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  • Review Article
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Building membrane nanopores

Abstract

Membrane nanopores—hollow nanoscale barrels that puncture biological or synthetic membranes—have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.

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Figure 1: Protein pores and applications.
Figure 2: Peptide pores.
Figure 3: DNA nanopores composed of aligned duplexes.
Figure 4: Synthetic organic nanopores.

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References

  1. Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016).

    CAS  Google Scholar 

  2. Cherf, G. M. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat. Biotechnol. 30, 344–348 (2012).

    Article  CAS  Google Scholar 

  3. Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349–353 (2012).

    Article  CAS  Google Scholar 

  4. Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016).

    CAS  Google Scholar 

  5. Howorka, S. & Siwy, Z. Nanopore analytics: sensing of single molecules. Chem. Soc. Rev. 38, 2360–2384 (2009).

    CAS  Google Scholar 

  6. Wang, G., Wang, L., Han, Y., Zhou, S. & Guan, X. Nanopore stochastic detection: diversity, sensitivity, and beyond. Acc. Chem. Res. 46, 2867–2877 (2013).

    CAS  Google Scholar 

  7. Stoloff, D. H. & Wanunu, M. Recent trends in nanopores for biotechnology. Curr. Opin. Biotechnol. 24, 699–704 (2013).

    CAS  Google Scholar 

  8. Reiner, J. E. et al. Disease detection and management via single nanopore-based sensors. Chem. Rev. 112, 6431–6451 (2012).

    CAS  Google Scholar 

  9. Miles, B. N. et al. Single molecule sensing with solid-state nanopores: novel materials, methods, and applications. Chem. Soc. Rev. 42, 15–28 (2013).

    CAS  Google Scholar 

  10. Movileanu, L. Interrogating single proteins through nanopores: challenges and opportunities. Trends Biotechnol. 27, 333–341 (2009).

    CAS  Google Scholar 

  11. Litvinchuk, S. et al. Synthetic pores with reactive signal amplifiers as artificial tongues. Nat. Mater. 6, 576–580 (2007).

    CAS  Google Scholar 

  12. Banghart, M., Borges, K., Isacoff, E., Trauner, D. & Kramer, R. H. Light-activated ion channels for remote control of neuronal firing. Nat. Neurosci. 7, 1381–1386 (2004).

    CAS  Google Scholar 

  13. Volgraf, M. et al. Allosteric control of an ionotropic glutamate receptor with an optical switch. Nat. Chem. Biol. 2, 47–52 (2006).

    CAS  Google Scholar 

  14. Burns, J. R., Seifert, A., Fertig, N. & Howorka, S. A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane. Nat. Nanotech. 11, 152–156 (2016).

    CAS  Google Scholar 

  15. Zhang, Y. et al. Computational design and experimental characterization of peptides intended for pH-dependent membrane insertion and pore formation. ACS Chem. Biol. 10, 1082–1093 (2015).

    CAS  Google Scholar 

  16. Fernandez-Lopez, S. et al. Antibacterial agents based on the cyclic D,L-α-peptide architecture. Nature 412, 452–455 (2001).

    CAS  Google Scholar 

  17. Dekker, C. Solid-state nanopores. Nat. Nanotech. 2, 209–215 (2007).

    CAS  Google Scholar 

  18. Heerema, S. J. & Dekker, C. Graphene nanodevices for DNA sequencing. Nat. Nanotech. 11, 127–136 (2016).

    CAS  Google Scholar 

  19. Lindsay, S. The promises and challenges of solid-state sequencing. Nat. Nanotech. 11, 109–111 (2016).

    CAS  Google Scholar 

  20. Feng, J. et al. Identification of single nucleotides in MoS2 nanopores. Nat. Nanotech. 10, 1070–1076 (2015).

    CAS  Google Scholar 

  21. Bell, N. A. & Keyser, U. F. Digitally encoded DNA nanostructures for multiplexed, single-molecule protein sensing with nanopores. Nat. Nanotech. 11, 645–651 (2016).

    CAS  Google Scholar 

  22. Mayer, M. & Yang, J. Engineered ion channels as emerging tools for chemical biology. Acc. Chem. Res. 46, 2998–3008 (2013).

    CAS  Google Scholar 

  23. Langecker, M., Arnaut, V., List, J. & Simmel, F. C. DNA nanostructures interacting with lipid bilayer membranes. Acc. Chem. Res. 47, 1807–1815 (2014).

    CAS  Google Scholar 

  24. Fyles, T. M. Synthetic ion channels in bilayer membranes. Chem. Soc. Rev. 36, 335–347 (2007).

    CAS  Google Scholar 

  25. Gokel, G. W. & Negin, S. Synthetic ion channels: from pores to biological applications. Acc. Chem. Res. 46, 2824–2833 (2013).

    CAS  Google Scholar 

  26. Sakai, N. & Matile, S. Synthetic ion channels. Langmuir 29, 9031–9040 (2013).

    CAS  Google Scholar 

  27. Bell, N. A. & Keyser, U. F. Nanopores formed by DNA origami: a review. FEBS Lett. 588, 3564–3570 (2014).

    CAS  Google Scholar 

  28. Shi, W., Friedman, A. K. & Baker, L. A. Nanopore sensing. Anal. Chem. 89, 157–188 (2017).

    CAS  Google Scholar 

  29. Majd, S. et al. Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Curr. Opin. Biotechnol. 21, 439–476 (2010).

    CAS  Google Scholar 

  30. Ayub, M. & Bayley, H. Engineered transmembrane pores. Curr. Opin. Chem. Biol. 34, 117–126 (2016).

    CAS  Google Scholar 

  31. Meier, W., Nardin, C. & Winterhalter, M. Reconstitution of channel proteins in (polymerized) ABA triblock copolymer membranes. Angew. Chem. Int. Ed. 39, 4599–4602 (2000).

    CAS  Google Scholar 

  32. Nardin, C., Winterhalter, M. & Meier, W. Giant free-standing ABA triblock copolymer membranes. Langmuir 16, 7708–7712 (2010).

    Google Scholar 

  33. Mosgaard, L. D. & Heimburg, T. Lipid ion channels and the role of proteins. Acc. Chem. Res. 46, 2966–2976 (2013).

    CAS  Google Scholar 

  34. Reiss, P. & Koert, U. Ion-channels: goals for function-oriented synthesis. Acc. Chem. Res. 46, 2773–2780 (2013).

    CAS  Google Scholar 

  35. De Riccardis, F., Izzo, I., Montesarchio, D. & Tecilla, P. Ion transport through lipid bilayers by synthetic ionophores: modulation of activity and selectivity. Acc. Chem. Res. 46, 2781–2790 (2013).

    CAS  Google Scholar 

  36. Li, H. et al. Efficient, non-toxic anion transport by synthetic carriers in cells and epithelia. Nat. Chem. 8, 24–32 (2016).

    CAS  Google Scholar 

  37. Schmidt, J. Membrane platforms for biological nanopore sensing and sequencing. Curr. Opin. Biotechnol. 39, 17–27 (2016).

    CAS  Google Scholar 

  38. Urban, M. et al. Highly parallel transport recordings on a membrane-on-nanopore chip at single molecule resolution. Nano Lett. 14, 1674–1680 (2014).

    CAS  Google Scholar 

  39. Funakoshi, K., Suzuki, H. & Takeuchi, S. Lipid bilayer formation by contacting monolayers in a microfluidic device for membrane protein analysis. Anal. Chem. 78, 8169–8174 (2006).

    CAS  Google Scholar 

  40. Holden, M. A., Needham, D. & Bayley, H. Functional bionetworks from nanoliter water droplets. J. Am. Chem. Soc. 129, 8650–8655 (2007).

    CAS  Google Scholar 

  41. Jeon, T. J., Malmstadt, N. & Schmidt, J. J. Hydrogel-encapsulated lipid membranes. J. Am. Chem. Soc. 128, 42–43 (2006).

    CAS  Google Scholar 

  42. Shim, J. W. & Gu, L. Q. Stochastic sensing on a modular chip containing a single-ion channel. Anal. Chem. 79, 2207–2213 (2007).

    CAS  Google Scholar 

  43. Daly, S. M., Heffernan, L. A., Barger, W. R. & Shenoy, D. K. Photopolymerization of mixed monolayers and black lipid membranes containing gramicidin A and diacetylenic phospholipids. Langmuir 22, 1215–1222 (2006).

    CAS  Google Scholar 

  44. Heitz, B. A., Jones, I. W., Hall, H. K. Jr, Aspinwall, C. A. & Saavedra, S. S. Fractional polymerization of a suspended planar bilayer creates a fluid, highly stable membrane for ion channel recordings. J. Am. Chem. Soc. 132, 7086–7093 (2010).

    CAS  Google Scholar 

  45. Wei, R. S., Gatterdam, V., Wieneke, R., Tampe, R. & Rant, U. Stochastic sensing of proteins with receptor-modified solid-state nanopores. Nat. Nanotech. 7, 257–263 (2012).

    CAS  Google Scholar 

  46. Wang, Y., Zheng, D., Tan, Q., Wang, M. X. & Gu, L. Q. Nanopore-based detection of circulating microRNAs in lung cancer patients. Nat. Nanotech. 6, 668–674 (2011).

    CAS  Google Scholar 

  47. Traversi, F. et al. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nat. Nanotech. 8, 939–945 (2013).

    CAS  Google Scholar 

  48. Wanunu, M. et al. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat. Nanotech. 5, 807–814 (2010).

    CAS  Google Scholar 

  49. Yusko, E. C. et al. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat. Nanotech. 6, 253–260 (2011).

    CAS  Google Scholar 

  50. Moreau, C. J., Dupuis, J. P., Revilloud, J., Arumugam, K. & Vivaudou, M. Coupling ion channels to receptors for biomolecule sensing. Nat. Nanotech. 3, 620–625 (2008).

    CAS  Google Scholar 

  51. Chen, M., Khalid, S., Sansom, M. S. & Bayley, H. Outer membrane protein G: engineering a quiet pore for biosensing. Proc. Natl Acad. Sci. USA 105, 6272–6277 (2008).

    CAS  Google Scholar 

  52. Soskine, M. et al. An engineered ClyA nanopore detects folded target proteins by selective external association and pore entry. Nano Lett. 12, 4895–4900 (2012).

    CAS  Google Scholar 

  53. Spicer, C. D. & Davis, B. G. Selective chemical protein modification. Nat. Commun. 5, 4740 (2014).

    CAS  Google Scholar 

  54. Valiyaveetil, F. I., Leonetti, M., Muir, T. W. & MacKinnon, R. Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation. Science 314, 1004–1007 (2006).

    CAS  Google Scholar 

  55. Focke, P. J. & Valiyaveetil, F. I. Studies of ion channels using expressed protein ligation. Curr. Opin. Chem. Biol. 14, 797–802 (2010).

    CAS  Google Scholar 

  56. Lee, J. & Bayley, H. Semisynthetic protein nanoreactor for single-molecule chemistry. Proc. Natl Acad. Sci. USA 112, 13768–13773 (2015).

    CAS  Google Scholar 

  57. Clayton, D. et al. Total chemical synthesis and electrophysiological characterization of mechanosensitive channels from Escherichia coli and Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA 101, 4764–4769 (2004).

    CAS  Google Scholar 

  58. Song, L. et al. Structure of staphylococcal α-hemolysin, a heptameric transmembrane pore. Science 274, 1859–1866 (1996).

    CAS  Google Scholar 

  59. Faller, M., Niederweis, M. & Schulz, G. E. The structure of a mycobacterial outer-membrane channel. Science 303, 1189–1192 (2004).

    CAS  Google Scholar 

  60. Goyal, P. et al. Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG. Nature 516, 250–253 (2014).

    CAS  Google Scholar 

  61. Mueller, M., Grauschopf, U., Maier, T., Glockshuber, R. & Ban, N. The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. Nature 459, 726–730 (2009).

    CAS  Google Scholar 

  62. Liang, B. & Tamm, L. K. Structure of outer membrane protein G by solution NMR spectroscopy. Proc. Natl Acad. Sci. USA 104, 16140–16145 (2007).

    CAS  Google Scholar 

  63. Cowan, S. W. et al. Crystal structures explain functional properties of two E. coli porins. Nature 358, 727–733 (1992).

    CAS  Google Scholar 

  64. Dong, C. et al. Wza the translocon for E. coli capsular polysaccharides defines a new class of membrane protein. Nature 444, 226–229 (2006).

    CAS  Google Scholar 

  65. Cao, C. et al. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore. Nat. Nanotech. 11, 713–718 (2016).

    CAS  Google Scholar 

  66. Doyle, D. A. et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280, 69–77 (1998).

    CAS  Google Scholar 

  67. Chang, G., Spencer, R. H., Lee, A. T., Barclay, M. T. & Rees, D. C. Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. Science 282, 2220–2226 (1998).

    CAS  Google Scholar 

  68. Haque, F., Geng, J., Montemagno, C. & Guo, P. Incorporation of a viral DNA-packaging motor channel in lipid bilayers for real-time, single-molecule sensing of chemicals and double-stranded DNA. Nat. Protoc. 8, 373–392 (2013).

    CAS  Google Scholar 

  69. Dunstone, M. A. & Tweten, R. K. Packing a punch: the mechanism of pore formation by cholesterol dependent cytolysins and membrane attack complex/perforin-like proteins. Curr. Opin. Struct. Biol. 22, 342–349 (2012).

    CAS  Google Scholar 

  70. Laszlo, A. H. et al. Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc. Natl Acad. Sci. USA 110, 18904–18909 (2013).

    CAS  Google Scholar 

  71. Bayley, H. & Cremer, P. S. Stochastic sensors inspired by biology. Nature 413, 226–230 (2001).

    CAS  Google Scholar 

  72. Braha, O. et al. Designed protein pores as components for biosensors. Chem. Biol. 4, 497–505 (1997).

    CAS  Google Scholar 

  73. Gu, L. Q., Braha, O., Conlan, S., Cheley, S. & Bayley, H. Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter. Nature 398, 686–690 (1999).

    CAS  Google Scholar 

  74. Gu, L. Q., Cheley, S. & Bayley, H. Capture of a single molecule in a nanocavity. Science 291, 636–640 (2001).

    CAS  Google Scholar 

  75. Kang, X. F., Cheley, S., Guan, X. & Bayley, H. Stochastic detection of enantiomers. J. Am. Chem. Soc. 128, 10684–10685 (2006).

    CAS  Google Scholar 

  76. Howorka, S., Cheley, S. & Bayley, H. Sequence-specific detection of individual DNA-strands using engineered nanopores. Nat. Biotechnol. 19, 636–639 (2001).

    CAS  Google Scholar 

  77. Rotem, D., Jayasinghe, L., Salichou, M. & Bayley, H. Protein detection by nanopores equipped with aptamers. J. Am. Chem. Soc. 134, 2781–2787 (2012).

    CAS  Google Scholar 

  78. Howorka, S. et al. A protein pore with a single polymer chain tethered within the lumen. J. Am. Chem. Soc. 122, 2411–2416 (2000).

    CAS  Google Scholar 

  79. Movileanu, L., Howorka, S., Braha, O. & Bayley, H. Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore. Nat. Biotechnol. 18, 1091–1095 (2000).

    CAS  Google Scholar 

  80. Loudwig, S. & Bayley, H. Photoisomerization of an individual azobenzene molecule in water: an on-off switch triggered by light at a fixed wavelength. J. Am. Chem. Soc. 128, 12404–12405 (2006).

    CAS  Google Scholar 

  81. Lu, S., Li, W. W., Rotem, D., Mikhailova, E. & Bayley, H. A primary hydrogen–deuterium isotope effect observed at the single-molecule level. Nat. Chem. 2, 921–928 (2010).

    CAS  Google Scholar 

  82. Shin, S. H., Steffensen, M. B., Claridge, T. D. & Bayley, H. Formation of a chiral center and pyramidal inversion at the single-molecule level. Angew. Chem. Int. Ed. 46, 7412–7416 (2007).

    CAS  Google Scholar 

  83. Pulcu, G. S., Mikhailova, E., Choi, L. S. & Bayley, H. Continuous observation of the stochastic motion of an individual small-molecule walker. Nat. Nanotech. 10, 76–83 (2015).

    CAS  Google Scholar 

  84. Maglia, G., Restrepo, M. R., Mikhailova, E. & Bayley, H. Enhanced translocation of single DNA molecules through alpha-hemolysin nanopores by manipulation of internal charge. Proc. Natl Acad. Sci. USA 105, 19720–19725 (2008).

    CAS  Google Scholar 

  85. Kocer, A., Walko, M., Meijberg, W. & Feringa, B. L. A light-actuated nanovalve derived from a channel protein. Science 309, 755–758 (2005).

    CAS  Google Scholar 

  86. Jung, Y., Bayley, H. & Movileanu, L. Temperature-responsive protein pores. J. Am. Chem. Soc. 128, 15332–15340 (2006).

    CAS  Google Scholar 

  87. Maglia, G. et al. Droplet networks with incorporated protein diodes show collective properties. Nat. Nanotech. 4, 437–440 (2009).

    CAS  Google Scholar 

  88. Miedema, H. et al. A biological porin engineered into a molecular, nanofluidic diode. Nano Lett. 7, 2886–2891 (2007).

    CAS  Google Scholar 

  89. Bondalapati, S., Jbara, M. & Brik, A. Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins. Nat. Chem. 8, 407–418 (2016).

    CAS  Google Scholar 

  90. Stoddart, D. et al. Functional truncated membrane pores. Proc. Natl Acad. Sci. USA 111, 2425–2430 (2014).

    CAS  Google Scholar 

  91. Reimer, J. M., Aloise, M. N., Harrison, P. M. & Schmeing, T. M. Synthetic cycle of the initiation module of a formylating nonribosomal peptide synthetase. Nature 529, 239–242 (2016).

    CAS  Google Scholar 

  92. Montenegro, J., Ghadiri, M. R. & Granja, J. R. Ion channel models based on self-assembling cyclic peptide nanotubes. Acc. Chem. Res. 46, 2955–2965 (2013).

    CAS  Google Scholar 

  93. Ketchem, R. R., Hu, W. & Cross, T. A. High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. Science 261, 1457–1460 (1993).

    CAS  Google Scholar 

  94. Cifu, A. S., Koeppe, R. E. II & Andersen, O. S. On the supramolecular organization of gramicidin channels. The elementary conducting unit is a dimer. Biophys. J. 61, 189–203 (1992).

    CAS  Google Scholar 

  95. Inoue, M. et al. Total synthesis of the large non-ribosomal peptide polytheonamide B. Nat. Chem. 2, 280–285 (2010).

    CAS  Google Scholar 

  96. Leitgeb, B., Szekeres, A., Manczinger, L., Vagvolgyi, C. & Kredics, L. The history of alamethicin: a review of the most extensively studied peptaibol. Chem. Biodivers. 4, 1027–1051 (2007).

    CAS  Google Scholar 

  97. Pieta, P., Mirza, J. & Lipkowski, J. Direct visualization of the alamethicin pore formed in a planar phospholipid matrix. Proc. Natl Acad. Sci. USA 109, 21223–21227 (2012).

    CAS  Google Scholar 

  98. Mayer, M., Kriebel, J. K., Tosteson, M. T. & Whitesides, G. M. Microfabricated teflon membranes for low-noise recordings of ion channels in planar lipid bilayers. Biophys. J. 85, 2684–2695 (2003).

    CAS  Google Scholar 

  99. Fjell, C. D., Hiss, J. A., Hancock, R. E. & Schneider, G. Designing antimicrobial peptides: form follows function. Nat. Rev. Drug. Discov. 11, 37–51 (2012).

    CAS  Google Scholar 

  100. Cornell, B. A. et al. A biosensor that uses ion-channel switches. Nature 387, 580–583 (1997).

    CAS  Google Scholar 

  101. Macrae, M. X. et al. A semi-synthetic ion channel platform for detection of phosphatase and protease activity. ACS Nano 3, 3567–3580 (2009).

    CAS  Google Scholar 

  102. Mayer, M., Semetey, V., Gitlin, I., Yang, J. & Whitesides, G. M. Using ion channel-forming peptides to quantify protein-ligand interactions. J. Am. Chem. Soc. 130, 1453–1465 (2008).

    CAS  Google Scholar 

  103. Sakai, N., Mareda, J. & Matile, S. Artificial β-barrels. Acc. Chem. Res. 41, 1354–1365 (2008).

    CAS  Google Scholar 

  104. Thomson, A. R. et al. Computational design of water-soluble α-helical barrels. Science 346, 485–488 (2014).

    CAS  Google Scholar 

  105. Joh, N. H. et al. De novo design of a transmembrane Zn2+-transporting four-helix bundle. Science 346, 1520–1524 (2014).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  107. Burns, J., Stulz, E. & Howorka, S. Self-assembled DNA nanopores that span lipid bilayers. Nano Lett. 13, 2351–2356 (2013).

    CAS  Google Scholar 

  108. Howorka, S. Changing of the guard. Science 352, 890–891 (2016).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  111. Chen, Y. J., Groves, B., Muscat, R. A. & Seelig, G. DNA nanotechnology from the test tube to the cell. Nat. Nanotech. 10, 748–760 (2015).

    CAS  Google Scholar 

  112. Pinheiro, A. V., Han, D., Shih, W. M. & Yan, H. Challenges and opportunities for structural DNA nanotechnology. Nat. Nanotech. 6, 763–772 (2011).

    CAS  Google Scholar 

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

    Google Scholar 

  114. Douglas, S. M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  120. 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 

  121. 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 

  122. Gopfrich, K. et al. DNA-tile structures induce ionic currents through lipid membranes. Nano Lett. 15, 3134–3138 (2015).

    CAS  Google Scholar 

  123. Gopfrich, K. et al. Large-conductance transmembrane porin made from DNA origami. ACS Nano 10, 8207–8214 (2016).

    CAS  Google Scholar 

  124. Krishnan, S. et al. Molecular transport through large-diameter DNA nanopores. Nat. Commun. 7, 12787 (2016).

    CAS  Google Scholar 

  125. Seifert, A. et al. Bilayer-spanning DNA nanopores with voltage-switching between open and closed state. ACS Nano 9, 1117–1126 (2015).

    CAS  Google Scholar 

  126. Bell, N. A. et al. DNA origami nanopores. Nano Lett. 12, 512–517 (2012).

    CAS  Google Scholar 

  127. Wei, R., Martin, T. G., Rant, U. & Dietz, H. DNA origami gatekeepers for solid-state nanopores. Angew. Chem. Int. Ed. 51, 4864–4867 (2012).

    CAS  Google Scholar 

  128. Czogalla, A. et al. Amphipathic DNA origami nanoparticles to scaffold and deform lipid membrane vesicles. Angew. Chem. Int. Ed. 54, 6501–6505 (2015).

    CAS  Google Scholar 

  129. Kocabey, S. et al. Membrane-assisted growth of DNA origami nanostructure arrays. ACS Nano 9, 3530–3539 (2015).

    CAS  Google Scholar 

  130. Johnson-Buck, A., Jiang, S., Yan, H. & Walter, N. G. DNA-cholesterol barges as programmable membrane-exploring agents. ACS Nano 8, 5641–5649 (2014).

    CAS  Google Scholar 

  131. Yang, Y. et al. Self-assembly of size-controlled liposomes on DNA nanotemplates. Nat. Chem. 8, 476–483 (2016).

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  133. Mura, S., Nicolas, J. & Couvreur, P. Stimuli-responsive nanocarriers for drug delivery. Nat. Mater. 12, 991–1003 (2013).

    CAS  Google Scholar 

  134. Villar, G., Graham, A. D. & Bayley, H. A tissue-like printed material. Science 340, 48–52 (2013).

    CAS  Google Scholar 

  135. Maingi, V., Lelimousin, M., Howorka, S. & Sansom, M. S. Gating-like motions and wall porosity in a DNA nanopore scaffold revealed by molecular simulations. ACS Nano 9, 11209–11217 (2015).

    CAS  Google Scholar 

  136. Yoo, J. & Aksimentiev, A. Molecular dynamics of membrane-spanning DNA channels: conductance mechanism, electro-osmotic transport, and mechanical gating. J. Phys. Chem. Lett. 6, 4680–4687 (2015).

    CAS  Google Scholar 

  137. Maingi, V. et al. Stability and dynamics of membrane-spanning DNA nanopores. Nat. Commun. 8, 14784 (2017).

    CAS  Google Scholar 

  138. Gopfrich, K. et al. Ion channels made from a single membrane-spanning DNA duplex. Nano Lett. 16, 4665–4669 (2016).

    CAS  Google Scholar 

  139. Ackermann, D. & Famulok, M. Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology. Nucleic Acids Res. 41, 4729–4739 (2013).

    CAS  Google Scholar 

  140. Edwardson, T. G., Carneiro, K. M., McLaughlin, C. K., Serpell, C. J. & Sleiman, H. F. Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly. Nat. Chem. 5, 868–875 (2013).

    CAS  Google Scholar 

  141. Chui, J. K. & Fyles, T. M. Ionic conductance of synthetic channels: analysis, lessons, and recommendations. Chem. Soc. Rev. 41, 148–175 (2012).

    CAS  Google Scholar 

  142. Sakaki, Y., Mareda, J. & Matile, S. Ion channels and pores, made from scratch. Mol. Biosys. 3, 658–666 (2007).

    Google Scholar 

  143. Barboiu, M. & Gilles, A. From natural to bioassisted and biomimetic artificial water channel systems. Acc. Chem. Res. 46, 2814–2823 (2013).

    CAS  Google Scholar 

  144. Geng, J. et al. Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes. Nature 514, 612–615 (2014).

    CAS  Google Scholar 

  145. Negin, S., Daschbach, M. M., Kulikov, O. V., Rath, N. & Gokel, G. W. Pore formation in phospholipid bilayers by branched-chain pyrogallol[4]arenes. J. Am. Chem. Soc. 133, 3234–3237 (2011).

    CAS  Google Scholar 

  146. Das, R. N., Kumar, Y. P., Schutte, O. M., Steinem, C. & Dash, J. A DNA-inspired synthetic ion channel based on G–C base pairing. J. Am. Chem. Soc. 137, 34–37 (2015).

    CAS  Google Scholar 

  147. Fyles, T. M. How do amphiphiles form ion-conducting channels in membranes? Lessons from linear oligoesters. Acc. Chem. Res. 46, 2847–2855 (2013).

    CAS  Google Scholar 

  148. Meillon, J. C. & Voyer, N. A synthetic transmembrane channel active in lipid bilayers. Angew. Chem. Int. Ed. 36, 967–969 (1997).

    CAS  Google Scholar 

  149. Gilles, A. & Barboiu, M. Highly selective artificial K+ channels: an example of selectivity-induced transmembrane potential. J. Am. Chem. Soc. 138, 426–432 (2016).

    CAS  Google Scholar 

  150. Kumaki, J. et al. AFM snapshots of synthetic multifunctional pores with polyacetylene blockers: pseudorotaxanes and template effects. Angew. Chem. Int. Ed. 44, 6154–6157 (2005).

    CAS  Google Scholar 

  151. Talukdar, P., Bollot, G., Mareda, J., Sakai, N. & Matile, S. Synthetic ion channels with rigid-rod π-stack architecture that open in response to charge-transfer complex formation. J. Am. Chem. Soc. 127, 6528–6529 (2005).

    CAS  Google Scholar 

  152. Shen, Y. X. et al. Highly permeable artificial water channels that can self-assemble into two-dimensional arrays. Proc. Natl Acad. Sci. USA 112, 9810–9815 (2015).

    CAS  Google Scholar 

  153. Liu, H. et al. Translocation of single-stranded DNA through single-walled carbon nanotubes. Science 327, 64–67 (2010).

    CAS  Google Scholar 

  154. Tunuguntla, R. H., Allen, F. I., Kim, K., Belliveau, A. & Noy, A. Ultrafast proton transport in sub-1-nm diameter carbon nanotube porins. Nat. Nanotech. 11, 639–644 (2016).

    CAS  Google Scholar 

  155. Lang, C. et al. Biomimetic transmembrane channels with high stability and transporting efficiency from helically folded macromolecules. Angew. Chem. Int. Ed. 55, 9723–9727 (2016).

    CAS  Google Scholar 

  156. Bhosale, S. et al. Photoproduction of proton gradients with pi-stacked fluorophore scaffolds in lipid bilayers. Science 313, 84–86 (2006).

    CAS  Google Scholar 

  157. Hall, A. R. et al. Hybrid pore formation by directed insertion of α-haemolysin into solid-state nanopores. Nat. Nanotech. 5, 874–877 (2010).

    CAS  Google Scholar 

  158. Mantri, S., Sapra, K. T., Cheley, S., Sharp, T. H. & Bayley, H. An engineered dimeric protein pore that spans adjacent lipid bilayers. Nat. Commun. 4, 1725 (2013).

    Google Scholar 

  159. Burton, A. J., Thomson, A. R., Dawson, W. M., Brady, R. L. & Woolfson, D. N. Installing hydrolytic activity into a completely de novo protein framework. Nat. Chem. 8, 837–844 (2016).

    CAS  Google Scholar 

  160. Costa, T. R. et al. Secretion systems in Gram-negative bacteria: structural and mechanistic insights. Nat. Rev. Microbiol. 13, 343–359 (2015).

    CAS  Google Scholar 

  161. Franceschini, L., Soskine, M., Biesemans, A. & Maglia, G. A nanopore machine promotes the vectorial transport of DNA across membranes. Nat. Commun. 4, 2415 (2013).

    Google Scholar 

  162. Watson, M. A. & Cockroft, S. L. Man-made molecular machines: membrane bound. Chem. Soc. Rev. 45, 6118–6129 (2016).

    CAS  Google Scholar 

  163. Nivala, J., Marks, D. B. & Akeson, M. Unfoldase-mediated protein translocation through an α-hemolysin nanopore. Nat. Biotechnol. 31, 247–250 (2013).

    CAS  Google Scholar 

  164. Noji, H., Yasuda, R., Yoshida, M. & Kinosita, K. Jr Direct observation of the rotation of F1-ATPase. Nature 386, 299–302 (1997).

    CAS  Google Scholar 

  165. Bakelar, J., Buchanan, S. K. & Noinaj, N. The structure of the β-barrel assembly machinery complex. Science 351, 180–186 (2016).

    CAS  Google Scholar 

  166. Blake, S., Capone, R., Mayer, M. & Yang, J. Chemically reactive derivatives of gramicidin A for developing ion channel-based nanoprobes. Bioconj. Chem. 19, 1614–1624 (2008).

    CAS  Google Scholar 

  167. Hendrickson, W. A. Atomic-level analysis of membrane-protein structure. Nat. Struct. Mol. Biol. 23, 464–467 (2016).

    CAS  Google Scholar 

  168. Williams, J. K., Tietze, D., Lee, M., Wang, J. & Hong, M. Solid-state NMR investigation of the conformation, proton conduction, and hydration of the influenza B virus M2 transmembrane proton channel. J. Am. Chem. Soc. 138, 8143–8155 (2016).

    CAS  Google Scholar 

  169. Hodel, A. W., Leung, C., Dudkina, N. V., Saibil, H. R. & Hoogenboom, B. W. Atomic force microscopy of membrane pore formation by cholesterol dependent cytolysins. Curr. Opin. Struct. Biol. 39, 8–15 (2016).

    CAS  Google Scholar 

  170. Zhu, R. et al. Nanopharmacological force sensing to reveal allosteric coupling in transporter binding sites. Angew. Chem. Int. Ed. 55, 1719–1722 (2016).

    CAS  Google Scholar 

  171. Krasilnikov, O. V., Rodrigues, C. G. & Bezrukov, S. M. Single polymer molecules in a protein nanopore in the limit of a strong polymer–pore attraction. Phys. Rev. Lett. 97, 018301 (2006).

    Google Scholar 

  172. Merzlyak, P. G., Capistrano, M. F. P., Valeva, A., Kasianowicz, J. J. & Krasilnikov, O. V. Conductance and ion selectivity of a mesoscopic protein nanopore probed with cysteine scanning mutagenesis. Biophys. J. 89, 3059–3070 (2005).

    CAS  Google Scholar 

  173. Huang, S., Romero-Ruiz, M., Castell, O. K., Bayley, H. & Wallace, M. I. High-throughput optical sensing of nucleic acids in a nanopore array. Nat. Nanotech. 10, 986–991 (2015).

    CAS  Google Scholar 

  174. Andersen, O. S. & Koeppe, R. E. II Bilayer thickness and membrane protein function: an energetic perspective. Annu. Rev. Biophys. Biomol. Struct. 36, 107–130 (2007).

    CAS  Google Scholar 

  175. Saliba, A. E., Vonkova, I. & Gavin, A. C. The systematic analysis of protein-lipid interactions comes of age. Nat. Rev. Mol. Cell. Biol. 16, 753–761 (2015).

    CAS  Google Scholar 

  176. Miles, A. J. & Wallace, B. A. Circular dichroism spectroscopy of membrane proteins. Chem. Soc. Rev. 45, 4859–4872 (2016).

    CAS  Google Scholar 

  177. Laganowsky, A. et al. Membrane proteins bind lipids selectively to modulate their structure and function. Nature 510, 172–175 (2014).

    CAS  Google Scholar 

  178. Maffeo, C., Bhattacharya, S., Yoo, J., Wells, D. & Aksimentiev, A. Modeling and simulation of ion channels. Chem. Rev. 112, 6250–6284 (2012).

    CAS  Google Scholar 

  179. Stansfeld, P. J. et al. MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes. Structure 23, 1350–1361 (2015).

    CAS  Google Scholar 

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Acknowledgements

I thank J. R. Burns for rendering and producing DNA pore images, A. Hodel for providing membrane particle system, K. Ahmad and J. Donnelly for help with peptide images, R. Morgan and Z. Siwy for critically reading the manuscript. Supported by UK Engineering and Physical Sciences Research Council grant EP/N009282/1 and Biotechnology and Biological Sciences Research Council grants BB/M025373/1 and BB/N017331/1, the Leverhulme Trust research grant RPG-2017-015 and Oxford Nanopore Technologies.

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Correspondence to Stefan Howorka.

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The research group of S.H. receives funding from Oxford Nanopore Technologies.

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Howorka, S. Building membrane nanopores. Nature Nanotech 12, 619–630 (2017). https://doi.org/10.1038/nnano.2017.99

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