Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation

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Abstract

Nucleic acids have attracted widespread attention due to the simplicity with which they can be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of DNA/RNA nanotechnology offer numerous opportunities for in-cell and in-vivo applications, and the technology holds great promise to advance the growing field of synthetic biology. Many elegant examples have revealed the potential in integrating nucleic acid nanostructures in cells and in vivo where they can perform important physiological functions. In this Review, we summarize the current abilities of DNA/RNA nanotechnology to realize applications in live cells and then discuss the key problems that must be solved to fully exploit the useful properties of nanostructures. Finally, we provide viewpoints on how to integrate the tools provided by DNA/RNA nanotechnology and related new technologies to construct nucleic acid nanostructure-based molecular circuitry for synthetic biology.

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Figure 1: Representative examples of promising DNA nanostructures for synthetic biology.
Figure 2: DNA/RNA nanotechnology-enabled toolbox for synthetic circuits.
Figure 3: Typical AND gate circuits.
Figure 4: I/O interface scheme for synthetic circuits.
Figure 5: Nucleic acid nanostructures as information storage media.
Figure 6: The scheme of an integrated live-cell circuit enabled by DNA/RNA nanotechnology.

References

  1. 1

    Jones, M. R., Seeman, N. C. & Mirkin, C. A. Programmable materials and the nature of the DNA bond. Science 347, 1260901 (2015).

  2. 2

    Gerling, T., Wagenbauer, K. F., Neuner, A. M. & Dietz, H. Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components. Science 347, 1446–1452 (2015).

  3. 3

    Benner, S. A. & Sismour, A. M. Synthetic biology. Nat. Rev. Genet. 6, 533–543 (2005).

  4. 4

    Church, G. M., Elowitz, M. B., Smolke, C. D., Voigt, C. A. & Weiss, R. Realizing the potential of synthetic biology. Nat. Rev. Mol. Cell Biol. 15, 289–294 (2014).

  5. 5

    Wilner, O. I. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nanotechnol. 4, 249–254 (2009).

  6. 6

    Myhrvold, C. & Silver, P. A. Using synthetic RNAs as scaffolds and regulators. Nat. Struct. Mol. Biol. 22, 8–10 (2015).

  7. 7

    Perrault, S. D. & Shih, W. M. Virus-inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. ACS Nano 8, 5132–5140 (2014).

  8. 8

    Ye, D., Zuo, X. & Fan, C. DNA Nanostructure-Based Engineering of the Biosensing Interface for Biomolecular Detection. Prog. Chem. 29, 36–46 (2017).

  9. 9

    Fu, J. et al. Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. Nat. Nanotechnol. 9, 531–536 (2014).

  10. 10

    Fu, Y. M. et al. Single-step rapid assembly of DNA origami nanostructures for addressable nanoscale bioreactors. J. Am. Chem. Soc. 135, 696–702 (2013).

  11. 11

    Fu, J. L., Liu, M. H., Liu, Y., Woodbury, N. W. & Yan, H. Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. J. Am. Chem. Soc. 134, 5516–5519 (2012).

  12. 12

    Pal, S. et al. DNA directed self-assembly of anisotropic plasmonic nanostructures. J. Am. Chem. Soc. 133, 17606–17609 (2011).

  13. 13

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

  14. 14

    Zhao, Z. et al. Nano-caged enzymes with enhanced catalytic activity and increased stability against protease digestion. Nat. Commun. 7, 10619 (2016).

  15. 15

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

  16. 16

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

  17. 17

    Benenson, Y. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 13, 455–468 (2012).

  18. 18

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

  19. 19

    Douglas, S. M., Bachelet, I. & Church, G. M. A logic-gated nanorobot for targeted transport of molecular payloads. Science 335, 831–834 (2012).

  20. 20

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

  21. 21

    Mao, C. D., LaBean, T. H., Reif, J. H. & Seeman, N. C. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules. Nature 407, 493–496 (2000).

  22. 22

    Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303–17314 (2009).

  23. 23

    Ge, Z. et al. Hybridization chain reaction amplification of MicroRNA detection with a tetrahedral DNA nanostructure-based electrochemical biosensor. Anal. Chem. 86, 2124–2130 (2014).

  24. 24

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

  25. 25

    Zhou, M. G., Liang, X. G., Mochizuki, T. & Asanuma, H. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion. Angew. Chem. Int. Ed. 49, 2167–2170 (2010).

  26. 26

    Lohmann, F., Weigandt, J., Valero, J. & Famulok, M. Logic gating by macrocycle displacement using a double-stranded DNA [3]rotaxane shuttle. Angew. Chem. Int. Ed. 53, 10372–10376 (2014).

  27. 27

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

  28. 28

    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).

  29. 29

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

  30. 30

    Willner, I., Shlyahovsky, B., Zayats, M. & Willner, B. DNAzymes for sensing, nanobiotechnology and logic gate applications. Chem. Soc. Rev. 37, 1153–1165 (2008).

  31. 31

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

  32. 32

    Soloveichik, D., Seelig, G. & Winfree, E. DNA as a universal substrate for chemical kinetics. Proc. Natl Acad. Sci. USA 107, 5393–5398 (2010).

  33. 33

    Groves, B. et al. Computing in mammalian cells with nucleic acid strand exchange. Nat. Nanotechnol. 11, 287–294 (2015).

  34. 34

    Genot, A. J., Bath, J. & Turberfield, A. J. Reversible logic circuits made of DNA. J. Am. Chem. Soc. 133, 20080–20083 (2011).

  35. 35

    Li, T., Lohmann, F. & Famulok, M. Interlocked DNA nanostructures controlled by a reversible logic circuit. Nat. Commun. 5, 4940 (2014).

  36. 36

    Walsh, A. S., Yin, H., Erben, C. M., Wood, M. J. & Turberfield, A. J. DNA cage delivery to mammalian cells. ACS Nano 5, 5427–5432 (2011).

  37. 37

    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).

  38. 38

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

  39. 39

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

  40. 40

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

  41. 41

    Li, J., Fan, C., Pei, H., Shi, J. & Huang, Q. Smart drug delivery nanocarriers with self-assembled DNA nanostructures. Adv. Mater. 25, 4386–4396 (2013).

  42. 42

    Ohta, S., Glancy, D. & Chan, W. C. DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction. Science 351, 841–845 (2016).

  43. 43

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

  44. 44

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

  45. 45

    Myhrvold, C., Dai, M., Silver, P. A. & Yin, P. Isothermal self-assembly of complex DNA structures under diverse and biocompatible conditions. Nano Lett. 13, 4242–4248 (2013).

  46. 46

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

  47. 47

    Hao, C. H. et al. Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat. Commun. 5, 3890 (2014).

  48. 48

    Grabow, W. W. & Jaeger, L. RNA self-assembly and RNA nanotechnology. Acc. Chem. Res. 47, 1871–1880 (2014).

  49. 49

    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).

  50. 50

    Elbaz, J., Yin, P. & Voigt, C. A. Genetic encoding of DNA nanostructures and their self-assembly in living bacteria. Nat. Commun. 7, 11179 (2016).

  51. 51

    Praetorius, F. & Dietz, H. Self-assembly of genetically encoded DNA–protein hybrid nanoscale shapes. Science 355, 1283 (2017).

  52. 52

    Gaj, T., Gersbach, C. A. & Barbas, C. F. 3rd ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31, 397–405 (2013).

  53. 53

    Cong, L. et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science 339, 819–823 (2013).

  54. 54

    Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

  55. 55

    Jinek, M. et al. RNA-programmed genome editing in human cells. Elife 2, e00471 (2013).

  56. 56

    Kiani, S. et al. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat. Methods 11, 723–726 (2014).

  57. 57

    Tsai, S. Q. et al. Dimeric CRISPR RNA-guided Fokl nucleases for highly specific genome editing. Nat. Biotechnol. 32, 569–576 (2014).

  58. 58

    Gilbert, L. A. et al. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154, 442–451 (2013).

  59. 59

    Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).

  60. 60

    Wright, A. V., Nunez, J. K. & Doudna, J. A. Biology and applications of CRISPR systems: harnessing nature's toolbox for genome engineering. Cell 164, 29–44 (2016).

  61. 61

    Paige, J. S., Wu, K. Y. & Jaffrey, S. R. RNA mimics of green fluorescent protein. Science 333, 642–646 (2011).

  62. 62

    Filonov, G. S., Moon, J. D., Svensen, N. & Jaffrey, S. R. Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. J. Am. Chem. Soc. 136, 16299–16308 (2014).

  63. 63

    Paige, J. S., Nguyen-Duc, T., Song, W. & Jaffrey, S. R. Fluorescence imaging of cellular metabolites with RNA. Science 335, 1194 (2012).

  64. 64

    Tye, K. M. & Deisseroth, K. Optogenetic investigation of neural circuits underlying brain disease in animal models. Nat. Rev. Neurosci. 13, 251–266 (2012).

  65. 65

    Antaris, A. L. et al. A small-molecule dye for NIR-II imaging. Nat. Mater. 15, 235–242 (2016).

  66. 66

    Rinaudo, K. et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol. 25, 795–801 (2007).

  67. 67

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

  68. 68

    Lucks, J. B., Qi, L., Mutalik, V. K., Wang, D. & Arkin, A. P. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc. Natl. Acad. Sci. USA 108, 8617–8622 (2011).

  69. 69

    Chappell, J., Takahashi, M. K. & Lucks, J. B. Creating small transcription activating RNAs. Nat. Chem. Biol. 11, 214–220 (2015).

  70. 70

    Mutalik, V. K., Qi, L., Guimaraes, J. C., Lucks, J. B. & Arkin, A. P. Rationally designed families of orthogonal RNA regulators of translation. Nat. Chem. Biol. 8, 447–454 (2012).

  71. 71

    Takahashi, M. K. & Lucks, J. B. A modular strategy for engineering orthogonal chimeric RNA transcription regulators. Nucleic Acids Res. 41, 7577–7588 (2013).

  72. 72

    Bayer, T. S. & Smolke, C. D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 23, 337–343 (2005).

  73. 73

    Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A. & Breaker, R. R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428, 281–286 (2004).

  74. 74

    Isaacs, F. J., Dwyer, D. J. & Collins, J. J. RNA synthetic biology. Nat. Biotechnol. 24, 545–554 (2006).

  75. 75

    Callura, J. M., Cantor, C. R. & Collins, J. J. Genetic switchboard for synthetic biology applications. Proc. Natl. Acad. Sci. USA 109, 5850–5855 (2012).

  76. 76

    Heath, J. R., Kuekes, P. J., Snider, G. S. & Williams, R. S. A defect-tolerant computer architecture: Opportunities for nanotechnology. Science 280, 1716–1721 (1998).

  77. 77

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

  78. 78

    Fujibayashi, K., Zhang, D. Y., Winfree, E. & Murata, S. Error suppression mechanisms for DNA tile self-assembly and their simulation. Nat. Comput. 8, 589–612 (2008).

  79. 79

    Schulman, R., Wright, C. & Winfree, E. Increasing redundancy exponentially reduces error rates during algorithmic self-assembly. ACS Nano 9, 5760–5771 (2015).

  80. 80

    Mayer, C., McInroy, G. R., Murat, P., Van Delft, P. & Balasubramanian, S. An epigenetics-inspired DNA-based data storage system. Angew. Chem. Int. Ed. 55, 11144–11148 (2016).

  81. 81

    Brouns, S. J. J. et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321, 960–964 (2008).

  82. 82

    Zhu, G. Z. et al. Noncanonical self-assembly of multifunctional DNA nanoflowers for biomedical applications. J. Am. Chem. Soc. 135, 16438–16445 (2013).

  83. 83

    Hu, R. et al. DNA nanoflowers for multiplexed cellular imaging and traceable targeted drug delivery. Angew. Chem. Int. Ed. 53, 5821–5826 (2014).

  84. 84

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

  85. 85

    Bhatia, D., Surana, S., Chakraborty, S., Koushika, S. P. & Krishnan, Y. A synthetic icosahedral DNA-based host-cargo complex for functional in vivo imaging. Nat. Commun. 2, 339 (2011).

  86. 86

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

  87. 87

    Chen, B. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479–1491 (2013).

  88. 88

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

  89. 89

    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).

  90. 90

    Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat. Methods 11, 313-U292 (2014).

  91. 91

    Liu, Y. et al. Synthesizing AND gate genetic circuits based on CRISPR-Cas9 for identification of bladder cancer cells. Nat. Commun. 5, 5393 (2014).

  92. 92

    Bindewald, E. et al. Multistrand structure prediction of nucleic acid assemblies and design of RNA switches. Nano Lett. 16, 1726–1735 (2016).

  93. 93

    Daniel, R., Rubens, J. R., Sarpeshkar, R. & Lu, T. K. Synthetic analog computation in living cells. Nature 497, 619–623 (2013).

  94. 94

    Damle, S. S. & Davidson, E. H. Synthetic in vivo validation of gene network circuitry. Proc. Natl. Acad. Sci. USA 109, 1548–1553 (2012).

  95. 95

    Auslander, S., Auslander, D., Muller, M., Wieland, M. & Fussenegger, M. Programmable single-cell mammalian biocomputers. Nature 487, 123–127 (2012).

  96. 96

    Nielsen, A. A. et al. Genetic circuit design automation. Science 352, aac7341 (2016).

  97. 97

    Lipton, R. J. DNA solution of hard computational problems. Science 268, 542–545 (1995).

  98. 98

    Ouyang, Q., Kaplan, P. D., Liu, S. & Libchaber, A. DNA solution of the maximal clique problem. Science 278, 446–449 (1997).

  99. 99

    Liu, Q. et al. DNA computing on surfaces. Nature 403, 175–179 (2000).

  100. 100

    Sakamoto, K. et al. Molecular computation by DNA hairpin formation. Science 288, 1223–1226 (2000).

  101. 101

    Chandran, H., Gopalkrishnan, N., Phillips, A. & Reif, J. In 17th Int. Conf. DNA Comput. Molecular Program (eds Cardelli, L. & Shih, W.) 64–83 (Springer, 2011).

  102. 102

    Weizmann, Y., Elnathan, R., Lioubashevski, O. & Willner, I. Endonuclease-based logic gates and sensors using magnetic force-amplified readout of DNA scission on cantilevers. J. Am. Chem. Soc. 127, 12666–12672 (2005).

  103. 103

    Bonnet, J., Yin, P., Ortiz, M. E., Subsoontorn, P. & Endy, D. Amplifying genetic logic gates. Science 340, 599–603 (2013).

  104. 104

    Siuti, P., Yazbek, J. & Lu, T. K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).

  105. 105

    Qian, L. & Winfree, E. A simple DNA gate motif for synthesizing large-scale circuits. J. R. Soc. Interface 8, 1281–1297 (2011).

  106. 106

    Genot, A. J. et al. High-resolution mapping of bifurcations in nonlinear biochemical circuits. Nat. Chem. 8, 760–767 (2016).

  107. 107

    Song, T. Q., Garg, S., Mokhtar, R., Bui, H. & Reif, J. Analog computation by DNA strand displacement circuits. ACS Synth. Biol. 5, 898–912 (2016).

  108. 108

    Vinkenborg, J. L., Karnowski, N. & Famulok, M. Aptamers for allosteric regulation. Nat. Chem. Biol. 7, 519–527 (2011).

  109. 109

    Pardee, K. et al. Paper-based synthetic gene networks. Cell 159, 940–954 (2014).

  110. 110

    Zhang, Z. et al. A DNA-origami chip platform for label-free SNP genotyping using toehold-mediated strand displacement. Small 6, 1854–1858 (2010).

  111. 111

    Subramanian, H. K. K., Chakraborty, B., Sha, R. & Seeman, N. C. The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami. Nano Lett. 11, 910–913 (2011).

  112. 112

    Lin, C. et al. Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat. Chem. 4, 832–839 (2012).

  113. 113

    Goldman, N. et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494, 77–80 (2013).

  114. 114

    Church, G. M., Gao, Y. & Kosuri, S. Next-generation digital information storage in DNA. Science 337, 1628 (2012).

  115. 115

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

  116. 116

    Boettiger, A. N. et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422 (2016).

  117. 117

    Edwardson, T. G. W., Lau, K. L., Bousmail, D., Serpell, C. J. & Sleiman, H. F. Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles. Nat. Chem. 8, 162–170 (2016).

  118. 118

    Farzadfard, F. & Lu, T. K. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346, 1256272 (2014).

  119. 119

    Kim, K. R. et al. Sentinel lymph node imaging by a fluorescently labeled DNA tetrahedron. Biomaterials 34, 5226–5235 (2013).

  120. 120

    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).

  121. 121

    Kim, J., Lee, J., Hamada, S., Murata, S. & Ha Park, S. Self-replication of DNA rings. Nat. Nanotechnol. 10, 528–533 (2015).

  122. 122

    Tam, D. Y. & Lo, P. K. Multifunctional DNA nanomaterials for biomedical applications. J. Nanomater. 2015, 765492 (2015).

  123. 123

    Chen, C. H. et al. A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila. Science 316, 597–600 (2007).

  124. 124

    Kemmer, C. et al. Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat. Biotechnol. 28, 355–360 (2010).

  125. 125

    Ren, K. et al. A DNA dual lock-and-key strategy for cell-subtype-specific siRNA delivery. Nat. Commun. 7, 13580 (2016).

  126. 126

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

  127. 127

    Hamblin, G. D., Carneiro, K. M. M., Fakhoury, J. F., Bujold, K. E. & Sleiman, H. F. Rolling circle amplification-templated DNA nanotubes show increased stability and cell penetration ability. J. Am. Chem. Soc. 134, 2888–2891 (2012).

  128. 128

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

  129. 129

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

  130. 130

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

  131. 131

    Hu, L., Lu, C. H. & Willner, I. Switchable catalytic DNA catenanes. Nano Lett. 15, 2099–2103 (2015).

  132. 132

    Cassinelli, V. et al. One-step formation of “chain-armor”-stabilized DNA nanostructures. Angew. Chem. Int. Ed. 54, 7795–7798 (2015).

  133. 133

    Brglez, J., Nikolov, P., Angelin, A. & Niemeyer, C. M. Designed intercalators for modification of DNA origami surface properties. Chem. Eur. J. 21, 9440–9446 (2015).

  134. 134

    Cutler, J. I., Auyeung, E. & Mirkin, C. A. Spherical nucleic acids. J. Am. Chem. Soc. 134, 1376–1391 (2012).

  135. 135

    Yan, J. et al. Growth and origami folding of DNA on nanoparticles for high-efficiency molecular transport in cellular imaging and drug delivery. Angew. Chem. Int. Ed. 54, 2431–2435 (2015).

  136. 136

    Sun, W. J. et al. Cocoon-like self-degradable DNA nanoclew for anticancer drug delivery. J. Am. Chem. Soc. 136, 14722–14725 (2014).

  137. 137

    Lu, C. H. & Willner, I. Stimuli-responsive DNA-functionalized nano-/microcontainers for switchable and controlled release. Angew. Chem. Int. Ed. 54, 12212–12235 (2015).

  138. 138

    Banerjee, A. et al. Controlled release of encapsulated cargo from a DNA icosahedron using a chemical trigger. Angew. Chem. Int. Ed. 52, 6854–6857 (2013).

  139. 139

    LeProust, E. M. et al. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res. 38, 2522–2540 (2010).

  140. 140

    Kosuri, S. & Church, G. M. Large-scale de novo DNA synthesis: technologies and applications. Nat. Methods 11, 499–507 (2014).

  141. 141

    Schmidt, T. L. et al. Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries. Nat. Commun. 6, 8634 (2015).

  142. 142

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

  143. 143

    Zhao, Z., Liu, Y. & Yan, H. Organizing DNA origami tiles into larger structures using preformed scaffold frames. Nano Lett. 11, 2997–3002 (2011).

  144. 144

    Nelissen, F. H. et al. Fast production of homogeneous recombinant RNA--towards large-scale production of RNA. Nucleic Acids Res. 40, e102 (2012).

  145. 145

    Ponchon, L. & Dardel, F. Recombinant RNA technology: the tRNA scaffold. Nat. Methods 4, 571–576 (2007).

  146. 146

    Suzuki, H., Ando, T., Umekage, S., Tanaka, T. & Kikuchi, Y. Extracellular production of an RNA aptamer by ribonuclease-free marine bacteria harboring engineered plasmids: a proposal for industrial RNA drug production. Appl. Environ. Microbiol. 76, 786–793 (2010).

  147. 147

    Chan, M. S. & Lo, P. K. Nanoneedle-assisted delivery of site-selective peptide-functionalized DNA nanocages for targeting mitochondria and nuclei. Small 10, 1255–1260 (2014).

  148. 148

    Patel, P. C., Giljohann, D. A., Seferos, D. S. & Mirkin, C. A. Peptide antisense nanoparticles. Proc. Natl. Acad. Sci. USA 105, 17222–17226 (2008).

  149. 149

    Crawford, R. et al. Non-covalent single transcription factor encapsulation inside a DNA cage. Angew. Chem. Int. Ed. 52, 2284–2288 (2013).

  150. 150

    Nakata, E. et al. Zinc-finger proteins for site-specific protein positioning on DNA-origami structures. Angew. Chem. Int. Ed. 51, 2421–2424 (2012).

  151. 151

    Tamsir, A., Tabor, J. J. & Voigt, C. A. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 469, 212–215 (2011).

  152. 152

    Gantz, V. M. & Bier, E. The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science 348, 442–444 (2015).

  153. 153

    Niu, Y. et al. Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell 156, 836–843 (2014).

  154. 154

    Sun, W. J. et al. Self-assembled DNA nanoclews for the efficient delivery of CRISPR-Cas9 for genome editing. Angew. Chem. Int. Ed. 54, 12029–12033 (2015).

  155. 155

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

  156. 156

    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).

  157. 157

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

  158. 158

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

  159. 159

    Ke, Y., Ong, L. L., Shih, W. M. & Yin, P. Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177–1183 (2012).

  160. 160

    Zhang, F. et al. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nat. Nanotechnol. 10, 779–784 (2015).

  161. 161

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

  162. 162

    Benson, E. et al. DNA rendering of polyhedral meshes at the nanoscale. Nature 523, 441–444 (2015).

  163. 163

    Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

  164. 164

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

  165. 165

    Stojanovic, M. N. et al. Deoxyribozyme-based ligase logic gates and their initial circuits. J. Am. Chem. Soc. 127, 6914–6915 (2005).

  166. 166

    Stojanovic, M. N., Mitchell, T. E. & Stefanovic, D. Deoxyribozyme-based logic gates. J. Am. Chem. Soc. 124, 3555–3561 (2002).

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Acknowledgements

Financial support from the Ministry of Science and Technology of China (2013CB932803, 2013CB933802, 2016YFA0201200, 2016YFA0400900), the National Science Foundation of China (21390414, 21227804, 21329501, U1532119) and the Chinese Academy of Sciences (QYZDJ-SSW-SLH031, KJCX2-EW-N03) are acknowledged. Hao Yan also acknowledges financial support from the US National Science Foundation, the National Institutes of Health, the Army Research Office, the Office of Naval Research and funds from Arizona State University. A.A.G. acknowledges financial support from the US National Science Foundation, the Gates Foundation, the Arizona Biomedical Research Commission, an Alfred P. Sloan Research Fellowship (FG-2017-9108) and Arizona State University.

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Correspondence to Alexander A. Green or Hao Yan or Chunhai Fan.

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Li, J., Green, A., Yan, H. et al. Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation. Nature Chem 9, 1056–1067 (2017) doi:10.1038/nchem.2852

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