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The Atomic Force Microscopy as a Lithographic Tool: Nanografting of DNA Nanostructures for Biosensing Applications

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Book cover DNA Nanotechnology

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

Abstract

Current in vitro techniques cannot accurately identify small differences in concentration in samples containing few molecules in single or few cells. Nanotechnology overcomes these limitations with the possibility of measuring protein amounts down to a hundred molecules and subnanomolar concentrations and in nanoliter to picoliter volumes. The nanoscale approach, therefore, permits measurements in samples consisting of single or few cells. Atomic force microscopy (AFM) nanografting can be utilized to prepare DNA nanopatches of different sizes (from few hundreds of nanometers to few microns in size) onto which DNA–antibody conjugates can be anchored through DNA-directed immobilization. AFM height measurements are used to assess the binding of the proteins as well as their subsequent interaction with other components, such as specific proteins from the serum. Recent results have contributed to demonstrate that nanografted patch arrays are well suited for application in biosensing and could enable the fabrication of multifeature protein nanoarrays.

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References

  1. Jonkheijm, P., Weinrich, D., Schroder, H., Niemeyer, C. M., Waldmann, H. (2008) Chemical Strategies for Generating Protein Biochips Angewandte Chemie-International Edition 47, 9618–9647.

    Google Scholar 

  2. Sobek, J., Bartscherer, K., Jacob, A., Hoheisel, J. D., Angenendt, P. (2006) Microarray technology as a universal tool for high-throughput analysis of biological systems Combinatorial Chemistry & High Throughput Screening 9, 365–380.

    Google Scholar 

  3. Phizicky, E., Bastiaens, P. I. H., Zhu, H., Snyder, M., Fields, S. (2003) Protein analysis on a proteomic scale Nature 422, 208–215.

    Google Scholar 

  4. Tomizaki, K.-Y., Usui, K., Mihara, H. (2005) Protein-Detecting Microarrays: Current Accomplishments and Requirements ChemBioChem 6, 782–799.

    Google Scholar 

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

    Google Scholar 

  6. Lim, J.-H., Ginger, D. S., Lee, K.-B., Heo, J., Nam, J.-M., Mirkin, C. A. (2003) Direct-Write Dip-Pen Nanolithography of Proteins on Modified Silicon Oxide Surfaces13 Angewandte Chemie International Edition 42, 2309–2312.

    Google Scholar 

  7. Salaita, K., Wang, Y. H., Mirkin, C. A. (2007) Applications of dip-pen nanolithography Nature Nanotechnology 2, 145–155.

    Google Scholar 

  8. Leggett, G. J. (2005) Biological nanostructures: platforms for analytical chemistry at the sub-zeptomolar level Analyst 130, 259–264.

    Google Scholar 

  9. Coyer, S. R., Garcia, A. J., Delamarche, E. (2007) Facile preparation of complex protein architectures with sub-100-nm resolution on surfaces Angewandte Chemie-International Edition 46, 6837–6840.

    Google Scholar 

  10. Mirmomtaz, E., Castronovo, M., Grunwald, C., Bano, F., Scaini, D., Ensafi, A. A., Scoles, G., Casalis, L. (2008) Quantitative Study of the Effect of Coverage on the Hybridization Efficiency of Surface-Bound DNA Nano­structures Nano Letters 8, 4134–4139.

    Google Scholar 

  11. Liu, M. Z., Liu, G. Y. (2005) Hybridization with nanostructures of single-stranded DNA Langmuir 21, 1972–1978.

    Google Scholar 

  12. Xu, S., Miller, S., Laibinis, P. E., Liu, G. Y. (1999) Fabrication of nanometer scale patterns within self-assembled monolayers by nanografting Langmuir 15, 7244–7251.

    Google Scholar 

  13. Liu, M. Z., Amro, N. A., Chow, C. S., Liu, G. Y. (2002) Production of nanostructures of DNA on surfaces Nano Letters 2, 863–867.

    Google Scholar 

  14. Castronovo, M., Radovic, S., Grunwald, C., Casalis, L., Morgante, M., Scoles, G. (2008) Control of Steric Hindrance on Restriction Enzyme Reactions with Surface-Bound DNA Nanostructures Nano Letters 8, 4140–4145.

    Google Scholar 

  15. Niemeyer, C. M., Sano, T., Smith, C. L., Cantor, C. R. (1994) Oligonucleotide-directed self-assembly of proteins: semisynthetic DNA – streptavidin hybrid molecules as connectors for the generation of macroscopic arrays and the construction of supramolecular bioconjugates Nucl Acids Res 22, 5530–5539.

    Google Scholar 

  16. Becker, C. F. W., Wacker, R., Bouschen, W., Seidel, R., Kolaric, B., Lang, P., Schroeder, H., Müller, O., Niemeyer, C. M., Spengler, B., Goody, R. S., Engelhard, M. (2005) Direct Readout of Protein-Protein Interactions by Mass Spectrometry from Protein-DNA Microarrays13 Angewandte Chemie International Edition 44, 7635–7639.

    Google Scholar 

  17. Fruk, L., Müller, J., Weber, G., Narvaez, A., Dominguez, E., Niemeyer, C. M. (2007) DNA-Directed immobilization of horseradish peroxidase-DNA conjugates on microelectrode arrays: Towards electrochemical screening of enzyme libraries Chemistry-a European Journal 13, 5223–5231.

    Google Scholar 

  18. Schroeder, H., Adler, M., Gerigk, K., Müller-Chorus, B., Götz, F., Niemeyer, C. M. (2009) User Configurable Microfluidic Device for Multiplexed Immunoassays Based on DNA-Directed Assembly Analytical Chemistry 81, 1275–1279.

    Google Scholar 

  19. Schroeder, H., Ellinger, B., Becker, C. F. W., Waldmann, H., Niemeyer, C. M. (2007) Generation of live-cell microarrays by means of DNA-directed immobilization of specific cell-surface ligands Angewandte Chemie-International Edition 46, 4180–4183.

    Google Scholar 

  20. Wacker, R., Niemeyer, C. M. (2004) DDI-μFIA – A Readily Configurable Microarray-Fluorescence Immunoassay Based on DNA-Directed Immobilization of Proteins ChemBioChem 5, 453–459.

    Google Scholar 

  21. Wacker, R., Schröder, H., Niemeyer, C. M. (2004) Performance of antibody microarrays fabricated by either DNA-directed immobilization, direct spotting, or streptavidin-biotin attachment: a comparative study Analytical Biochemistry 330, 281–287.

    Google Scholar 

  22. Liu, M., Amro, N. A., Liu, G. Y. (2008) Nanografting for surface physical chemistry Annual Review of Physical Chemistry 59, 367–386.

    Google Scholar 

  23. Niemeyer, C. M. (2007) Functional devices from DNA and proteins Nano Today 2, 42–52.

    Google Scholar 

  24. Bano, F., Fruk, L., Sanavio, B., Glettenberg, M., Casalis, L., Niemeyer, C. M., Scoles, G. (2009) Toward Multiprotein Nanoarrays Using Nanografting and DNA Directed Immobilization of Proteins Nano Letters 9, 2614–2618.

    Google Scholar 

  25. Gupta, P., Loos, K., Korniakov, A., Spagnoli, C., Cowman, M., Ulman, A. (2004) Facile route to ultraflat SAM-protected gold surfaces by “amphiphile splitting” Angewandte Chemie-International Edition 43, 520–523.

    Google Scholar 

  26. Generally EG terminated SAMs resist the unspecific adsorption of biomolecules. (a) Kane, R. S.; Deschatelets, P.; Whitesides, G. M. Langmuir 2003, 19, 2388. (b) Harder, P.; Grunze, M.; Dahint, R.; Whitesides, G. M.; Laibinis, P. E. J. Phys. Chem. B 1998, 102, 426.

    Google Scholar 

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Acknowledgments

The authors are grateful to Dr. Loredana Casalis (ELETTRA Synchrotron Laboratory, Trieste, Italy), Prof. Giacinto Scoles (ICS-UNIDO and SISSA, Trieste, Italy and Temple University, Philadelphia, PA), the SISSA – Scuola Internazionale Superiore di Studi Avanzati (Trieste, Italy), the Italian Institute of Technology (Trieste Unit @ SISSA, Trieste, Italy), the CBM S.c.r.l. – Cluster in Molecular Biomedicine (Trieste, Italy), Dr. Jian Liang, (Columbia University, NY), and Prof. Gang-yu Liu (UC Davis, CA).

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Correspondence to Matteo Castronovo .

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Castronovo, M., Scaini, D. (2011). The Atomic Force Microscopy as a Lithographic Tool: Nanografting of DNA Nanostructures for Biosensing Applications. 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_15

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  • DOI: https://doi.org/10.1007/978-1-61779-142-0_15

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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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