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Controlled Confinement of DNA at the Nanoscale: Nanofabrication and Surface Bio-Functionalization

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DNA Nanotechnology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 749))

Abstract

Nanopatterned arrays of biomolecules are a powerful tool to address fundamental issues in many areas of biology. DNA nanoarrays, in particular, are of interest in the study of DNA–protein interactions and for biodiagnostic investigations. In this context, achieving a highly specific nanoscale assembly of oligonucleotides at surfaces is critical. In this chapter, we describe a method to control the immobilization of DNA on nanopatterned surfaces; the nanofabrication and the bio-functionalization involved in the process will be discussed.

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References

  1. Whitesides, G. M. (2003) The ‘right’ size in nanobiotechnology, Nat Biotechnol 21, 1161–1165.

    Article  CAS  Google Scholar 

  2. Torres, A. J., Wu, M., Holowka, D., and Baird, B. (2008) Nanobiotechnology and cell biology: Micro- and nanofabricated surfaces to investigate receptor-mediated signaling, Ann Rev Biophys 37, 265–288.

    Article  CAS  Google Scholar 

  3. Rosi, N. L., and Mirkin, C. A. (2005) Nanostructures in biodiagnostics, Chem Rev 105, 1547–1562.

    Article  CAS  Google Scholar 

  4. Langer, R., and Tirrell, D. A. (2004) Designing materials for biology and medicine, Nature 428, 487–492.

    Article  CAS  Google Scholar 

  5. Wong, L. S., Khan, F., and Micklefield, J. (2009) Selective Covalent Protein Immobilization: Strategies and Applications, Chem Rev 109, 4025–4053.

    Article  CAS  Google Scholar 

  6. Williams, B. A. R., Lund, K., Liu, Y., Yan, H., and Chaput, J. C. (2007) Self-assembled peptide nanoarrays: An approach to studying protein-protein interactions, Angew Chem Int Edit 46, 3051–3054.

    Article  CAS  Google Scholar 

  7. Winssinger, N., Pianowski, Z., and Debaene, F. (2007) Probing biology with small molecule microarrays (SMM), Top Curr Chem 278, 311–342.

    Article  CAS  Google Scholar 

  8. (2004) Nanobiotechnology Wiley-VCH, Weinheim.

    Google Scholar 

  9. (2005) Nanofabrication Towards Biomedical Applications, Wiley-VCH, Weinheim.

    Google Scholar 

  10. Tan, P. K., Downey, T. J., Spitznagel, E. L., Xu, P., Fu, D., Dimitrov, D. S., Lempicki, R. A., Raaka, B. M., and Cam, M. C. (2003) Evaluation of gene expression measurements from commercial microarray platforms, Nucleic Acids Res 31, 5676–5684.

    Article  CAS  Google Scholar 

  11. Becerril, H. A., and Woolley, A. T. (2009) DNA-templated nanofabrication, Chem Soc Rev 38, 329–337.

    Article  CAS  Google Scholar 

  12. Niemeyer, C. M. (2001) Nanoparticles, proteins, and nucleic acids: Biotechnology meets materials science, Angew Chem Int Edit 40, 4128–4158.

    Article  CAS  Google Scholar 

  13. Drummond, T. G., Hill, M. G., and Barton, J. K. (2003) Electrochemical DNA sensors, Nat Biotechnol 21, 1192–1199.

    Article  CAS  Google Scholar 

  14. Rant, U., Arinaga, K., Scherer, S., Pringsheim, E., Fujita, S., Yokoyama, N., Tornow, M., and Abstreiter, G. (2007) Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets, P Natl Acad Sci USA 104, 17364–17369.

    Article  CAS  Google Scholar 

  15. Brucale, M., Zuccheri, G., and Samori, B. (2006) Mastering the complexity of DNA nanostructures, Trends Biotechnol 24, 235–243.

    Article  CAS  Google Scholar 

  16. (2002) Methods in Molecular Biology Vol. 170, Humana Press, Totowa, NJ.

    Google Scholar 

  17. (2007) Nanobiotechnology II, Wiley-VCH, Weinheim.

    Google Scholar 

  18. Heise, C., and Bier, F. F. (2005) Immobilization of DNA on microarrays, Top Curr Chem 261, 1–25.

    CAS  Google Scholar 

  19. Luderer, F., and Walschus, U. (2005) Immobilization of oligonucleoticles for biochemical sensing by self-assembled monolayers: Thiol-organic bonding on gold and silanization on silica surfaces, Top Curr Chem 260, 37–56.

    Article  CAS  Google Scholar 

  20. Murphy, J. N., Cheng, A. K. H., Yu, H. Z., and Bizzotto, D. (2009) On the Nature of DNA Self-Assembled Monolayers on Au: Measuring Surface Heterogeneity with Electrochemical in Situ Fluorescence Microscopy, J Am Chem Soc 131, 4042–4050.

    Article  CAS  Google Scholar 

  21. Shumaker-Parry, J. S., Zareie, M. H., Aebersold, R., and Campbell, C. T. (2004) Microspotting streptavidin and double-stranded DNA Arrays on gold for high-throughput studies of protein-DNA interactions by surface plasmon resonance microscopy, Anal Chem 76, 918–929.

    Article  CAS  Google Scholar 

  22. Smith, C. L., Milea, J. S., and Nguyen, G. H. (2005) Immobilization of nucleic acids using biotin-strept(avidin) systems, Top Curr Chem 261, 63–90.

    Article  CAS  Google Scholar 

  23. Takahashi, S., Matsuno, H., Furusawa, H., and Okahata, Y. (2007) Kinetic analyses of divalent cation-dependent EcoRV digestions on a DNA-immobilized quartz crystal microbalance, Anal Biochem 361, 210–217.

    Article  CAS  Google Scholar 

  24. Ladd, J., Boozer, C., Yu, Q. M., Chen, S. F., Homola, J., and Jiang, S. (2004) DNA-directed protein immobilization on mixed self-assembled monolayers via a Streptavidin bridge, Langmuir 20, 8090–8095.

    Article  CAS  Google Scholar 

  25. Whitesides, G. M., Ostuni, E., Takayama, S., Jiang, X. Y., and Ingber, D. E. (2001) Soft lithography in biology and biochemistry, Annu Rev Biomed Eng 3, 335–373.

    Article  CAS  Google Scholar 

  26. Noh, H., Hung, A. M., Choi, C., Lee, J. H., Kim, J. Y., Jin, S., and Cha, J. N. (2009) 50 nm DNA Nanoarrays Generated from Uniform Oligonucleotide Films, Acs Nano 3, 2376–2382.

    Article  CAS  Google Scholar 

  27. Yu, A. A., Savas, T. A., Taylor, G. S., Guiseppe-Elie, A., Smith, H. I., and Stellacci, F. (2005) Supramolecular nanostamping: Using DNA as movable type, Nano Lett 5, 1061–1064.

    Article  CAS  Google Scholar 

  28. Demers, L. M., Ginger, D. S., Park, S. J., Li, Z., Chung, S. W., and Mirkin, C. A. (2002) Direct patterning of modified oligonucleotides on metals and insulators by dip-pen nanolithography, Science 296, 1836–1838.

    Article  CAS  Google Scholar 

  29. Rodolfa, K. T., Bruckbauer, A., Zhou, D. J., Korchev, Y. E., and Klenerman, D. (2005) Two-component graded deposition of biomolecules with a double-barreled ­nanopipette, Angew Chem Int Edit 44, 6854–6859.

    Article  CAS  Google Scholar 

  30. Cherniavskaya, O., Chen, C. J., Heller, E., Sun, E., Provezano, J., Kam, L., Hone, J., Sheetz, M. P., and Wind, S. J. (2005) Fabrication and surface chemistry of nanoscale bioarrays designed for the study of cytoskeletal protein binding interactions and their effect on cell motility, J Vac Sci Technol B 23, 2972–2978.

    Article  CAS  Google Scholar 

  31. (1990) Methods in Enzymology Vol. 184, Academic press.

    Google Scholar 

  32. Nelson, K. E., Gamble, L., Jung, L. S., Boeckl, M. S., Naeemi, E., Golledge, S. L., Sasaki, T., Castner, D. G., Campbell, C. T., and Stayton, P. S. (2001) Surface characterization of mixed self-assembled monolayers designed for streptavidin immobilization, Langmuir 17, 2807–2816.

    Article  CAS  Google Scholar 

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Acknowledgments

We gratefully acknowledge support from the office of Naval Research under award number N00014-09-1-1117, National Institutes of Health through award number PN2EY016586 under the NIH Roadmap for Medical Research, and from the National Science Foundation under NSF award number EF-05-07086 and award number CHE-0936923. Additional support from the Nanoscale Science and Engineering Initiative of the National Science Foundation under NSF Award Number CHE-0641523 and from the New York State Office of Science, Technology, and Academic Research (NYSTAR) is also gratefully acknowledged.

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Correspondence to Matteo Palma .

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Palma, M. et al. (2011). Controlled Confinement of DNA at the Nanoscale: Nanofabrication and Surface Bio-Functionalization. In: Zuccheri, G., Samorì, B. (eds) DNA Nanotechnology. Methods in Molecular Biology, vol 749. Humana Press. https://doi.org/10.1007/978-1-61779-142-0_12

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  • DOI: https://doi.org/10.1007/978-1-61779-142-0_12

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-141-3

  • Online ISBN: 978-1-61779-142-0

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