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Tunable non-equilibrium gating of flexible DNA nanochannels in response to transport flux

Nature Nanotechnology volume 2, pages 366–371 (2007)Cite this article

Abstract

Biological nanochannels made from proteins play a central role in cellular signalling1,2,3,4,5,6,7,8,9. The rapid emergence of DNA nanotechnology in recent years10,11,12,13 has opened up the possibility of making similar nanochannels from DNA. Building on previous work on switchable DNA nanocompartment14,15, we have constructed complex DNA nanosystems to investigate the gating behaviour of these nanochannels. Here we show that DNA nanochannels can be gated by stress exerted by permeating solute particles at non-equilibrium states due to the high flexibility of the nanochannels. This novel gating mechanism results in tunable ratchet-like transport of solute particles through the nanochannels. A simple model that couples non-equilibrium channel gating with transport flux can quantitatively explain a number of the phenomena we observe. With only one set of model parameters, we can reproduce diverse gating behaviours, modulated by an inherent gating threshold. This work could lead to the development of new devices based on DNA nanochannels.

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Figure 1: Experimental observations of ratchet-like thionine transport through DNA nanochannels.
Figure 2: Theoretical modelling of the gating dynamics of DNA channels.
Figure 3: Behaviour of the gating threshold C* in relation to Cmax.
Figure 4: Modulation of gating behaviours of DNA channels.

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Acknowledgements

We thank A. G. Cherstvy for a critical review and helpful comments on the manuscript. This work is partly supported by the Ministry of Science and Technology of China, and the Chinese Natural Science Foundation.

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Authors and Affiliations

  1. School of Physics and Center for Theoretical Biology, Peking University, Beijing, 100871, China

    Youdong Mao, Song Chang, Shaoxuan Yang & Qi Ouyang

  2. National Center for Nanoscience and Technology, Beijing, 100080, China

    Youdong Mao

  3. Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100080, China

    Lei Jiang

Authors
  1. Youdong Mao
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  2. Song Chang
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  3. Shaoxuan Yang
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  4. Qi Ouyang
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Contributions

Y.M. designed the experiments, established the theoretical model and performed the numerical calculations. Y.M. and S.Y. carried out the experiments. Y.M. and Q.O. analysed the data. S.C. and Y.M. performed the simulation on the mean residence number of solute particle inside channels. Y.M. wrote the manuscript, and Q.O. and L.J. proofread it. Q.O. and L.J. supervised the research project.

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Correspondence to Qi Ouyang or Lei Jiang.

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The authors declare no competing financial interests.

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Supplementary figures S1–S14 (PDF 1810 kb)

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Mao, Y., Chang, S., Yang, S. et al. Tunable non-equilibrium gating of flexible DNA nanochannels in response to transport flux. Nature Nanotech 2, 366–371 (2007). https://doi.org/10.1038/nnano.2007.148

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