature Cited

  1. 1.  Watson JD, Crick FH 1953. Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737–38
    [Google Scholar]
  2. 2.  Shipman SL, Nivala J, Macklis JD, Church GM 2017. CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 547:345–49
    [Google Scholar]
  3. 3.  Seeman NC 1982. Nucleic acid junctions and lattices. J. Theor. Biol. 99:237–47
    [Google Scholar]
  4. 4.  Modi S, Swetha MG, Goswami D, Gupta GD, Mayor S, Krishnan Y 2009. A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nat. Nanotechnol. 4:325–30
    [Google Scholar]
  5. 5.  Jungmann R, Avendano MS, Woehrstein JB, Dai MJ, Shih WM, Yin P 2014. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11:313–18
    [Google Scholar]
  6. 6.  Douglas SM, Bachelet I, Church GM 2012. A logic-gated nanorobot for targeted transport of molecular payloads. Science 335:831
    [Google Scholar]
  7. 7.  Kallenbach NR, Ma RI, Seeman NC 1983. An immobile nucleic-acid junction constructed from oligonucleotides. Nature 305:829–31
    [Google Scholar]
  8. 8.  Ma RI, Kallenbach NR, Sheardy RD, Petrillo ML, Seeman NC 1986. Three-arm nucleic acid junctions are flexible. Nucleic Acids Res 14:9745–53
    [Google Scholar]
  9. 9.  Wang YL, Mueller JE, Kemper B, Seeman NC 1991. Assembly and characterization of five-arm and six-arm DNA branched junctions. Biochemistry 30:5667–74
    [Google Scholar]
  10. 10.  Wang X, Seeman NC 2007. Assembly and characterization of 8-arm and 12-arm DNA branched junctions. J. Am. Chem. Soc. 129:8169–76
    [Google Scholar]
  11. 11.  Fu TJ, Seeman NC 1993. DNA double-crossover molecules. Biochemistry 32:3211–20
    [Google Scholar]
  12. 12.  Winfree E, Liu F, Wenzler LA, Seeman NC 1998. Design and self-assembly of two-dimensional DNA crystals. Nature 394:539–44
    [Google Scholar]
  13. 13.  Yan H, Park SH, Finkelstein G, Reif JH, LaBean TH 2003. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301:1882–84
    [Google Scholar]
  14. 14.  He Y, Chen Y, Liu H, Ribbe AE, Mao C 2005. Self-assembly of hexagonal DNA two-dimensional (2D) arrays. J. Am. Chem. Soc. 127:12202–3
    [Google Scholar]
  15. 15.  He Y, Tian Y, Ribbe AE, Mao C 2006. Highly connected two-dimensional crystals of DNA six-point-stars. J. Am. Chem. Soc. 128:15978–79
    [Google Scholar]
  16. 16.  He Y, Ye T, Su M, Zhang C, Ribbe AE et al. 2008. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452:198–201
    [Google Scholar]
  17. 17.  Zhang C, Su M, He Y, Zhao X, Fang PA et al. 2008. Conformational flexibility facilitates self-assembly of complex DNA nanostructures. PNAS 105:10665–69
    [Google Scholar]
  18. 18.  Zheng J, Birktoft JJ, Chen Y, Wang T, Sha R et al. 2009. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461:74–77
    [Google Scholar]
  19. 19.  Ke YG, Ong LL, Shih WM, Yin P 2012. Three-dimensional structures self-assembled from DNA bricks. Science 338:1177–83
    [Google Scholar]
  20. 20.  Wei B, Dai MJ, Yin P 2012. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485:623–26
    [Google Scholar]
  21. 21.  Zhang C, Wu W, Li X, Tian C, Qian H et al. 2012. Controlling the chirality of DNA nanocages. Angew. Chem. Int. Ed. Engl. 51:7999–8002
    [Google Scholar]
  22. 22.  Ke Y, Ong LL, Sun W, Song J, Dong M et al. 2014. DNA brick crystals with prescribed depths. Nat. Chem. 6:994–1002
    [Google Scholar]
  23. 23.  Tian C, Li X, Liu Z, Jiang W, Wang G, Mao C 2014. Directed self-assembly of DNA tiles into complex nanocages. Angew. Chem. Int. Ed. Engl. 53:8041–44
    [Google Scholar]
  24. 24.  Wang P, Wu S, Tian C, Yu G, Jiang W et al. 2016. Retrosynthetic analysis–guided breaking tile symmetry for the assembly of complex DNA nanostructures. J. Am. Chem. Soc. 138:13579–85
    [Google Scholar]
  25. 25.  Zhang C, Ko SH, Su M, Leng Y, Ribbe AE et al. 2009. Symmetry controls the face geometry of DNA polyhedra. J. Am. Chem. Soc. 131:1413–15
    [Google Scholar]
  26. 26.  He Y, Su M, Fang PA, Zhang C, Ribbe AE et al. 2010. On the chirality of self-assembled DNA octahedra. Angew. Chem. Int. Ed. Engl. 49:748–51
    [Google Scholar]
  27. 27.  He Y, Tian Y, Chen Y, Deng Z, Ribbe AE, Mao C 2005. Sequence symmetry as a tool for designing DNA nanostructures. Angew. Chem. Int. Ed. Engl. 44:6694–96
    [Google Scholar]
  28. 28.  Zhang F, Liu Y, Yan H 2013. Complex Archimedean tiling self-assembled from DNA nanostructures. J. Am. Chem. Soc. 135:7458–61
    [Google Scholar]
  29. 29.  Zhang F, Jiang S, Li W, Hunt A, Liu Y, Yan H 2016. Self-assembly of complex DNA tessellations by using low-symmetry multi-arm DNA tiles. Angew. Chem. Int. Ed. Engl. 55:8860–63
    [Google Scholar]
  30. 30.  Rothemund PWK 2006. Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302
    [Google Scholar]
  31. 31.  Yan H, LaBean TH, Feng L, Reif JH 2003. Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices. PNAS 100:8103–8
    [Google Scholar]
  32. 32.  Shih WM, Quispe J, Joyce G 2004. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427:618–21
    [Google Scholar]
  33. 33.  Ke YG, Douglas SM, Liu MH, Sharma J, Cheng AC et al. 2009. Multilayer DNA origami packed on a square lattice. J. Am. Chem. Soc. 131:15903–8
    [Google Scholar]
  34. 34.  Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM 2009. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459:414–18
    [Google Scholar]
  35. 35.  Ke YG, Voigt NV, Gothelf KV, Shih WM 2012. Multilayer DNA origami packed on hexagonal and hybrid lattices. J. Am. Chem. Soc. 134:1770–74
    [Google Scholar]
  36. 36.  Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R et al. 2009. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459:73–76
    [Google Scholar]
  37. 37.  Ke Y, Sharma J, Liu M, Jahn K, Liu Y, Yan H 2009. Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano Lett 9:2445–47
    [Google Scholar]
  38. 38.  Han D, Pal S, Nangreave J, Deng Z, Liu Y, Yan H 2011. DNA origami with complex curvatures in three-dimensional space. Science 332:342–46
    [Google Scholar]
  39. 39.  Dietz H, Douglas SM, Shih WM 2009. Folding DNA into twisted and curved nanoscale shapes. Science 325:725–30
    [Google Scholar]
  40. 40.  Han D, Pal S, Yang Y, Jiang S, Nangreave J et al. 2013. DNA gridiron nanostructures based on four-arm junctions. Science 339:1412–15
    [Google Scholar]
  41. 41.  Zhao Z, Yan H, Liu Y 2010. A route to scale up DNA origami using DNA tiles as folding staples. Angew. Chem. Int. Ed. Engl. 49:1414–17
    [Google Scholar]
  42. 42.  Liu W, Zhong H, Wang R, Seeman NC 2011. Crystalline two-dimensional DNA-origami arrays. Angew. Chem. Int. Ed. Engl. 50:264–67
    [Google Scholar]
  43. 43.  Zhao Z, Liu Y, Yan H 2011. Organizing DNA origami tiles into larger structures using preformed scaffold frames. Nano Lett 11:2997–3002
    [Google Scholar]
  44. 44.  Zhang HL, Chao J, Pan D, Liu HJ, Huang Q, Fan CH 2012. Folding super-sized DNA origami with scaffold strands from long-range PCR. Chem. Commun. 48:6405–7
    [Google Scholar]
  45. 45.  Iinuma R, Ke Y, Jungmann R, Schlichthaerle T, Woehrstein JB, Yin P 2014. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344:65–69
    [Google Scholar]
  46. 46.  Marchi AN, Saaem I, Vogen BN, Brown S, LaBean TH 2014. Toward larger DNA origami. Nano Lett 14:5740–47
    [Google Scholar]
  47. 47.  Benson E, Mohammed A, Gardell J, Masich S, Czeizler E et al. 2015. DNA rendering of polyhedral meshes at the nanoscale. Nature 523:441–44
    [Google Scholar]
  48. 48.  Gerling T, Wagenbauer KF, Neuner AM, Dietz H 2015. Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components. Science 347:1446–52
    [Google Scholar]
  49. 49.  Zhang F, Jiang S, Wu S, Li Y, Liu Y, Mao C 2015. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nat. Nanotechnol. 10:779–84
    [Google Scholar]
  50. 50.  Liu W, Halverson J, Tian Y, Tkachenko AV, Gang O 2016. Self-organized architectures from assorted DNA-framed nanoparticles. Nat. Chem. 8:867–73
    [Google Scholar]
  51. 51.  Veneziano R, Ratanalert S, Zhang K, Zhang F, Yan H et al. 2016. Designer nanoscale DNA assemblies programmed from the top down. Science 352:1534–48
    [Google Scholar]
  52. 52.  Wang P, Gaitanaros S, Lee S, Bathe M, Shih WM, Ke Y 2016. Programming self-assembly of DNA origami honeycomb two-dimensional lattices and plasmonic metamaterials. J. Am. Chem. Soc. 138:7733–40
    [Google Scholar]
  53. 53.  Kocabey S, Kempter S, List J, Xing Y, Bae W et al. 2015. Membrane-assisted growth of DNA origami nanostructure arrays. ACS Nano 9:3530–39
    [Google Scholar]
  54. 54.  Aghebat Rafat A, Pirzer T, Scheible MB, Kostina A, Simmel FC 2014. Surface-assisted large-scale ordering of DNA origami tiles. Angew. Chem. Int. Ed. Engl. 53:7665–68
    [Google Scholar]
  55. 55.  Suzuki Y, Endo M, Sugiyama H 2015. Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures. Nat. Commun. 6:8052
    [Google Scholar]
  56. 56.  Woo S, Rothemund PWK 2014. Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion. Nat. Commun. 5:4889
    [Google Scholar]
  57. 57.  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 37:5001–6
    [Google Scholar]
  58. 58.  Castro CE, Su HJ, Marras AE, Zhou L, Johnson J 2015. Mechanical design of DNA nanostructures. Nanoscale 7:5913–21
    [Google Scholar]
  59. 59.  Bustamante C, Marko JF, Siggia ED, Smith S 1994. Entropic elasticity of lambda-phage DNA. Science 265:1599–600
    [Google Scholar]
  60. 60.  Wang MD, Yin H, Landick R, Gelles J, Block SM 1997. Stretching DNA with optical tweezers. Biophys. J. 72:1335–46
    [Google Scholar]
  61. 61.  Pan J, Li F, Cha TG, Chen H, Choi JH 2015. Recent progress on DNA based walkers. Curr. Opin. Biotechnol. 34:56–64
    [Google Scholar]
  62. 62.  Sherman WB, Seeman NC 2004. A precisely controlled DNA biped walking device. Nano Lett 4:1203–7
    [Google Scholar]
  63. 63.  Shin JS, Pierce NA 2004. A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126:10834–35
    [Google Scholar]
  64. 64.  Omabegho T, Sha R, Seeman NC 2009. A bipedal DNA Brownian motor with coordinated legs. Science 324:67–71
    [Google Scholar]
  65. 65.  Green SJ, Bath J, Turberfield AJ 2008. Coordinated chemomechanical cycles: a mechanism for autonomous molecular motion. Phys. Rev. Lett. 101:238101
    [Google Scholar]
  66. 66.  Jung C, Allen PB, Ellington AD 2016. A stochastic DNA walker that traverses a microparticle surface. Nat. Nanotechnol. 11:157–63
    [Google Scholar]
  67. 67.  Yin P, Choi HM, Calvert CR, Pierce NA 2008. Programming biomolecular self-assembly pathways. Nature 451:318–22
    [Google Scholar]
  68. 68.  Bath J, Green SJ, Turberfield AJ 2005. A free-running DNA motor powered by a nicking enzyme. Angew. Chem. Int. Ed. Engl. 44:4358–61
    [Google Scholar]
  69. 69.  Bath J, Green SJ, Allen K, Turberfield AJ 2009. Mechanism for a directional, processive, and reversible DNA motor. Small 5:1513–16
    [Google Scholar]
  70. 70.  Cha TG, Pan J, Chen H, Salgado J, Li X et al. 2014. A synthetic DNA motor that transports nanoparticles along carbon nanotubes. Nat. Nanotechnol. 9:39–43
    [Google Scholar]
  71. 71.  Zhou C, Duan X, Liu N 2015. A plasmonic nanorod that walks on DNA origami. Nat. Commun. 6:8102
    [Google Scholar]
  72. 72.  Yehl K, Mugler A, Vivek S, Liu Y, Zhang Y et al. 2016. High-speed DNA-based rolling motors powered by RNase H. Nat. Nanotechnol. 11:184–90
    [Google Scholar]
  73. 73.  Zhang Z, Olsen EM, Kryger M, Voigt NV, Torring T et al. 2011. A DNA tile actuator with eleven discrete states. Angew. Chem. Int. Ed. Engl. 50:3983–87
    [Google Scholar]
  74. 74.  Ranallo S, Prévost-Tremblay C, Idili A, Vallée-Bélisle A, Ricci F 2017. Antibody-powered nucleic acid release using a DNA-based nanomachine. Nat. Commun. 8:15150
    [Google Scholar]
  75. 75.  Gu H, Yang W, Seeman NC 2010. DNA scissors device used to measure MutS binding to DNA mis-pairs. J. Am. Chem. Soc. 132:4352–57
    [Google Scholar]
  76. 76.  Modi S, Nizak C, Surana S, Halder S, Krishnan Y 2013. Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nat. Nanotechnol. 8:459–67
    [Google Scholar]
  77. 77.  Chatterjee G, Dalchau N, Muscat RA, Phillips A, Seelig G 2017. A spatially localized architecture for fast and modular DNA computing. Nat. Nanotechnol. 12:920–27
    [Google Scholar]
  78. 78.  Kopperger E, Pirzer T, Simmel FC 2015. Diffusive transport of molecular cargo tethered to a DNA origami platform. Nano Lett 15:2693–99
    [Google Scholar]
  79. 79.  Zhang F, Nangreave J, Liu Y, Yan H 2012. Reconfigurable DNA origami to generate quasifractal patterns. Nano Lett 12:3290–95
    [Google Scholar]
  80. 80.  Song J, Li Z, Wang P, Meyer T, Mao C, Ke Y 2017. Reconfiguration of DNA molecular arrays driven by information relay. Science 357:eaan3377
    [Google Scholar]
  81. 81.  Zadegan RM, Jepsen MD, Thomsen KE, Okholm AH, Schaffert DH et al. 2012. Construction of a 4 zeptoliters switchable 3D DNA box origami. ACS Nano 6:10050–53
    [Google Scholar]
  82. 82.  Banerjee A, Bhatia D, Saminathan A, Chakraborty S, Kar S, Krishnan Y 2013. Controlled release of encapsulated cargo from a DNA icosahedron using a chemical trigger. Angew. Chem. Int. Ed. Engl. 52:6854–57
    [Google Scholar]
  83. 83.  Kohman RE, Han X 2015. Light sensitization of DNA nanostructures via incorporation of photo-cleavable spacers. Chem. Commun. 51:5747–50
    [Google Scholar]
  84. 84.  Kuzyk A, Schreiber R, Zhang H, Govorov AO, Liedl T, Liu N 2014. Reconfigurable 3D plasmonic metamolecules. Nat. Mater. 13:862–66
    [Google Scholar]
  85. 85.  Sobczak JP, Martin TG, Gerling T, Dietz H 2012. Rapid folding of DNA into nanoscale shapes at constant temperature. Science 338:1458–61
    [Google Scholar]
  86. 86.  Ketterer P, Willner EM, Dietz H 2016. Nanoscale rotary apparatus formed from tight-fitting 3D DNA components. Sci. Adv. 2:e1501209
    [Google Scholar]
  87. 87.  Marras AE, Zhou L, Su HJ, Castro CE 2015. Programmable motion of DNA origami mechanisms. PNAS 112:713–18
    [Google Scholar]
  88. 88.  Ke Y, Meyer T, Shih WM, Bellot G 2016. Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator. Nat. Commun. 7:10935
    [Google Scholar]
  89. 89.  Zhou L, Marras AE, Su HJ, Castro CE 2015. Direct design of an energy landscape with bistable DNA origami mechanisms. Nano Lett 15:1815–21
    [Google Scholar]
  90. 90.  Gu H, Chao J, Xiao SJ, Seeman NC 2010. A proximity-based programmable DNA nanoscale assembly line. Nature 465:202–5
    [Google Scholar]
  91. 91.  Yin P, Yan H, Daniell XG, Turberfield AJ, Reif JH 2004. A unidirectional DNA walker that moves autonomously along a track. Angew. Chem. Int. Ed. Engl. 43:4906–11
    [Google Scholar]
  92. 92.  Lund K, Manzo AJ, Dabby N, Michelotti N, Johnson-Buck A et al. 2010. Molecular robots guided by prescriptive landscapes. Nature 465:206–10
    [Google Scholar]
  93. 93.  Pan J, Cha TG, Li F, Chen H, Bragg NA, Choi JH 2017. Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers. Sci. Adv. 3:e1601600
    [Google Scholar]
  94. 94.  Li N, Zheng J, Li C, Wang X, Ji X, He Z 2017. An enzyme-free DNA walker that moves on the surface of functionalized magnetic microparticles and its biosensing analysis. Chem. Commun. 53:8486–88
    [Google Scholar]
  95. 95.  Jung C, Allen PB, Ellington AD 2017. A simple, cleated DNA walker that hangs on to surfaces. ACS Nano 11:8047–54
    [Google Scholar]
  96. 96.  Wickham SF, Endo M, Katsuda Y, Hidaka K, Bath J et al. 2011. Direct observation of stepwise movement of a synthetic molecular transporter. Nat. Nanotechnol. 6:166–69
    [Google Scholar]
  97. 97.  Yang Y, Goetzfried MA, Hidaka K, You M, Tan W et al. 2015. Direct visualization of walking motions of photocontrolled nanomachine on the DNA nanostructure. Nano Lett 15:6672–76
    [Google Scholar]
  98. 98.  Schnitzer MJ, Block SM 1997. Kinesin hydrolyses one ATP per 8-nm step. Nature 388:386–90
    [Google Scholar]
  99. 99.  Wang C, Tao Y, Song G, Ren J, Qu X 2012. Speeding up a bidirectional DNA walking device. Langmuir 28:14829–37
    [Google Scholar]
  100. 100.  Saha S, Prakash V, Halder S, Chakraborty K, Krishnan Y 2015. A pH-independent DNA nanodevice for quantifying chloride transport in organelles of living cells. Nat. Nanotechnol. 10:645–51
    [Google Scholar]
  101. 101.  Surana S, Bhat JM, Koushika SP, Krishnan Y 2011. An autonomous DNA nanomachine maps spatiotemporal pH changes in a multicellular living organism. Nat. Commun. 2:340
    [Google Scholar]
  102. 102.  Surana S, Shenoy AR, Krishnan Y 2015. Designing DNA nanodevices for compatibility with the immune system of higher organisms. Nat. Nanotechnol. 10:741–47
    [Google Scholar]
  103. 103.  Peng P, Shi L, Wang H, Li T 2017. A DNA nanoswitch-controlled reversible nanosensor. Nucleic Acids Res 45:541–46
    [Google Scholar]
  104. 104.  Wei B, Ong LL, Chen J, Jaffe AS, Yin P 2014. Complex reconfiguration of DNA nanostructures. Angew. Chem. Int. Ed. Engl. 53:7475–79
    [Google Scholar]
  105. 105.  Hao Y, Kristiansen M, Sha R, Birktoft JJ, Hernandez C et al. 2017. A device that operates within a self-assembled 3D DNA crystal. Nat. Chem. 9:824–27
    [Google Scholar]
  106. 106.  Andersen ES, Dong M, Nielsen MM, Jahn K, Subramani R et al. 2009. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459:73–76
    [Google Scholar]
  107. 107.  Perrault SD, Shih WM 2014. Virus-inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. ACS Nano 8:5132–40
    [Google Scholar]
  108. 108.  Ponnuswamy N, Bastings MMC, Nathwani B, Ryu JH, Chou LYT et al. 2017. Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation. Nat. Commun. 8:15654
    [Google Scholar]
  109. 109.  Lee H, Lytton-Jean AK, Chen Y, Love KT, Park AI et al. 2012. Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery. Nat. Nanotechnol. 7:389–93
    [Google Scholar]
  110. 110.  Zhang Q, Jiang Q, Li N, Dai L, Liu Q et al. 2014. DNA origami as an in vivo drug delivery vehicle for cancer therapy. ACS Nano 8:6633–43
    [Google Scholar]
  111. 111.  Funke JJ, Dietz H 2016. Placing molecules with Bohr radius resolution using DNA origami. Nat. Nanotechnol. 11:47–52
    [Google Scholar]
  112. 112.  Marras AE, Zhou L, Kolliopoulos V, Su HJ, Castro CE 2016. Directing folding pathways for multi-component DNA origami nanostructures with complex topology. New J. Phys. 18:055005
    [Google Scholar]
  113. 113.  Gerling T, Wagenbauer KF, Neuner AM, Dietz H 2015. Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components. Science 347:1446–52
    [Google Scholar]
  114. 114.  Zhou L, Marras AE, Su HJ, Castro CE 2013. DNA origami compliant nanostructures with tunable mechanical properties. ACS Nano 8:27–34
    [Google Scholar]
  115. 115.  Zhou L, Marras AE, Castro CE, Su H-J 2016. Pseudorigid-body models of compliant DNA origami mechanisms. J. Mech. Robot. 8:051013
    [Google Scholar]
  116. 116.  Liedl T, Högberg B, Tytell J, Ingber DE, Shih WM 2010. Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat. Nanotechnol. 5:520–24
    [Google Scholar]
  117. 117.  Shi Z, Castro CE, Arya G 2017. Conformational dynamics of mechanically compliant DNA nanostructures from coarse-grained molecular dynamics simulations. ACS Nano 11:4617–30
    [Google Scholar]
  118. 118.  Yurke B, Turberfield AJ, Mills AP Jr., Simmel FC, Neumann JL 2000. A DNA-fuelled molecular machine made of DNA. Nat 406:605–8
    [Google Scholar]
  119. 119.  Liu M, Fu J, Hejesen C, Yang Y, Woodbury NW et al. 2013. A DNA tweezer–actuated enzyme nanoreactor. Nat. Commun. 4:2127
    [Google Scholar]
  120. 120.  Kuzyk A, Urban MJ, Idili A, Ricci F, Liu N 2017. Selective control of reconfigurable chiral plasmonic metamolecules. Sci. Adv. 3:e1602803
    [Google Scholar]
  121. 121.  Yang Y, Endo M, Hidaka K, Sugiyama H 2012. Photo-controllable DNA origami nanostructures assembling into predesigned multiorientational patterns. J. Am. Chem. Soc. 134:20645–53
    [Google Scholar]
  122. 122.  Hudoba MW, Luo Y, Zacharias A, Poirier MG, Castro CE 2017. Dynamic DNA origami device for measuring compressive depletion forces. ACS Nano 11:6566–73
    [Google Scholar]
  123. 123.  Zhang DY, Seelig G 2011. Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3:103–13
    [Google Scholar]
  124. 124.  Srinivas N, Ouldridge TE, Sulc P, Schaeffer JM, Yurke B et al. 2013. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res 41:10641–58
    [Google Scholar]
  125. 125.  Kuzyk A, Yang Y, Duan X, Stoll S, Govorov AO et al. 2016. A light-driven three-dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nat. Commun. 7:10591
    [Google Scholar]
  126. 126.  Yang Y, Tashiro R, Suzuki Y, Emura T, Hidaka K et al. 2017. A photoregulated DNA-based rotary system and direct observation of its rotational movement. Chemistry 23:3979–85
    [Google Scholar]
  127. 127.  Asanuma H, Liang X, Nishioka H, Matsunaga D, Liu M, Komiyama M 2007. Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription. Nat. Protoc. 2:203–12
    [Google Scholar]
  128. 128.  List J, Weber M, Simmel FC 2014. Hydrophobic actuation of a DNA origami bilayer structure. Angew. Chem. Int. Ed. Engl. 53:4236–39
    [Google Scholar]
  129. 129.  Mukherjea M, Llinas P, Kim H, Travaglia M, Safer D et al. 2009. Myosin VI dimerization triggers an unfolding of a three-helix bundle in order to extend its reach. Mol. Cell 35:305–15
    [Google Scholar]
  130. 130.  Yildiz A, Tomishige M, Gennerich A, Vale RD 2008. Intramolecular strain coordinates kinesin stepping behavior along microtubules. Cell 134:1030–41
    [Google Scholar]
  131. 131.  Kinosita K Jr., Yasuda R, Noji H, Adachi K 2000. A rotary molecular motor that can work at near 100% efficiency. Philos. Trans. R. Soc. B 355:473–89
    [Google Scholar]
  132. 132.  List J, Falgenhauer E, Kopperger E, Pardatscher G, Simmel FC 2016. Long-range movement of large mechanically interlocked DNA nanostructures. Nat. Commun. 7:12414
    [Google Scholar]
  133. 133.  Sun L, Zhang X, Gao S, Rao PA, Padilla-Sanchez V et al. 2015. Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Nat. Commun. 6:7548
    [Google Scholar]
  134. 134.  Gligoris T, Lowe J 2016. Structural insights into ring formation of cohesin and related Smc complexes. Trends Cell Biol 26:680–93
    [Google Scholar]
  135. 135.  Corbett KD, Harrison SC 2016. Molecular architecture of the yeast monopolin complex. Cell Rep 17:929
    [Google Scholar]
  136. 136.  Le JV, Luo Y, Darcy MA, Lucas CR, Goodwin MF et al. 2016. Probing nucleosome stability with a DNA origami nanocaliper. ACS Nano 10:7073–84
    [Google Scholar]
  137. 137.  Funke JJ, Ketterer P, Lieleg C, Schunter S, Korber P, Dietz H 2016. Uncovering the forces between nucleosomes using DNA origami. Sci. Adv. 2:e1600974
    [Google Scholar]
  138. 138.  Chen Y-J, Groves B, Muscat RA, Seelig G 2015. DNA nanotechnology from the test tube to the cell. Nat. Nanotechnol. 10:748–60
    [Google Scholar]
  139. 139.  Groves B, Chen YJ, Zurla C, Pochekailov S, Kirschman JL et al. 2016. Computing in mammalian cells with nucleic acid strand exchange. Nat. Nanotechnol. 11:287–94
    [Google Scholar]
  140. 140.  Wang K, Tang Z, Yang CJ, Kim Y, Fang X et al. 2009. Molecular engineering of DNA: molecular beacons. Angew. Chem. Int. Ed. Engl. 48:856–70
    [Google Scholar]
  141. 141.  Li D, Song S, Fan C 2010. Target-responsive structural switching for nucleic acid–based sensors. Acc. Chem. Res. 43:631–41
    [Google Scholar]
  142. 142.  Bell NA, Engst CR, Ablay M, Divitini G, Ducati C et al. 2012. DNA origami nanopores. Nano Lett 12:512–17
    [Google Scholar]
  143. 143.  Endo M, Sugiyama H 2014. Single-molecule imaging of dynamic motions of biomolecules in DNA origami nanostructures using high-speed atomic force microscopy. Acc. Chem. Res. 47:1645–53
    [Google Scholar]
  144. 144.  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 319:180–83
    [Google Scholar]
  145. 145.  Kuzuya A, Sakai Y, Yamazaki T, Xu Y, Komiyama M 2011. Nanomechanical DNA origami “single-molecule beacons” directly imaged by atomic force microscopy. Nat. Commun. 2:449
    [Google Scholar]
  146. 146.  Walter HK, Bauer J, Steinmeyer J, Kuzuya A, Niemeyer CM, Wagenknecht HA 2017. “DNA origami traffic lights” with a split aptamer sensor for a bicolor fluorescence readout. Nano Lett 17:2467–72
    [Google Scholar]
  147. 147.  Liu M, Fu J, Hejesen C, Yang Y, Woodbury NW et al. 2013. A DNA tweezer–actuated enzyme nanoreactor. Nat. Commun. 4:2127
    [Google Scholar]
  148. 148.  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 10:4756–61
    [Google Scholar]
  149. 149.  Jungmann R, Avendano MS, Dai MJ, Woehrstein JB, Agasti SS et al. 2016. Quantitative super-resolution imaging with qPAINT. Nat. Methods 13:439–42
    [Google Scholar]
  150. 150.  Bhatia D, Arumugam S, Nasilowski M, Joshi H, Wunder C et al. 2016. Quantum dot–loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. Nat. Nanotechnol. 11:1112–19
    [Google Scholar]
  151. 151.  Jiang Q, Song C, Nangreave J, Liu X, Lin L et al. 2012. DNA origami as a carrier for circumvention of drug resistance. J. Am. Chem. Soc. 134:13396–403
    [Google Scholar]
  152. 152.  Zhao Y-X, Shaw A, Zeng X, Benson E, Nyström AM, Högberg B 2012. DNA origami delivery system for cancer therapy with tunable release properties. ACS Nano 6:8684–91
    [Google Scholar]
  153. 153.  Zhang Q, Jiang Q, Li N, Dai L, Liu Q et al. 2014. DNA origami as an in vivo drug delivery vehicle for cancer therapy. ACS Nano 8:6633–43
    [Google Scholar]
  154. 154.  Schüller VJ, Heidegger S, Sandholzer N, Nickels PC, Suhartha NA et al. 2011. Cellular immunostimulation by CpG-sequence-coated DNA origami structures. ACS Nano 5:9696–702
    [Google Scholar]
  155. 155.  Kohman RE, Cha SS, Man HY, Han X 2016. Light-triggered release of bioactive molecules from DNA nanostructures. Nano Lett 16:2781–85
    [Google Scholar]
  156. 156.  Li F, Chen H, Pan J, Cha TG, Medintz IL, Choi JH 2016. A DNAzyme-mediated logic gate for programming molecular capture and release on DNA origami. Chem. Commun. 52:8369–72
    [Google Scholar]
/content/journals/10.1146/annurev-bioeng-062117-120904
Loading
/content/journals/10.1146/annurev-bioeng-062117-120904
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error