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A double-stranded DNA rotaxane

Abstract

Mechanically interlocked molecules such as rotaxanes and catenanes have potential as components of molecular machinery. Rotaxanes consist of a dumb-bell-shaped molecule encircled by a macrocycle that can move unhindered along the axle, trapped by bulky stoppers. Previously, rotaxanes have been made from a variety of molecules, but not from DNA. Here, we report the design, assembly and characterization of rotaxanes in which both the dumb-bell-shaped molecule and the macrocycle are made of double-stranded DNA, and in which the axle of the dumb-bell is threaded through the macrocycle by base pairing. The assembly involves the formation of pseudorotaxanes, in which the macrocycle and the axle are locked together by hybridization. Ligation of stopper modules to the axle leads to the characteristic dumb-bell topology. When an oligonucleotide is added to release the macrocycle from the axle, the pseudorotaxanes are either converted to mechanically stable rotaxanes, or they disassemble by means of a slippage mechanism to yield a dumb-bell and a free macrocycle. Our DNA rotaxanes allow the fields of mechanically interlocked molecules and DNA nanotechnology to be combined, thus opening new possibilities for research into molecular machines and synthetic biology.

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Figure 1: Architecture of DNA–pseudorotaxanes with single-ring stoppers.
Figure 2: Architecture of a DNA pseudo[3]rotaxane.
Figure 3: Architecture of DNA–rotaxanes with spherical stoppers.
Figure 4: Rotaxane stability and macrocycle mobility studies.

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Acknowledgements

The authors would like to thank S. Verma and A. Schmitz for helpful discussions, and F. Vögtle for critical reading of this manuscript. This work was supported by grants from the Deutsche Forschungsgemeinschaft, the SFB 624, the Fonds der Chemischen Industrie (to M.F.) and Exc 115 (to A.H. and T.L.S). C.S.P. thanks the Alexander von Humboldt foundation for a postdoctoral fellowship.

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Contributions

D.A. performed and designed, with M.F., most of the included studies. C.S.P. performed the dethreading experiments. J.H. provided conceptual input. T.L.S. performed the AFM studies, assisted by A.H. M.F. supervised the research project and assisted in the experimental design. All authors discussed the experimental results. D.A., J.H. and M.F. wrote the manuscript.

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Correspondence to Michael Famulok.

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The authors declare no competing financial interests.

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Ackermann, D., Schmidt, T., Hannam, J. et al. A double-stranded DNA rotaxane. Nature Nanotech 5, 436–442 (2010). https://doi.org/10.1038/nnano.2010.65

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