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Research Article

Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components

Science
27 Mar 2015
Vol 347, Issue 6229
pp. 1446-1452

Reconfigurable DNA structures

DNA origami—nanostructures created by programming the assembly of single-stranded DNA through base pairing—can create intricate structures. However, such structures lack the flexible and reversible interactions more typical of biomolecular recognition. Gerling et al. created three-dimensional DNA nanostructures that assemble though nucleotide base-stacking interactions (see the Perspective by Shih). These structures cycled from open to closed states with changes in salt concentration or temperature.
Science, this issue p. 1446; see also p. 1417

Abstract

We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.

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Supplementary Material

Summary

Materials and Methods
Supplementary Text S1 to S7
Figs. S1 to S103
Movies S1 to S8
List of Oligonucleotides
Overview of Strand Diagrams
References (3032)

Resources

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File (aaa5372s8.avi)
File (gerling.sm.pdf)
File (oligonucleotides.xlsx)
File (strand_diagrams.pdf)

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Information & Authors

Information

Published In

Science
Volume 347 | Issue 6229
27 March 2015

Submission history

Received: 19 December 2014
Accepted: 9 February 2015
Published in print: 27 March 2015

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Acknowledgments

We thank E. Stahl, T. Martin, J. Funke, M. Schickinger, F. Kilchherr, C. Wachauf, L. Meregalli, and V. Hechtl for technical assistance. F. Praetorius is acknowledged for scaffold DNA preparations. This work was supported by a European Research Council Starting Grant to H.D. (GA no.256270) and the Deutsche Forschungsgemeinschaft through grants provided within the Excellence Clusters CIPSM (Center for Integrated Protein Science Munich), NIM (Nanosystems Initiative Munich), the Sonderforschungsbereich SFB863, the Technische Universität München (TUM) Institute for Advanced Study, and the TUM International Graduate School of Science and Engineering (IGSSE). K.F.W. and H.D. are grateful for additional support from the Hans L. Merkle Foundation. T.G., K.F.W., and A.N. performed research. H.D. designed research and wrote the manuscript. T.G., K.F.W., and H.D. prepared figures. T.G., K.F.W., and H.D. analyzed and discussed data and edited the manuscript. We confirm no competing financial interests. The data reported in this paper are tabulated in the supplementary materials.

Authors

Affiliations

Thomas Gerling
Physik Department, Walter Schottky Institute, Technische Universität München Am Coulombwall 4a, 85748 Garching near Munich, Germany
Klaus F. Wagenbauer
Physik Department, Walter Schottky Institute, Technische Universität München Am Coulombwall 4a, 85748 Garching near Munich, Germany
Andrea M. Neuner
Physik Department, Walter Schottky Institute, Technische Universität München Am Coulombwall 4a, 85748 Garching near Munich, Germany
Hendrik Dietz* [email protected]
Physik Department, Walter Schottky Institute, Technische Universität München Am Coulombwall 4a, 85748 Garching near Munich, Germany

Notes

*
Corresponding author. E-mail: [email protected]

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