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A nanomechanical device based on the B–Z transition of DNA

Abstract

The assembly of synthetic, controllable molecular mechanical systems1,2,3,4,5,6,7 is one of the goals of nanotechnology. Protein-based molecular machines, often driven by an energy source such as ATP, are abundant in biology8,9. It has been shown previously that branched motifs of DNA can provide components for the assembly of nanoscale objects10, links11 and arrays12. Here we show that such structures can also provide the basis for dynamic assemblies: switchable molecular machines. We have constructed a supramolecular device consisting of two rigid DNA ‘double-crossover’ (DX) molecules connected by 4.5 double-helical turns. One domain of each DX molecule is attached to the connecting helix. To effect switchable motion in this assembly, we use the transition between the B and Z13,14 forms of DNA. In conditions that favour B-DNA, the two unconnected domains of the DX molecules lie on the same side of the central helix. In Z-DNA-promoting conditions, however, these domains switch to opposite sides of the helix. This relative repositioning is detected by means of fluorescence resonance energy transfer spectroscopy, which measures the relative proximity of two dye molecules attached to the free ends of the DX molecules. The switching event induces atomic displacements of 20–60 Å.

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Figure 1: Design of the nanomechanical device.
Figure 2: FRET demonstration of nanomechanical motion.

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References

  1. Dado, G. & Gellman, S. H. Redox control of secondary structure in a designed peptide. J. Am. Chem. Soc. 115, 12609–12610 (1993).

    Article  CAS  Google Scholar 

  2. Handel, T. M., Williams, S. A. & deGrado, W. F. Metal ion dependent modulation of the dynamics of a designed protein. Science 261, 879–885 (1993).

    Article  ADS  CAS  Google Scholar 

  3. Bissell, R. A., Códova, E., Kalfer, A. E. & Stoddart, J. F. Achemically and electrochemically switchable molecular shuttle. Nature 369, 133–137 (1994).

    Article  ADS  CAS  Google Scholar 

  4. Zelkovich, L., Libman, J. & Shanzer, A. Molecular redox switches based on chemical triggering of iron translocation in triple-stranded helical complexes. Nature 374, 790–792 (1995).

    Article  ADS  Google Scholar 

  5. Livoreil, A. et al. Electrochemically and photochemically driven ring motions in a dissymmetrical copper [2] catenate. J. Am. Chem. Soc. 119, 12114–12124 (1997).

    Article  CAS  Google Scholar 

  6. Murakami, M., Kawabuchi, A., Kotoo, K., Kumitake, M. & Nakashima, N. Alight-driven molecular shuttle based on a rotaxane. J. Am. Chem. Soc. 119, 7605–7606 (1997).

    Article  CAS  Google Scholar 

  7. Zahn, S. & Canary, J. W. Redox-switched exciton-coupled circular dichroism: A novel strategy for binary molecular switching. Angew. Chem. Int. Edn 37, 305–307 (1998).

    Article  CAS  Google Scholar 

  8. Nedelec, F. J., Surrey, T., Maggs, A. C. & Leibler, S. Self-organization of microtubules and motors. Nature 389, 305–308 (1997).

    Article  ADS  CAS  Google Scholar 

  9. Alberts, B. The cell as a collection of protein machines. Cell 92, 291–294 (1998).

    Article  CAS  Google Scholar 

  10. Chen, J. & Seeman, N. C. The synthesis from DNA of a molecule with the connectivity of a cube. Nature 350, 631–633 (1991).

    Article  ADS  CAS  Google Scholar 

  11. Mao, C., Sun, W. & Seeman, N. C. Assembly of Borromean rings from DNA. Nature 386, 137–138 (1997).

    Article  ADS  CAS  Google Scholar 

  12. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998).

    Article  ADS  CAS  Google Scholar 

  13. Rich, A., Nordheim, A. & Wang, A. H.-J. The chemistry and biology of left-handed Z-DNA. Annu. Rev. Biochem. 53, 791–846 (1984).

    Article  CAS  Google Scholar 

  14. Pohl, F. M. & Jovin, T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J. Mol. Biol. 67, 375–396 (1972).

    Article  CAS  Google Scholar 

  15. Seeman, N. C. in Biomolecular Materials (ed. Viney, C., Case, S. T. & Waite, J. H.) 123–134 (Symp. Proc. Vol. 292, Materials Research Soc, (1993)).

    Google Scholar 

  16. Li, X., Yang, X., Qi, J. & Seeman, N. C. Antiparallel DNA double crossover molecules as components for nanoconstruction. J. Am. Chem. Soc. 118, 6131–6140 (1996).

    Article  CAS  Google Scholar 

  17. Fu, T.-J. & Seeman, N. C. DNA double crossover structures. Biochemistry 32, 3211–3220 (1993).

    Article  CAS  Google Scholar 

  18. Sheardy, R. D. et al. Sequence dependence of the free energy of B-Z junction formation in deoxyoligonucleotides. J. Mol. Biol. 231, 475–488 (1993).

    Article  CAS  Google Scholar 

  19. Jares-Erijman, E. A. & Jovin, T. M. Determination of DNA helical handedness by fluorescence resonance energy transfer. J. Mol. Biol. 257, 597–617 (1996).

    Article  CAS  Google Scholar 

  20. Ma, R.-I., Kallenbach, N. R., Sheardy, R. D., Petrillo, M. L. & Seeman, N. C. 3-arm nucleic acid junctions are flexible. Nucleic Acids Res. 14, 9745–9753 (1986).

    Article  CAS  Google Scholar 

  21. Behe, M. & Felsenfeld, G. Effects of methylation on a synthetic polynucleotide: The B-Z transition in poly (dG-m5dC).poly (dG-m5dC). Proc. Natl Acad. Sci. USA 78, 1619–1623 (1981).

    Article  ADS  CAS  Google Scholar 

  22. Seeman, N. C. Physical models for exploring DNA topology. J. Biol. Struct. Dyn. 5, 997–1004 (1988).

    Article  CAS  Google Scholar 

  23. Seeman, N. C. DNA nanotechnology: novel DNA constructions. Annu. Rev. Biophys. Biomol. Struct. 27, 225–248 (1998).

    Article  CAS  Google Scholar 

  24. Smith, S. S. et al. Nucleoprotein-based nanoscale assembly. Proc. Natl Acad. Sci. USA 94, 2162–2167 (1997).

    Article  ADS  CAS  Google Scholar 

  25. Yang, X., Liu, B., Vologodskii, A. V., Kemper, B. & Seeman, N. C. Torsional control of double stranded DNA branch migration. Biopolymers 45, 69–83 (1998).

    Article  CAS  Google Scholar 

  26. Clegg, R. M. et al. Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction. Biochemistry 31, 4846–4856 (1992).

    Article  CAS  Google Scholar 

  27. Chattopadhyaya, R., Grzeskowiak, K. & Dickerson, R. E. Structure of a T4hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops. J. Mol. Biol. 211, 189–210 (1990).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank S. Zhang for work done on previous systems, and D. Millar, N. Geacintov and R. Sheardy for advice and for the use of equipment. This work was supported by the Office of Naval Research, the National Institute of General Medical Sciences, the National Science Foundation/DARPA and the Information Directorate of the Air Force Research Laboratory (Rome, NY).

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Correspondence to Nadrian C. Seeman.

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Mao, C., Sun, W., Shen, Z. et al. A nanomechanical device based on the B–Z transition of DNA. Nature 397, 144–146 (1999). https://doi.org/10.1038/16437

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