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

Methods in Molecular Biology

Volumn 749, Issue , 2011, Pages 169-185

  Palma, Matteo ^a   Abramson, Justin J ^b   Gorodetsky, Alon A ^b   Nuckolls, Colin ^b   Sheetz, Michael P ^b   Wind, Shalom J ^b   Hone, James ^b  

^a Howard Hughes Medical Institute   (United States)

^b NONE

Author keywords

DNA; Fluorescence microscopy; Nanoscale; Nanotechnology; Self assembly

Indexed keywords

DNA; DNA BINDING PROTEIN; GLASS; GOLD; NANOMATERIAL; PALLADIUM;

ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY; IMMOBILIZATION; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; SURFACE PROPERTY;

DNA; DNA-BINDING PROTEINS; GLASS; GOLD; IMMOBILIZATION; MICROSCOPY, ATOMIC FORCE; NANOSTRUCTURES; NANOTECHNOLOGY; PALLADIUM; SURFACE PROPERTIES;

EID: 84855166358     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-142-0_12     Document Type: Chapter

References (32)

1. Whitesides, G. M. (2003) The ‘right’ size in nanobiotechnology, Nat Biotechnol 21, 1161–1165.
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.
3. Rosi, N. L., and Mirkin, C. A. (2005) Nanostructures in biodiagnostics, Chem Rev 105, 1547–1562.
4. Langer, R., and Tirrell, D. A. (2004) Designing materials for biology and medicine, Nature 428, 487–492.
5. Wong, L. S., Khan, F., and Micklefield, J. (2009) Selective Covalent Protein Immobilization: Strategies and Applications, Chem Rev 109, 4025–4053.
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.
7. Winssinger, N., Pianowski, Z., and Debaene, F. (2007) Probing biology with small molecule microarrays (SMM), Top Curr Chem 278, 311–342.
8. Nanobiotechnology Wiley-VCH, Weinheim.
9. Nanofabrication Towards Biomedical Applications, Wiley-VCH, Weinheim.
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.
11. Becerril, H. A., and Woolley, A. T. (2009) DNA-templated nanofabrication, Chem Soc Rev 38, 329–337.
12. Niemeyer, C. M. (2001) Nanoparticles, proteins, and nucleic acids: Biotechnology meets materials science, Angew Chem Int Edit 40, 4128–4158.
13. Drummond, T. G., Hill, M. G., and Barton, J. K. (2003) Electrochemical DNA sensors, Nat Biotechnol 21, 1192–1199.
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.
15. Brucale, M., Zuccheri, G., and Samori, B. (2006) Mastering the complexity of DNA nanostructures, Trends Biotechnol 24, 235–243.
16. Methods in Molecular Biology Vol. 170, Humana Press, Totowa, NJ.
17. Nanobiotechnology II, Wiley-VCH, Weinheim.
18. Heise, C., and Bier, F. F. (2005) Immobilization of DNA on microarrays, Top Curr Chem 261, 1–25.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
31. Methods in Enzymology Vol. 184, Academic press.
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.