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Routing of individual polymers in designed patterns

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.

References

  1. 1

    Heeger, A. J. Semiconducting and metallic polymers: the fourth generation of polymeric materials. Synthetic Met. 125, 23–42 (2001).

    Article  Google Scholar 

  2. 2

    Heeger, A. J. Semiconducting polymers: the third generation. Chem. Soc. Rev. 39, 2354–2371 (2010).

    CAS  Article  Google Scholar 

  3. 3

    Facchetti, A. π-Conjugated polymers for organic electronics and photovoltaic cell applications. Chem. Mater. 23, 733–758 (2011).

    CAS  Article  Google Scholar 

  4. 4

    Baeg, K.-J. et al. High speeds complementary integrated circuits fabricated with all-printed polymeric semiconductors. J. Polym. Sci. B 49, 62–67 (2011).

    CAS  Article  Google Scholar 

  5. 5

    Gong, S., Yang, C. & Qin, J. Efficient phosphorescent polymer light-emitting diodes by suppressing triplet energy back transfer. Chem. Soc. Rev. 41, 4797–4807 (2012).

    CAS  Article  Google Scholar 

  6. 6

    Zheng, H. et al. All-solution processed polymer light-emitting diode displays. Nature Commun. 4, 1–7 (2013).

    CAS  Google Scholar 

  7. 7

    Günes, S., Neugebauer, H. & Sariciftci, N. S. Conjugated polymer-based organic solar cells. Chem. Rev. 107, 1324–1338 (2007).

    Article  Google Scholar 

  8. 8

    Thomas, S. W., Joly, G. D. & Swager, T. M. Chemical sensors based on amplifying fluorescent conjugated polymers. Chem. Rev. 107, 1339–1386 (2007).

    CAS  Article  Google Scholar 

  9. 9

    Barbara, P. F., Gesquiere, A. J., Park, S. J. & Lee, Y. J. Single-molecule spectroscopy of conjugated polymers. Acc. Chem. Res. 38, 602–610 (2005).

    CAS  Article  Google Scholar 

  10. 10

    Hugel, T. et al. Single-molecule optomechanical cycle. Science 296, 1103–1106 (2002).

    Article  Google Scholar 

  11. 11

    Kawai, S. et al. Quantifying the atomic-level mechanics of single long physisorbed molecular chains. Proc. Natl Acad. Sci. USA 111, 3968–3972 (2014).

    CAS  Article  Google Scholar 

  12. 12

    Taniguchi, M. et al. Self-organized interconnect method for molecular devices. J. Am. Chem. Soc. 128, 15062–15063 (2006).

    CAS  Article  Google Scholar 

  13. 13

    Lafferentz, L. et al. Conductance of a single conjugated polymer as a continuous function of its length. Science 323, 1193–1197 (2009).

    CAS  Article  Google Scholar 

  14. 14

    Shimomura, T. et al. Conductivity measurement of insulated molecular wire formed by molecular nanotube and polyaniline. Synthetic Met. 153, 497–500 (2005).

    CAS  Article  Google Scholar 

  15. 15

    Kiriy, A. et al. Cascade of coil–globule conformational transitions of single flexible polyelectrolyte molecules in poor solvent. J. Am. Chem. Soc. 124, 13454–13462 (2002).

    CAS  Article  Google Scholar 

  16. 16

    Shimomura, T., Akai, T., Abe, T. & Ito, K. Atomic force microscopy observation of insulated molecular wire formed by conducting polymer and molecular nanotube. J. Chem. Phys. 116, 1753–1756 (2002).

    CAS  Article  Google Scholar 

  17. 17

    Ouchi, M., Badi, N., Lutz, J.-F. & Sawamoto, M. Single-chain technology using discrete synthetic macromolecules. Nature Chem. 3, 917–924 (2011).

    CAS  Article  Google Scholar 

  18. 18

    Müllen, K. Evolution of graphene molecules: structural and functional complexity as driving forces behind nanoscience. ACS Nano 8, 6531–6541 (2011).

    Article  Google Scholar 

  19. 19

    Palma, C.-A. & Samori, P. Blueprinting macromolecular electronics. Nature Chem. 3, 431–436 (2011).

    CAS  Article  Google Scholar 

  20. 20

    Lörtscher, E. Wiring molecules into circuits. Nature Nanotech. 8, 381–384 (2013).

    Article  Google Scholar 

  21. 21

    Peng, H., Zhang, L., Soeller, C. & Travas-Sejdic, J. Conducting polymers for electrochemical DNA sensing. Biomaterials 30, 2132–2148 (2009).

    CAS  Article  Google Scholar 

  22. 22

    Lo, P. K. & Sleiman, H. F. Nucleobase-templated polymerization: copying the chain length and polydispersity of living polymers into conjugated polymers. J. Am. Chem. Soc. 131, 4182–4183 (2009).

    CAS  Article  Google Scholar 

  23. 23

    Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    CAS  Article  Google Scholar 

  24. 24

    Tørring, T., Voigt, N. V., Nangreave, J., Yan, H. & Gothelf, K. V. DNA origami: a quantum leap for self-assembly of complex structures. Chem. Soc. Rev. 40, 5636–5646 (2011).

    Article  Google Scholar 

  25. 25

    Sacca, B. & Niemeyer, C. M. Functionalization of DNA nanostructures with proteins. Chem. Soc. Rev. 40, 5910–5921 (2011).

    CAS  Article  Google Scholar 

  26. 26

    Wang, Z. G. & Ding, B. Engineering DNA self-assemblies as templates for functional nanostructures. Acc. Chem. Res. 47, 1654–1662 (2014).

    CAS  Article  Google Scholar 

  27. 27

    Maune, H. T. et al. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nature Nanotech. 5, 61–66 (2010).

    CAS  Article  Google Scholar 

  28. 28

    Chaix, C., Minard-Basquin, C., Delair, T., Pichot, C. & Mandrand, B. Oligonucleotide synthesis on maleic anhydride copolymers covalently bound to silica spherical support and characterization of the obtained conjugates. J. Appl. Polym. Sci. 70, 2487 (1998).

    CAS  Article  Google Scholar 

  29. 29

    Henckens, A., Duyssens, I., Lutsen, L., Vanderzande, D. & Cleij, T. J. Synthesis of poly(p-phenylene vinylene) and derivatives via a new precursor route, the dithiocarbamate route. Polymer 47, 123–131 (2006).

    CAS  Article  Google Scholar 

  30. 30

    Vandenbergh, J. et al. Synthesis and characterization of water-soluble poly(p-phenylene vinylene) derivatives via the dithiocarbamate precursor route. Eur. Polym. J. 47, 1827–1835 (2011).

    CAS  Article  Google Scholar 

  31. 31

    Minard-Basquin, C., Chaix, C., Pichot, C. & Mandrand, B. Oligonucleotide−polymer conjugates: effect of the method of synthesis on their structure and performance in diagnostic assays. Bioconjugate Chem. 11, 795–805 (2000).

    CAS  Article  Google Scholar 

  32. 32

    Volcke, C. et al. Influence of DNA condensation state on transfection efficiency in DNA/polymer complexes: an AFM and DLS comparative study. J. Biotechnol. 125, 11–21 (2006).

    CAS  Article  Google Scholar 

  33. 33

    Zhang, S. et al. Coexistence of ribbon and helical fibrils originating from hIAPP20–29 revealed by quantitative nanomechanical atomic force microscopy. Proc. Natl Acad. Sci. USA 110, 2798–2803 (2013).

    CAS  Article  Google Scholar 

  34. 34

    Pfeffer, C. et al. Filamentous bacteria transport electrons over centimetre distances. Nature 491, 218–221 (2012).

    CAS  Article  Google Scholar 

  35. 35

    Sinensky, A. K. & Belcher, A. M. Label-free and high-resolution protein/DNA nanoarray analysis using Kelvin probe force microscopy. Nature Nanotech. 2, 653–659 (2007).

    CAS  Article  Google Scholar 

  36. 36

    Ke, Y., Lindsay, S., Chang, Y., Liu, Y. & Yan, H. Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319, 180–183 (2008).

    CAS  Article  Google Scholar 

  37. 37

    Shih, W. M. & Lin, C. Knitting complex weaves with DNA origami. Curr. Opin. Chem. Biol. 20, 276–282 (2010).

    CAS  Google Scholar 

  38. 38

    Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).

    CAS  Article  Google Scholar 

  39. 39

    Iinuma, R. et al. Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. Science 344, 65–69 (2014).

    CAS  Article  Google Scholar 

  40. 40

    Jungmann, R. et al. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nature Methods 11, 313 (2014).

    CAS  Article  Google Scholar 

  41. 41

    Jungmann, R. et al. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 10, 4756–4761 (2010).

    CAS  Article  Google Scholar 

  42. 42

    Kao, H. P. & Verkman, A. S. Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position. Biophys. J. 67, 1291–1300 (1994).

    CAS  Article  Google Scholar 

  43. 43

    Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008).

    CAS  Article  Google Scholar 

  44. 44

    Burns, P. L. et al. Chemical tuning of the electronic properties of poly(p-phenylenevinylene)-based copolymers. J. Am. Chem. Soc. 115, 10117–10124 (1993).

    Article  Google Scholar 

  45. 45

    Kershner, R. J. et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nature Nanotech. 4, 557–561 (2009).

    CAS  Article  Google Scholar 

Download references

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.

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Contributions

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.

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Correspondence to Mingdong Dong or Kurt V. Gothelf.

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The authors declare no competing financial interests.

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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). https://doi.org/10.1038/nnano.2015.190

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