DNA Nanotechnology

Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 733)

Abstract

The base sequence encoded in nucleic acids yields significant structural and functional properties into the biopolymer. The resulting nucleic acid nanostructures provide the basis for the rapidly developing area of DNA nanotechnology. Advances in this field will be exemplified by discussing the following topics: (i) Hemin/G-quadruplex DNA nanostructures exhibit unique electrocatalytic, chemiluminescence and photophysical properties. Their integration with electrode surfaces or semiconductor quantum dots enables the development of new electrochemical or optical bioanalytical platforms for sensing DNA. (ii) The encoding of structural information into DNA enables the activation of autonomous replication processes that enable the ultrasensitive detection of DNA. (iii) By the appropriate design of DNA nanostructures, functional DNA machines, acting as “tweezers”, “walkers” and “stepper” systems, can be tailored. (iv) The self-assembly of nucleic acid nanostructures (nanowires, strips, nanotubes) allows the programmed positioning of proteins on the DNA templates and the activation of enzyme cascades.

Keywords

DNA Nanotechnology Sensors Machines Nanostructures 

Notes

Acknowledgement

Our research in DNA nanotechnology is supported by the Israel Science Foundation and the EC projects NANOGNOSTICS and ECCell.

References

  1. Aldaye, F. A., Palmer, A. L., & Sleiman, H. F. (2008). Assembling materials with DNA as the guide. Science, 321, 1795–1799.PubMedCrossRefGoogle Scholar
  2. Andersen, E. S., Dong, M., Nielsen, M. M., et al. (2009). Self-assembly of a nanoscale DNA box with a controllable lid. Nature, 459, 73–76.PubMedCrossRefGoogle Scholar
  3. Bath, J., & Turberfield, A. J. (2007). DNA nanomachines. Nature Nanotechnology, 2, 275–284.PubMedCrossRefGoogle Scholar
  4. Bath, J., Green, S. J., Allen, K. E., & Turberfield, A. J. (2009). Mechanism for a directional, processive, and reversible DNA motor. Small, 5, 1513–1516.PubMedCrossRefGoogle Scholar
  5. Beissenhirtz, M. K., & Willner, I. (2006). DNA-based machines. Organic and Biomolecular Chemistry, 4, 3392–3401.PubMedCrossRefGoogle Scholar
  6. Breaker, R. R., & Joyce, G. F. (1994). A DNA enzyme that cleaves RNA. Chemistry and Biology, 1, 223–229.PubMedCrossRefGoogle Scholar
  7. Buranachai, C., Mckinney, S. A., & Ha, T. (2006). Single molecule nanometronome. Nano Letters, 6, 496–500.PubMedCrossRefGoogle Scholar
  8. Cheglakov, Z., Weizmann, Y., Braunschweig, A. B., Wilner, O. I., & Willner, I. (2007). Increasing the complexity of periodic protein nanostructures by the rolling-circle amplified synthesis of aptamers. Angewandte Chemie (International ed. in English), 47, 126–130.CrossRefGoogle Scholar
  9. Dietz, H., Douglas, S. M., & Shih, W. M. (2009). Folding DNA into twisted and curved nanoscale shapes. Science, 325, 725–730.PubMedCrossRefGoogle Scholar
  10. Dittmer, W. U., Reuter, A., & Simmel, F. C. (2004). A DNA-based machine that can cyclically bind and release thrombin. Angewandte Chemie (International ed. in English), 43, 3550–3553.CrossRefGoogle Scholar
  11. Drummond, T. G., Hill, M. G., & Barton, J. K. (2003). Electrochemical DNA sensors. Nature Biotechnology, 21, 1192–1199.PubMedCrossRefGoogle Scholar
  12. Elbaz, J., Wang, Z.-G., Orbach, R., & Willner, I. (2009). pH-stimulated concurrent mechanical activation of two DNA “tweezers”. A “SET-RESET” logic gate system. Nano Letters, 9, 4510–4514.PubMedCrossRefGoogle Scholar
  13. Ellington, A. D., & Szostak, J. W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818–822.PubMedCrossRefGoogle Scholar
  14. Freeman, R., Liu, X., & Willner, I. (2011). Chemiluminescent and chemiluminescence resonance energy transfer (CRET) detection of DNA, metal ions and aptamer-substrate complexes using hemin/G-quadruplex and CdSe/ZnS quantum dots. Journal of the American Chemical Society, 133(30), 11597–11604.PubMedCrossRefGoogle Scholar
  15. Fu, T. J., & Seeman, N. C. (1993). Symmetric immobile DNA branched junctions. Biochemistry, 32, 8062–8067.PubMedCrossRefGoogle Scholar
  16. Han, X., Zhou, Z., Yang, F., & Deng, Z. (2008). Catch and release: DNA tweezers that can capture, hold, and release an object under control. Journal of the American Chemical Society, 130, 14414–14415.PubMedCrossRefGoogle Scholar
  17. He, Y., & Liu, D. R. (2010). Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker. Nature Nanotechnology, 5, 778–782.PubMedCrossRefGoogle Scholar
  18. Keren, K., Berman, R. S., Buchstab, E., Sivan, U., & Braun, E. (2003). DNA-templated carbon nanotube field-effect transistor. Science, 302, 1380–1382.PubMedCrossRefGoogle Scholar
  19. LaBean, T. H., Yan, H., Kopatsch, J., et al. (2000). Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. Journal of the American Chemical Society, 122, 1848–1860.CrossRefGoogle Scholar
  20. Lin, C., Liu, Y., Rinker, S., & Yan, H. (2006). DNA tile based self-assembly: Building complex nanoarchitectures. ChemPhysChem, 7, 1641–1647.PubMedCrossRefGoogle Scholar
  21. Lo, P. K., Karam, P., Aldaye, F. A., McLaughlin, C. K., Hamblin, G. D., Cosa, G., & Sleiman, H. F. (2010). Loading and selective release of cargo in DNA nanotubes with longitudinal variation. Nature Chemistry, 2, 319–328.PubMedCrossRefGoogle Scholar
  22. Mathieu, F., Liao, S., Kopatsch, J., Wang, T., Mao, C., & Seeman, N. C. (2005). Six-helix bundles designed from DNA. Nano Letters, 5, 661–665.PubMedCrossRefGoogle Scholar
  23. Mayer, G. (2009). The chemical biology of aptamers. Angewandte Chemie (International ed. in English), 48, 2672–2689.CrossRefGoogle Scholar
  24. Pelossof, G., Tel-Vered, R., Elbaz, J., & Willner, I. (2010). Amplified biosensing using the horseradish peroxidase-mimicking DNAzyme as an electrocatalyst. Analytical Chemistry, 82, 4396–4402.PubMedCrossRefGoogle Scholar
  25. Phan, A. T., & Mergny, J. (2002). Human telomeric DNA: G-quadruplex, i-motif and Watson-crick double helix. Nucleic Acids Research, 30, 4618–4625.PubMedCrossRefGoogle Scholar
  26. Rothemund, P. W. K. (2006). Folding DNA to create nanoscale shapes and patterns. Nature, 440, 297–302.PubMedCrossRefGoogle Scholar
  27. Seeman, N. C. (2007). An overview of structural DNA nanotechnology. Molecular Biotechnology, 37, 246–257.PubMedCrossRefGoogle Scholar
  28. Seeman, N. C. (2010). Structural DNA nanotechnology: Growing along with nano letters. Nano Letters, 10, 1971–1978.PubMedCrossRefGoogle Scholar
  29. Sharma, J., Chhabra, R., Cheng, A., Brownell, J., Liu, Y., & Yan, H. (2009). Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science, 323, 112–116.PubMedCrossRefGoogle Scholar
  30. Sharon, E., Freeman, R., & Willner, I. (2010). CdSe/ZnS quantum dots-G-quadruplex/hemin hybrids as optical DNA sensors and aptasensors. Analytical Chemistry, 82, 7073–7077.PubMedCrossRefGoogle Scholar
  31. Shih, J., & Pierce, N. A. (2004). A synthetic DNA walker for molecular transport. Journal of the American Chemical Society, 126, 10834–10835.CrossRefGoogle Scholar
  32. Simmel, F. C. (2007). Towards biomedical applications for nucleic acid nanodevices. Nanomedicine, 2, 817–830.PubMedCrossRefGoogle Scholar
  33. Teller, C., & Willner, I. (2010). Functional nucleic acid nanostructures and DNA machines. Current Opinion in Biotechnology, 21, 376–391.PubMedCrossRefGoogle Scholar
  34. Tombelli, S., & Mascini, M. (2009). Aptamers as molecular tools for bioanalytical methods. Current Opinion in Molecular Therapeutics, 11, 179–188.PubMedGoogle Scholar
  35. Tuerk, C., & Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505–510.PubMedCrossRefGoogle Scholar
  36. Wang, Z.-G., Elbaz, J., Remacle, F., Levine, R. D., & Willner, I. (2010). All-DNA finite-state automata with finite memory. Proceedings of the National Academy of Sciences of the United States of America, 107, 21996–22001.PubMedCrossRefGoogle Scholar
  37. Wang, F., Elbaz, J., Teller, C., & Willner, I. (2011a). Amplified detection of DNA through an autocatalytic and catabolic DNAzyme-mediated process. Angewandte Chemie (International ed. in English), 50, 295–299.CrossRefGoogle Scholar
  38. Wang, Z.-G., Elbaz, J., & Willner, I. (2011b). DNA machines: Bipedal walker and stepper. Nano Letters, 11, 304–309.PubMedCrossRefGoogle Scholar
  39. Weizmann, Y., Beissenhirtz, M. K., Cheglakov, Z., Nowarski, R., Kotler, M., & Willner, I. (2006). A virus spotlighted by an autonomous DNA machine. Angewandte Chemie (International ed. in English), 45, 7384–7388.CrossRefGoogle Scholar
  40. Willner, I., & Zayats, M. (2007). Electronic aptamer-based sensors. Angewandte Chemie (International ed. in English), 46, 6408–6418.CrossRefGoogle Scholar
  41. Willner, I., Shlyahovsky, B., Zayats, M., & Willner, B. (2008). DNAzymes for sensing, nanobiotechnology and logic gate applications. Chemical Society Reviews, 37, 1153–1165.PubMedCrossRefGoogle Scholar
  42. Wilner, O. I., Weizmann, Y., Gill, R., Lioubashevski, O., Freeman, R., & Willner, I. (2009). Enzyme cascades activated on topologically programmed DNA scaffolds. Nature Nanotechnology, 4, 249–254.PubMedCrossRefGoogle Scholar
  43. Wilner, O. I., Henning, A., Shlyahovsky, B., & Willner, I. (2010). Covalently linked DNA nanotubes. Nano Letters, 10, 1458–1465.PubMedCrossRefGoogle Scholar
  44. Xiao, Y., Pavlov, V., Gill, R., & BourenkoT, W. I. (2004). Lighting up biochemiluminescence by the surface self-assembly of DNA-hemin complexes. ChemBioChem, 5, 374–379.PubMedCrossRefGoogle Scholar
  45. Yurke, B., Turberfield, A. J., Mills, A. P., Simmel, F. C., & Neumann, J. L. (2000). A DNA-fuelled molecular machine made of DNA. Nature, 406, 605–608.PubMedCrossRefGoogle Scholar
  46. Zhao, W., Gao, Y., Srinivas, A., et al. (2006). DNA polymerization on gold nanoparticles through rolling circle ­amplification: Towards novel scaffolds for three-dimensional periodic nanoassemblies. Angewandte Chemie (International ed. in English), 45, 2409–2413.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Ofer I. Wilner
    • 1
  • Bilha Willner
    • 1
  • Itamar Willner
    • 1
  1. 1.Institute of ChemistryThe Hebrew University of JerusalemJerusalemIsrael

Personalised recommendations