Abstract
Biological ion channels are molecular gatekeepers that control transport across cell membranes. Recreating the functional principle of such systems and extending it beyond physiological ionic cargo is both scientifically exciting and technologically relevant to sensing or drug release1,2. However, fabricating synthetic channels1,3 with a predictable structure remains a significant challenge. Here, we use DNA as a building material4,5,6,7,8 to create an atomistically determined molecular valve that can control when and which cargo is transported across a bilayer. The valve, which is made from seven concatenated DNA strands, can bind a specific ligand and, in response, undergo a nanomechanical change to open up the membrane-spanning channel. It is also able to distinguish with high selectivity the transport of small organic molecules that differ by the presence of a positively or negatively charged group. The DNA device could be used for controlled drug release and the building of synthetic cell-like or logic ionic networks9,10.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Litvinchuk, S. et al. Synthetic pores with reactive signal amplifiers as artificial tongues. Nature Mater. 6, 576–580 (2007).
Mayer, M. & Yang, J. Engineered ion channels as emerging tools for chemical biology. Acc. Chem. Res. 46, 2998–3008 (2013).
Thomson, A. R. et al. Computational design of water-soluble α-helical barrels. Science 346, 485–488 (2014).
Burns, J. R., Stulz, E. & Howorka, S. Self-assembled DNA nanopores that span lipid bilayers. Nano Lett. 13, 2351–2356 (2013).
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).
Burns, J. R. et al. Lipid bilayer-spanning DNA nanopores with a bifunctional porphyrin anchor. Angew. Chem. Int. Ed. 52, 12069–12072 (2013).
Seifert, A. et al. Bilayer-spanning DNA nanopores with voltage-switching between open and closed state. ACS Nano 9, 1117–1126 (2015).
Langecker, M. et al. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338, 932–936 (2012).
Maglia, G. et al. Droplet networks with incorporated protein diodes show collective properties. Nature Nanotech. 4, 437–440 (2009).
Villar, G., Graham, A. D. & Bayley, H. A tissue-like printed material. Science 340, 48–52 (2013).
Chowdhury, S., Jarecki, B. W. & Chanda, B. A molecular framework for temperature-dependent gating of ion channels. Cell 158, 1148–1158 (2014).
Kocer, A., Walko, M., Meijberg, W. & Feringa, B. L. A light-actuated nanovalve derived from a channel protein. Science 309, 755–758 (2005).
Howorka, S. & Siwy, Z. Nanopore analytics: sensing of single molecules. Chem. Soc. Rev. 38, 2360–2384 (2009).
Wang, Y., Zheng, D., Tan, Q., Wang, M. X. & Gu, L. Q. Nanopore-based detection of circulating microRNAs in lung cancer patients. Nature Nanotech. 6, 668–674 (2011).
Cherf, G. M. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nature Biotechnol. 30, 344–348 (2012).
Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nature Biotechnol. 30, 349–353 (2012).
Wei, R. S., Gatterdam, V., Wieneke, R., Tampe, R. & Rant, U. Stochastic sensing of proteins with receptor-modified solid-state nanopores. Nature Nanotech. 7, 257–263 (2012).
Traversi, F. et al. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nature Nanotech. 8, 939–945 (2013).
Geng, J. et al. Stochastic transport through carbon nanotubes in lipid bilayers and live cell membranes. Nature 514, 612–615 (2014).
Wanunu, M. et al. Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nature Nanotech. 5, 807–814 (2010).
Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009).
Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
Wollman, A. J., Sanchez-Cano, C., Carstairs, H. M., Cross, R. A. & Turberfield, A. J. Transport and self-organization across different length scales powered by motor proteins and programmed by DNA. Nature Nanotech. 9, 44–47 (2014).
Sacca, B. & Niemeyer, C. M. Functionalization of DNA nanostructures with proteins. Chem. Soc. Rev. 40, 5910–5921 (2011).
Andersen, E. S. et al. Self-assembly of a nanoscale DNA box with a controllable lid. Nature 459, 73–76 (2009).
Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science 324, 67–71 (2009).
Krishnan, S. & Simmel, F. C. Nanotechnology: deadly DNA. Nature Chem. 7, 17–18 (2014).
Eisenstein, M. Molecular engineering: changing the channel. Nature Methods 10, 10–11 (2013).
Yoo, J. & Aksimentiev, A. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations. Proc. Natl Acad. Sci. USA 110, 20099–20104 (2013).
Douglas, S. M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).
Bai, X. C., Martin, T. G., Scheres, S. H. & Dietz, H. Cryo-EM structure of a 3D DNA-origami object. Proc. Natl Acad. Sci. USA 109, 20012–20017 (2012).
Song, L. et al. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science 274, 1859–1866 (1996).
Rinker, S., Ke, Y. G., Liu, Y., Chhabra, R. & Yan, H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand–protein binding. Nature Nanotech. 3, 418–422 (2008).
Wilner, O. I. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nature Nanotech. 4, 249–254 (2009).
Bussiek, M., Mucke, N. & Langowski, J. Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution. Nucleic Acids Res. 31, e137 (2003).
Mitchell, N., Ebner, A., Hinterdorfer, P., Tampe, R. & Howorka, S. Chemical tags mediate the self-assembly of DNA strands into supramolecular structures. Small 6, 1732–1735 (2010).
Del Rio Martinez, J. M., Zaitseva, E., Petersen, S., Baaken, G. & Behrends, J. C. Automated formation of lipid membrane microarrays for ionic single-molecule sensing with protein nanopores. Small 11, 119–125 (2015).
Chen, R. F. & Knutson, J. R. Mechanism of fluorescence concentration quenching of carboxyfluorescein in liposomes: energy transfer to nonfluorescent dimers. Anal. Biochem. 172, 61–77 (1988).
Moscho, A., Orwar, O., Chiu, D. T., Modi, B. P. & Zare, R. N. Rapid preparation of giant unilamellar vesicles. Proc. Natl Acad. Sci. USA 93, 11443–11447 (1996).
Acknowledgements
This research was funded by the Leverhulme Trust (RPG-170), UCL Chemistry and the BBSRC (grant ref. BB/M012700/1). The authors thank A. Pyne and B. Hoogenboom from the London Centre for Nanotechnology for assistance with the AFM analysis of DNA nanopores, and H. Martin in aiding J.B. to render the images of the pores.
Author information
Authors and Affiliations
Contributions
J.B. and S.H. designed the DNA nanopores. J.B. carried out all experiments except nanopore recordings, which were conducted by A.S. N.F. co-supervised A.S. S.H. conceived the project, supervised J.B. and A.S., and wrote the manuscript with data input from J.B. and A.S.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Supplementary information
Supplementary information
Supplementary information (PDF 1789 kb)
Rights and permissions
About this article
Cite this article
Burns, J., Seifert, A., Fertig, N. et al. A biomimetic DNA-based channel for the ligand-controlled transport of charged molecular cargo across a biological membrane. Nature Nanotech 11, 152–156 (2016). https://doi.org/10.1038/nnano.2015.279
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nnano.2015.279
This article is cited by
-
Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations
Nature Communications (2023)
-
High-resolution discrimination of homologous and isomeric proteinogenic amino acids in nanopore sensors with ultrashort single-walled carbon nanotubes
Nature Communications (2023)
-
Creating complex protocells and prototissues using simple DNA building blocks
Nature Communications (2023)
-
Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility
Nature Communications (2022)
-
Highly shape- and size-tunable membrane nanopores made with DNA
Nature Nanotechnology (2022)