Routing of individual polymers in designed patterns

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Abstract

Synthetic polymers are ubiquitous in the modern world, but our ability to exert control over the molecular conformation of individual polymers is very limited. In particular, although the programmable self-assembly of oligonucleotides and proteins into artificial nanostructures has been demonstrated, we currently lack the tools to handle other types of synthetic polymers individually and thus the ability to utilize and study their single-molecule properties. Here we show that synthetic polymer wires containing short oligonucleotides that extend from each repeat can be made to assemble into arbitrary routings. The wires, which can be more than 200 nm in length, are soft and bendable, and the DNA strands allow individual polymers to self-assemble into predesigned routings on both two- and three-dimensional DNA origami templates. The polymers are conjugated and potentially conducting, and could therefore be used to create molecular-scale electronic or optical wires in arbitrary geometries.

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Figure 1: Synthesis of poly(APPV-DNA).
Figure 2: AFM characterization of the physical properties of poly(APPV-DNA).
Figure 3: Immobilization of the APPV-DNA polymer on origami by hybridization of the 9 nt DNA sequences extending from the polymer to patterns of ssDNA extending from the origami.
Figure 4: 3D DNA-PAINT super-resolution imaging of the APPV-DNA polymer immobilized on a 3D DNA nanostructure.

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Acknowledgements

We thank P.W.K. Rothemund for discussions. This work was funded by the Danish National Research Foundation (Centre for DNA Nanotechnology, DNRF81), Sino-Danish Centre for Education and Research, Carlsberg Foundation, Danish Research Council (V.B.) (Sapere Aude Starting Grant (A.N.Z. and V.B.), STENO grant and an individual post-doctorate grant (R.O.)), Villum Foundation (Young Investigator Program (M.D.)), and the Lundbeck Foundation (A.N.Z). R.J. acknowledges support from the Deutsche Forschungsgemeinschaft through the Emmy Noether program (DFG JU 2957/1–1) and the Max Planck Society. W.M.S. acknowledges support for the contributions to his laboratory from the National Science Foundation (CCF-1317291), Army Research Office (W911NF-12-1-0420) and the Wyss Institute for Biologically Inspired Engineering.

Author information

J.B.K. and M.M. synthesized and characterized the APPV-DNA polymer. L.L., J.S., Q.L. and J.V. conducted the SPM experiments. A.L.B.K. and A.K. designed the DNA origami and conducted the AFM experiments. A.A.A.S. and A.N.Z. assisted in performing and interpreting the GPC analysis. R.O. performed XPS and assisted in the interpretation. D.G. measured the fluorescence quantum yields of the polymer. M.M. designed and conducted the FRET experiments. J.B.W., R.J., S.F.J.W., W.M.S. and K.V.G. designed the DNA-PAINT experiments. S.F.J.W. and W.M.S. designed the 3D DNA origami samples, and S.F.J.W. assembled, purified and characterized the 3D DNA origami samples. J.B.W., M.T.S. and F.S. performed the DNA-PAINT experiments and analysed the data. M.T.S. wrote the 3D image analysis and fitting software. R.J. performed the class averaging. P.Y. and R.J. supervised the DNA-PAINT study. A.Z., V.B. and F.B. supervised parts of the project. M.D. supervised and analysed the SPM experiments. K.V.G. conceived and supervised the project. J.B.K., M.D., S.F.J.W., A.L.B.K., J.B.W., M.T.S., R.J. and K.V.G. wrote the paper.

Correspondence to Mingdong Dong or Kurt V. Gothelf.

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Knudsen, J., Liu, L., Bank Kodal, A. et al. Routing of individual polymers in designed patterns. Nature Nanotech 10, 892–898 (2015) doi:10.1038/nnano.2015.190

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