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DNA condensation in one dimension

Nature Nanotechnology volume 11, pages 1076–1081 (2016)Cite this article

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Abstract

DNA can be programmed to assemble into a variety of shapes and patterns on the nanoscale1,2,3,4,5 and can act as a template for hybrid nanostructures6 such as conducting wires7,8,9, protein arrays8 and field-effect transistors10,11. Current DNA nanostructures are typically in the sub-micrometre range, limited by the sequence space and length of the assembled strands. Here we show that on a patterned biochip12, DNA chains collapse into one-dimensional (1D) fibres that are 20 nm wide and around 70 µm long, each comprising approximately 35 co-aligned chains at its cross-section. Electron beam writing on a photocleavable monolayer was used to immobilize and pattern the DNA molecules, which condense into 1D bundles in the presence of spermidine. DNA condensation can propagate and split at junctions, cross gaps and create domain walls between counterpropagating fronts. This system is inherently adept at solving probabilistic problems and was used to find the possible paths through a maze and to evaluate stochastic switching circuits. This technique could be used to propagate biological or ionic signals13 in combination with sequence-specific DNA nanotechnology or for gene expression in cell-free DNA compartments14.

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Figure 1: Assembly and structure of nanobundles.
Figure 2: Structural properties of nuclei and 1D bundles.
Figure 3: Front propagation dynamics.
Figure 4: Condensation through a graphical representation of a maze.
Figure 5: 1D DNA condensation bridges over gap barriers.

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Acknowledgements

We gratefully acknowledge financial support by the Volkswagen Stiftung (G.P., F.C.S. and R.H.B.-Z., grant no. 86 395), the Israel Science Foundation (R.H.B.-Z.) and the Minerva Foundation (R.H.B.-Z).

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Author notes

  1. Günther Pardatscher and Dan Bracha: These authors contributed equally to this work

Authors and Affiliations

  1. Physics-Department and ZNN, Systems Biophysics and Bionanotechnology - E14, Technische Universität München, Garching, 85748, Germany

    Günther Pardatscher & Friedrich C. Simmel

  2. Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot, 76100, Israel

    Dan Bracha, Shirley S. Daube, Ohad Vonshak & Roy H. Bar-Ziv

  3. Nanosystems Initiative Munich, Munich, 80539, Germany

    Friedrich C. Simmel

Authors
  1. Günther Pardatscher
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Contributions

G.P., D.B., F.C.S. and R.H.B.-Z. planned and designed the experiments. G.P., D.B. and O.V. performed the experiments. G.P., D.B., S.S.D., F.C.S. and R.H.B.-Z. wrote the paper; all authors discussed the results and commented on the manuscript.

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Correspondence to Friedrich C. Simmel or Roy H. Bar-Ziv.

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The authors declare no competing financial interests.

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Pardatscher, G., Bracha, D., Daube, S. et al. DNA condensation in one dimension. Nature Nanotech 11, 1076–1081 (2016). https://doi.org/10.1038/nnano.2016.142

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