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DNA nanotechnology from the test tube to the cell

Nature Nanotechnology volume 10, pages 748–760 (2015)Cite this article

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Abstract

The programmability of Watson–Crick base pairing, combined with a decrease in the cost of synthesis, has made DNA a widely used material for the assembly of molecular structures and dynamic molecular devices. Working in cell-free settings, researchers in DNA nanotechnology have been able to scale up system complexity and quantitatively characterize reaction mechanisms to an extent that is infeasible for engineered gene circuits or other cell-based technologies. However, the most intriguing applications of DNA nanotechnology — applications that best take advantage of the small size, biocompatibility and programmability of DNA-based systems — lie at the interface with biology. Here, we review recent progress in the transition of DNA nanotechnology from the test tube to the cell. We highlight key successes in the development of DNA-based imaging probes, prototypes of smart therapeutics and drug delivery systems, and explore the future challenges and opportunities for cellular DNA nanotechnology.

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Figure 1: Applications of DNA nanotechnology at the interface with biology.
Figure 2: In situ imaging of mRNA in fixed cells.
Figure 3: Cell surface computation.
Figure 4: DNA nanomachines and logic gates in mammalian cells.
Figure 5: mRNA imaging in living cells.
Figure 6: Complexity break for cellular DNA nanodevices?

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References

  1. Bloomfield, V. A., Crothers, D. M. & Ignacio Tinoco, J. Nucleic Acids: Structures, Properties and Functions (University Science Books, 2000).

    Google Scholar 

  2. SantaLucia, J. & Hicks, D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415–440 (2004).

    CAS  Google Scholar 

  3. Carlson, R. The changing economics of DNA synthesis. Nature Biotechnol. 27, 1091–1094 (2009).

    CAS  Google Scholar 

  4. Dittmer, W. U., Reuter, A. & Simmel, F. C. A. DNA-based machine that can cyclically bind and release thrombin. Angew. Chem. Int. Ed. 43, 3550–3553 (2004).

    CAS  Google Scholar 

  5. Yurke, B., Mills, A. P. Jr & Cheng, S. L. DNA implementation of addition in which the input strands are separate from the operator strands. BioSystems 52, 165–174 (1999).

    CAS  Google Scholar 

  6. Benenson, Y., Gil, B., Ben-Dor, U., Adar, R. & Shapiro, E. An autonomous molecular computer for logical control of gene expression. Nature 429, 423–429 (2004).

    CAS  Google Scholar 

  7. Ko, S., Liu, H., Chen, Y. & Mao, C. DNA nanotubes as combinatorial vehicles for cellular delivery. Biomacromolecules 9, 3039–3043 (2008). Cellular uptake of large DNA nanostructures was first demonstrated in this work.

    CAS  Google Scholar 

  8. Seeman, N. C. Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).

    CAS  Google Scholar 

  9. Kallenbach, N. R., Ma, R.-I. & Seeman, N. C. An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829–831 (1983).

    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).

    CAS  Google Scholar 

  11. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  13. Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009).

    CAS  Google Scholar 

  14. 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 

  15. 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 

  16. 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 

  17. Rothemund, P. W. K., Papadakis, N. & Winfree, E. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, e424 (2004).

    Google Scholar 

  18. He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–201 (2008).

    CAS  Google Scholar 

  19. Yan, H., Park, S. H., Finkelstein, G., Reif, J. H. & LaBean, T. H. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882–1884 (2003).

    CAS  Google Scholar 

  20. Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    CAS  Google Scholar 

  21. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  25. Adleman, L. M. Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024 (1994).

    CAS  Google Scholar 

  26. Yurke, B., Turberfield, A. J., Mills, A. P. Jr, Simmel, F. C. & Neumann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000).

    CAS  Google Scholar 

  27. Seelig, G., Soloveichik, D., Zhang, D. Y. & Winfree, E. Enzyme-free nucleic acid logic circuits. Science 314, 1585–1588 (2006).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  29. Kay, E. R., Leigh, D. A & Zerbetto, F. Synthetic molecular motors and mechanical machines. Angew. Chem. Int. Ed. 46, 72–191 (2007).

    CAS  Google Scholar 

  30. Bath, J. & Turberfield, A. J. DNA nanomachines. Nature Nanotech. 2, 274–284 (2007).

    Google Scholar 

  31. Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science 324, 67–71 (2009).

    CAS  Google Scholar 

  32. Lund, K. et al. Molecular robots guided by prescriptive landscapes. Nature 465, 206–210 (2010).

    CAS  Google Scholar 

  33. Muscat, R. A., Bath, J. & Turberfield, A. J. A programmable molecular robot. Nano Lett. 11, 982–987 (2011).

    CAS  Google Scholar 

  34. Wickham, S. F. J. et al. A DNA-based molecular motor that can navigate a network of tracks. Nature Nanotech. 7, 169–173 (2012).

    CAS  Google Scholar 

  35. Chen, Y.-J. et al. Programmable chemical controllers made from DNA. Nature Nanotech. 8, 755–762 (2013).

    CAS  Google Scholar 

  36. Qian, L., Winfree, E. & Bruck, J. Neural network computation with DNA strand displacement cascades. Nature 475, 368–372 (2011).

    CAS  Google Scholar 

  37. Qian, L. & Winfree, E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 332, 1196–1201 (2011).

    CAS  Google Scholar 

  38. Elbaz, J. et al. DNA computing circuits using libraries of DNAzyme subunits. Nature Nanotech. 5, 417–422 (2010).

    CAS  Google Scholar 

  39. Pei, R., Matamoros, E., Liu, M., Stefanovic, D. & Stojanovic, M. N. Training a molecular automaton to play a game. Nature Nanotech. 5, 773–777 (2010).

    CAS  Google Scholar 

  40. Seelig, G., Yurke, B. & Winfree, E. Catalyzed relaxation of a metastable DNA fuel. J. Am. Chem. Soc. 128, 12211–12220 (2006).

    CAS  Google Scholar 

  41. Zhang, D. Y., Turberfield, A. J., Yurke, B. & Winfree, E. Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318, 1121–1125 (2007).

    CAS  Google Scholar 

  42. Zhang, D. Y. & Winfree, E. Dynamic allosteric control of noncovalent DNA catalysis reactions. J. Am. Chem. Soc. 130, 13921–13926 (2008).

    CAS  Google Scholar 

  43. Turberfield, A. J. et al. DNA fuel for free-running nanomachines. Phys. Rev. Lett. 90, 118102 (2003).

    CAS  Google Scholar 

  44. Bois, J. S. et al. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res. 33, 4090–4095 (2005).

    CAS  Google Scholar 

  45. Benenson, Y. et al. Programmable and autonomous computing machine made of biomolecules. Nature 414, 430–434 (2001).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  47. Conway, J. W., McLaughlin, C. K., Castor, K. J. & Sleiman, H. DNA nanostructure serum stability: greater than the sum of its parts. Chem. Commun. 49, 1172–1174 (2013).

    CAS  Google Scholar 

  48. Hahn, J., Wickham, S. F. J., Shih, W. M. & Perrault, S. D. Addressing the instability of DNA nanostructures in tissue culture. ACS Nano 8, 8765–8775 (2014).

    CAS  Google Scholar 

  49. Keum, J.-W. & Bermudez, H. Enhanced resistance of DNA nanostructures to enzymatic digestion. Chem. Commun. 7036–7038 (2009).

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

    CAS  Google Scholar 

  51. Choi, H. M. T. et al. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature Biotechnol. 28, 1208–1212 (2010).

    CAS  Google Scholar 

  52. Choi, H. M. T., Beck, V. A. & Pierce, N. A. Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 8, 4284–4294 (2014).

    CAS  Google Scholar 

  53. Levesque, M. J., Ginart, P., Wei, Y. & Raj, A. Visualizing SNVs to quantify allele-specific expression in single cells. Nature Methods 10, 865–867 (2013). Taking advantage of the specificity of toehold-mediated strand displacement reactions, this work demonstrated that single-nucleotide variants on single RNA transcripts can be detected using smFISH-based imaging probes.

    CAS  Google Scholar 

  54. Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nature Methods 5, 877–879 (2008).

    CAS  Google Scholar 

  55. Duose, D. Y. et al. Configuring robust DNA strand displacement reactions for in situ molecular analyses. Nucleic Acids Res. 40, 3289–3298 (2012).

    CAS  Google Scholar 

  56. Jungmann, R. et al. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 10, 4756–4761 (2010).

    CAS  Google Scholar 

  57. Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nature Methods 11, 313–318 (2014).

    CAS  Google Scholar 

  58. Keefe, A., Pai, S. & Ellington, A. Aptamers as therapeutics. Nature Rev. Drug Discov. 9, 537–550 (2010).

    CAS  Google Scholar 

  59. Rudchenko, M. et al. Autonomous molecular cascades for evaluation of cell surfaces. Nature Nanotech. 8, 580–586 (2013). This work successfully used strand displacement cascades to classify different cell types, thereby demonstrating a scalable approach for the analysis of cellular information.

    CAS  Google Scholar 

  60. Douglas, S. M., Bachelet, I. & Church, G. M. A logic-gated nanorobot for targeted transport of molecular payloads. Science 335, 831–834 (2012). Proof-of-principle demonstration of a novel class of conditional therapeutics that combine protective DNA origami structures with molecular logic.

    CAS  Google Scholar 

  61. Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505–510 (1990).

    CAS  Google Scholar 

  62. Ellington, A. D. & Szostak, J. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990).

    CAS  Google Scholar 

  63. Amir, Y. et al. Universal computing by DNA origami robots in a living animal. Nature Nanotech. 9, 353–357 (2014).

    CAS  Google Scholar 

  64. You, M. et al. DNA 'nano-claw': logic-based autonomous cancer targeting and therapy. J. Am. Chem. Soc. 136, 1256–1259 (2014).

    CAS  Google Scholar 

  65. You, M., Zhu, G., Chen, T., Donovan, M. J. & Tan, W. Programmable and multiparameter DNA-based logic platform for cancer recognition and targeted therapy. J. Am. Chem. Soc. 137, 667–674 (2015).

    CAS  Google Scholar 

  66. Shaw, A. et al. Spatial control of membrane receptor function using ligand nanocalipers. Nature Methods 11, 841–846 (2014). By showing that cells are sensitive to the spatial organization of protein ligands arranged on a DNA origami, the authors provide an intriguing example of the use of nanostructures as tools for cell biology.

    CAS  Google Scholar 

  67. Chandra, R. A., Douglas, E. S., Mathies, R. A., Bertozzi, C. R. & Francis, M. B. Programmable cell adhesion encoded by DNA hybridization. Angew. Chem. Int. Ed. 45, 896–901 (2006).

    CAS  Google Scholar 

  68. Saxon, E. & Bertozzi, C. R. Cell surface engineering by a modified Staudinger reaction. Science 287, 2007–2010 (2000).

    CAS  Google Scholar 

  69. Gartner, Z. J. & Bertozzi, C. R. Programmed assembly of 3-dimensional microtissues with defined cellular connectivity. Proc. Natl Acad. Sci. USA 106, 4606–4610 (2009). This work demonstrated a novel strategy for the bottom-up construction of 'microtissues' using DNA sequence-programmed connectivity.

    CAS  Google Scholar 

  70. Liu, J. S., Farlow, J. T., Paulson, A. K., Labarge, M. A. & Gartner, Z. J. Programmed cell-to-cell variability in Ras activity triggers emergent behaviors during mammary epithelial morphogenesis. Cell Rep. 2, 1461–1470 (2012).

    CAS  Google Scholar 

  71. Langecker, M. et al. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338, 932–936 (2012).

    CAS  Google Scholar 

  72. Burns, J. R. et al. Lipid-bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor. Angew. Chem. Int. Ed. 52, 12069–12072 (2013).

    CAS  Google Scholar 

  73. Burns, J. R., Al-Juffali, N., Janes, S. M. & Howorka, S. Membrane-spanning DNA nanopores with cytotoxic effect. Angew. Chem. Int. Ed. 53, 12466–12470 (2014).

    CAS  Google Scholar 

  74. Walsh, A. S. et al. DNA cage delivery to mammalian cells. ACS Nano 5, 5427–5432 (2011).

    CAS  Google Scholar 

  75. Schüller, V. J. et al. Cellular immunostimulation by CpG-sequence-coated DNA origami structures. ACS Nano 5, 9696–9702 (2011).

    Google Scholar 

  76. Liang, L. et al. Single-particle tracking and modulation of cell entry pathways of a tetrahedral DNA nanostructure in live cells. Angew. Chem. Int. Ed. 53, 7745–7750 (2014).

    CAS  Google Scholar 

  77. Mikkilä, J. et al. Virus-encapsulated DNA origami nanostructures for cellular delivery. Nano Lett. 14, 2196–2200 (2014).

    Google Scholar 

  78. Perrault, S. D. & Shih, W. M. Virus-inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. ACS Nano 8, 5132–5140 (2014). The authors showed that lipid encapsulation of DNA octahedrons results in a reduced immune response and greatly enhanced bioavailability in circulation in mouse models.

    CAS  Google Scholar 

  79. Hemmi, H. et al. A Toll-like receptor recognizes bacterial DNA. Nature 408, 740–745 (2000).

    CAS  Google Scholar 

  80. Nishikawa, M., Matono, M., Rattanakiat, S., Matsuoka, N. & Takakura, Y. Enhanced immunostimulatory activity of oligodeoxynucleotides by Y-shape formation. Immunology 124, 247–255 (2008). The first demonstration of drug delivery using DNA nanostructures; Y-shaped DNA nanostructures decorated with CpG motifs were used to trigger immune responses in living cells.

    CAS  Google Scholar 

  81. Rattanakiat, S., Nishikawa, M., Funabashi, H., Luo, D. & Takakura, Y. The assembly of a short linear natural cytosine-phosphate-guanine DNA into dendritic structures and its effect on immunostimulatory activity. Biomaterials 30, 5701–5706 (2009).

    CAS  Google Scholar 

  82. Mohri, K. et al. Design and development of nanosized DNA assemblies in polypod-like structures as efficient vehicles for immunostimulatory cpg motifs to immune cells. ACS Nano 6, 5931–5940 (2012).

    CAS  Google Scholar 

  83. Li, J. et al. Self-assembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides. ACS Nano 5, 8783–8789 (2011).

    CAS  Google Scholar 

  84. Liu, X. et al. A DNA nanostructure platform for directed assembly of synthetic vaccines. Nano Lett. 12, 4254–4259 (2012).

    CAS  Google Scholar 

  85. Davis, M. E., Chen, Z. (Georgia) & Shin, D. M. Nanoparticle therapeutics: an emerging treatment modality for cancer. Nature Rev. Drug Discov. 7, 771–782 (2008).

    CAS  Google Scholar 

  86. Chang, M., Yang, C.-S. & Huang, D.-M. Aptamer-conjugated DNA icosahedral nanoparticles as a carrier of doxorubicin for cancer therapy. ACS Nano 5, 6156–6163 (2011).

    CAS  Google Scholar 

  87. Jiang, Q. et al. DNA origami as a carrier for circumvention of drug resistance. J. Am. Chem. Soc. 134, 13396–13403 (2012).

    CAS  Google Scholar 

  88. Kim, K.-R. et al. Drug delivery by a self-assembled DNA tetrahedron for overcoming drug resistance in breast cancer cells. Chem. Commun. 49, 2010–2012 (2013).

    CAS  Google Scholar 

  89. Zhao, Y.-X. et al. DNA origami delivery system for cancer therapy with tunable release properties. ACS Nano 6, 8684–8691 (2012).

    CAS  Google Scholar 

  90. Zhu, G. et al. Self-assembled, aptamer-tethered DNA nanotrains for targeted transport of molecular drugs in cancer theranostics. Proc. Natl Acad. Sci. USA 110, 7998–8003 (2013).

    CAS  Google Scholar 

  91. Zhang, Q. et al. DNA origami as an in vivo drug delivery vehicle for cancer therapy. ACS Nano 8, 6633–6643 (2014).

    CAS  Google Scholar 

  92. Keum, J. W., Ahn, J. H. & Bermudez, H. Design, assembly, and activity of antisense DNA nanostructures. Small 7, 3529–3535 (2011).

    CAS  Google Scholar 

  93. Lee, H. et al. Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery. Nature Nanotech. 7, 389–393 (2012).

    CAS  Google Scholar 

  94. Chen, G. et al. Enzymatic synthesis of periodic DNA nanoribbons for intracellular pH sensing and gene silencing. J. Am. Chem. Soc. 137, 3844–3851 (2015).

    CAS  Google Scholar 

  95. Pei, H. et al. Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors. Angew. Chem. Int. Ed. 51, 9020–9024 (2012).

    CAS  Google Scholar 

  96. Modi, S. et al. A DNA nanomachine that maps spatial and temporal pH changes inside living cells. Nature Nanotech. 4, 325–330 (2009).

    CAS  Google Scholar 

  97. Modi, S., Nizak, C., Surana, S., Halder, S. & Krishnan, Y. Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nature Nanotech. 8, 459–467 (2013).

    CAS  Google Scholar 

  98. Tyagi, S. & Kramer, F. R. Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnol. 14, 303–308 (1996).

    CAS  Google Scholar 

  99. Chen, A. K., Davydenko, O., Behlke, M. A. & Tsourkas, A. Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells. Nucleic Acids Res. 38, e148 (2010).

    Google Scholar 

  100. Mhlanga, M. M., Vargas, D. Y., Fung, C. W., Kramer, F. R. & Tyagi, S. tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells. Nucleic Acids Res. 33, 1902–1912 (2005).

    CAS  Google Scholar 

  101. Zhang, X., Song, Y., Shah, A. & Lekova, V. Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells. Nucleic Acids Res. 41, e152 (2013).

    CAS  Google Scholar 

  102. Bratu, D. P., Cha, B.-J., Mhlanga, M. M., Kramer, F. R. & Tyagi, S. Visualizing the distribution and transport of mRNAs in living cells. Proc. Natl Acad. Sci. USA 100, 13308–13313 (2003).

    CAS  Google Scholar 

  103. Santangelo, P. J. et al. Single molecule–sensitive probes for imaging RNA in live cells. Nature Methods 6, 347–349 (2009).

    CAS  Google Scholar 

  104. Rosi, N. L. et al. Oligonucleotide-modified gold nanoparticles for intracellular gene regulation. Science 312, 1027–1030 (2006). Nanoflares provided the first example of strand displacement reactions with an endogenous RNA input inside living cells.

    CAS  Google Scholar 

  105. Alhasan, A. H., Patel, P. C., Choi, C. H. J. & Mirkin, C. A. Exosome encased spherical nucleic acid gold nanoparticle conjugates as potent microRNA regulation agents. Small 10, 186–192 (2014).

    CAS  Google Scholar 

  106. Prigodich, A. E. et al. Nano-flares for mRNA regulation and detection. ACS Nano 3, 2147–2152 (2009).

    CAS  Google Scholar 

  107. Halo, T. L. et al. NanoFlares for the detection, isolation, and culture of live tumor cells from human blood. Proc. Natl Acad. Sci. USA 111, 17104–17109 (2014).

    CAS  Google Scholar 

  108. Afonin, K. A. et al. Activation of different split functionalities on re-association of RNA–DNA hybrids. Nature Nanotech. 8, 296–304 (2013).

    CAS  Google Scholar 

  109. Chen, S. X., Zhang, D. Y. & Seelig, G. Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA. Nature Chem. 5, 782–789 (2013).

    CAS  Google Scholar 

  110. Xie, Z., Liu, S. J., Bleris, L. & Benenson, Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res. 38, 2692–2701 (2010).

    CAS  Google Scholar 

  111. Hochrein, L. M., Schwarzkopf, M., Shahgholi, M., Yin, P. & Pierce, N. A. Conditional dicer substrate formation via shape and sequence transduction with small conditional RNAs. J. Am. Chem. Soc. 135, 17322–17330 (2013).

    CAS  Google Scholar 

  112. Kumar, D., Kim, S. H. & Yokobayashi, Y. Combinatorially inducible RNA interference triggered by chemically modified oligonucleotides. J. Am. Chem. Soc. 133, 2783–2788 (2011).

    CAS  Google Scholar 

  113. Kahan-Hanum, M., Douek, Y., Adar, R. & Shapiro, E. A library of programmable DNAzymes that operate in a cellular environment. Sci. Rep. 3, 1535 (2013).

    Google Scholar 

  114. Hemphill, J. & Deiters, A. DNA computation in mammalian cells: microRNA logic operations. J. Am. Chem. Soc. 135, 10512–10518 (2013).

    CAS  Google Scholar 

  115. Yu, J., Liu, Z., Jiang, W., Wang, G. & Mao, C. De novo design of an RNA tile that self-assembles into a homo-octameric nanoprism. Nature Commun. 6, 1–6 (2015).

    Google Scholar 

  116. Lee, J. B., Hong, J., Bonner, D. K., Poon, Z. & Hammond, P. T. Self-assembled RNA interference microsponges for efficient siRNA delivery. Nature Mater. 11, 316–322 (2012).

    CAS  Google Scholar 

  117. Severcan, I. et al. A polyhedron made of tRNAs. Nature Chem. 2, 772–779 (2010).

    CAS  Google Scholar 

  118. Ohno, H. et al. Synthetic RNA-protein complex shaped like an equilateral triangle. Nature Nanotech. 6, 116–120 (2011).

    CAS  Google Scholar 

  119. Chworos, A. et al. Building programmable jigsaw puzzles with RNA. Science 306, 2068–2073 (2004).

    CAS  Google Scholar 

  120. Afonin, K. A. et al. In vitro assembly of cubic RNA-based scaffolds designed in silico. Nature Nanotechnol. 5, 676–682 (2010).

    CAS  Google Scholar 

  121. Geary, C., Rothemund, P. W. K. & Andersen, E. S. A single-stranded architecture for cotranscriptional folding of RNA nanostructures. Science 345, 799–804 (2014).

    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 333, 470–474 (2011). This work used self-assembled RNA scaffolds to increase the efficiency of hydrogen production in bacteria, thus demonstrating the functional use of RNA architectures in vivo.

    CAS  Google Scholar 

  123. Sachdeva, G., Garg, A., Godding, D., Way, J. C. & Silver, P. A. In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner. Nucleic Acids Res. 42, 9493–9503 (2014).

    CAS  Google Scholar 

  124. Bhadra, S. & Ellington, A. D. Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers. Nucleic Acids Res. 42, e58 (2014).

    CAS  Google Scholar 

  125. Isaacs, F. J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnol. 22, 841–847 (2004).

    CAS  Google Scholar 

  126. Green, A. A., Silver, P. A., Collins, J. J. & Yin, P. Toehold switches: de-novo-designed regulators of gene expression. Cell 159, 925–939 (2014).

    CAS  Google Scholar 

  127. Farzadfard, F. & Lu, T. K. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346, 6211 (2014).

    Google Scholar 

  128. Kelley, B. Industrialization of mAb production technology: the bioprocessing industry at a crossroads. MAbs 1, 440–449 (2009).

    Google Scholar 

  129. Kick, B., Praetorius, F., Dietz, H. & Weuster-Botz, D. Efficient production of single-stranded phage DNA as scaffolds for DNA origami. Nano Lett. 15, 4672–4676 (2015).

    CAS  Google Scholar 

  130. Ducani, C., Kaul, C., Moche, M., Shih, W. M. & Högberg, B. Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides. Nature Methods 10, 647–652 (2013).

    CAS  Google Scholar 

  131. Gu, H. & Breaker, R. R. Production of single-stranded DNAs by self-cleavage of rolling-circle amplification products. Biotechniques 54, 337–343 (2013).

    CAS  Google Scholar 

  132. Gilleron, J. et al. Image-based analysis of lipid nanoparticle–mediated siRNA delivery, intracellular trafficking and endosomal escape. Nature Biotechnol. 31, 638–646 (2013).

    CAS  Google Scholar 

  133. Sahay, G. et al. Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling. Nature Biotechnol. 31, 653–658 (2013).

    CAS  Google Scholar 

  134. Bao, G., Rhee, W. J. & Tsourkas, A. Fluorescent probes for live-cell RNA detection. Annu. Rev. Biomed. Eng. 11, 25–47 (2009).

    CAS  Google Scholar 

  135. Fisher, T. L., Terhorst, T., Cao, X. & Wagner, R. W. Intracellular disposition and metabolism of fluorescently-labeled unmodified and modified oligonucleotides microinjected into mammalian cells. Nucleic Acids Res. 21, 3857–3865 (1993).

    CAS  Google Scholar 

  136. Watts, J. K., Deleavey, G. F. & Damha, M. J. Chemically modified siRNA: tools and applications. Drug Discov. Today 13, 842–855 (2008).

    CAS  Google Scholar 

  137. Amarzguioui, M., Holen, T., Babaie, E. & Prydz, H. Tolerance for mutations and chemical modifications in a siRNA. Nucleic Acids Res. 31, 589–595 (2003).

    CAS  Google Scholar 

  138. Bramsen, J. B. et al. A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity. Nucleic Acids Res. 37, 2867–2881 (2009).

    CAS  Google Scholar 

  139. Lukacs, G. L. et al. Size-dependent DNA mobility in cytoplasm and nucleus. J. Biol. Chem. 275, 1625–1629 (2000).

    CAS  Google Scholar 

  140. Schoen, I., Krammer, H. & Braun, D. Hybridization kinetics is different inside cells. Proc. Natl Acad. Sci. USA 106, 21649–21654 (2009).

    CAS  Google Scholar 

  141. Manche, L., Green, S. R., Schmedt, C. & Mathews, M. B. Interactions between double-stranded RNA regulators and the protein kinase DAI. Mol. Cell. Biol. 12, 5238–5248 (1992).

    CAS  Google Scholar 

  142. Krieg, A. M. Therapeutic potential of Toll-like receptor 9 activation. Nature Rev. Drug Discov. 5, 471–484 (2006).

    CAS  Google Scholar 

  143. Shir, A. & Levitzki, A. Inhibition of glioma growth by tumor-specific activation of double-stranded RNA-dependent protein kinase PKR. Nature Biotechnol. 20, 895–900 (2002).

    CAS  Google Scholar 

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Acknowledgements

We would like to thank S. Douglas, N. Pierce, M. Schwarzkopf, S. Pun and D. Soloveichik for insightful comments and helpful feedback on the manuscript. This work was supported by NSF grants CCF-1317653 and CAREER CBET-0954566.

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Authors and Affiliations

  1. Department of Electrical Engineering, University of Washington, Seattle, 98195, Washington, USA

    Yuan-Jyue Chen, Benjamin Groves, Richard A. Muscat & Georg Seelig

  2. Department of Computer Science and Engineering, University of Washington, Seattle, 98195, Washington, USA

    Georg Seelig

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  1. Yuan-Jyue Chen
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  2. Benjamin Groves
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  4. Georg Seelig
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All authors contributed equally to this work.

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Correspondence to Georg Seelig.

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Chen, YJ., Groves, B., Muscat, R. et al. DNA nanotechnology from the test tube to the cell. Nature Nanotech 10, 748–760 (2015). https://doi.org/10.1038/nnano.2015.195

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