Nanotechnology

Moving From Microarrays Toward Nanoarrays

  • Protocol
Microarrays

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 381))

Abstract

Microarrays are important tools for high-throughput analysis of biomolecules. The use of microarrays for parallel screening of nucleic acid and protein profiles has become an industry standard. A few limitations of microarrays are the requirement for relatively large sample volumes and elongated incubation time, as well as the limit of detection. In addition, traditional microarrays make use of bulky instrumentation for the detection, and sample amplification and labeling are quite laborious, which increase analysis cost and delays the time for obtaining results. These problems limit microarray techniques from point-of-care and field applications. One strategy for overcoming these problems is to develop nanoarrays, particularly electronicsbased nanoarrays. With further miniaturization, higher sensitivity, and simplified sample preparation, nanoarrays could potentially be employed for biomolecular analysis in personal healthcare and monitoring of trace pathogens. In this chapter, it is intended to introduce the concept and advantage of nanotechnology and then describe current methods and protocols for novel nanoarrays in three aspects: (1) label-free nucleic acids analysis using nanoarrays, (2) nanoarrays for protein detection by conventional optical fluorescence microscopy as well as by novel label-free methods such as atomic force microscopy, and (3) nanoarray for enzymatic-based assay. These nanoarrays will have significant applications in drug discovery, medical diagnosis, genetic testing, environmental monitoring, and food safety inspection.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free ship** worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Li, J., Ng, H. T., and Chen, H. (2005) Carbon nanotube and nanowires for biological sensing, in Protein Nanotechnology, Protocols, Instrumentation and Applications, (Vo-Dinh, T., ed.), Humana, Totowa, NJ, pp. 191–223.

    Google Scholar 

  2. Li, J., Ng, H. T., Cassell, A., et al. (2003) Carbon nanotube nanoelectrode array for ultrasensitive DNA detection. Nano Lett. 3, 597–602.

    Article  CAS  Google Scholar 

  3. Koehne, J., Chen, H., Li, J., et al. (2003) Ultrasensitive label-free electronic method for DNA analysis using carbon nanotube nanoelectrode array. Nanotechnology 14, 1239–1245.

    Article  CAS  Google Scholar 

  4. Piner, R. D., Zhu, J., Xu, F., Hong, S., and Mirkin, C. A. (1999) “Dip-Pen” nanolithography. Science 283, 661

    Article  CAS  Google Scholar 

  5. Lee, K.-B., Park, S. J., Mirkin, C. A., Smith, J. C., and Mrksich, M. (2002) Protein nanoarrays generated by dip-pen nanolithography. Science 295, 1702.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Ginger, D. S., Zhang, H., and Mirkin, C. A. (2004) The evolution of Dip-Pen nanolithography. Angew. Chem., Int. Ed. 43, 30.

    Article  Google Scholar 

  8. Bruckbauer, A., Zhou, D., Kang, D. J., Korchev, Y. E., Abell, C., and Klenerman, D. (2004) An addressable antibody nanoarray produced on a nanostructured surface. J. Am. Chem. Soc. 126, 6508–6509.

    Article  CAS  Google Scholar 

  9. Lynch, M., Mosher, C., Huff, J., Nettikadan, S., Johnson, J., and Henderson, E. (2004) Functional protein nanoarrays for biomarker profiling. Proteomics 4, 1695–1702.

    Article  CAS  Google Scholar 

  10. Lee, K. B., Kim, E.-Y., Mirkin, C. A., and Wolinsky, S. M. (2004). The use of nanoarrays for highly sensitive and selective detection of human immunodeficiency Virus Type 1 in Plasma. Nano Lett. 4, 1869–1872.

    Article  CAS  Google Scholar 

  11. Wang, J. (2005) Carbon-nanotube based electrochemical biosensors: a review. Electroanalysis 17, 7–14.

    Article  CAS  Google Scholar 

  12. Dietrich, H. R., Knoll, J., van den Doel, L. R., et al. (2004) Nanoarrays: a method for performing enzymatic assays. Anal. Chem. 76, 4112–4117.

    Article  CAS  Google Scholar 

  13. Feynman, R. P. (1960) There’s plenty of room at the bottom: an invitation to enter a new field of physics. Engineering Sci: http://www.zyvex.com/nanotech/feynman.html (accessed Feb 2, 2005).

    Google Scholar 

  14. Drexler, K. E. (1986) Engines of Creation. Anchor Press/Doubleday, New York.

    Google Scholar 

  15. Iijima, S. (1991) Helical microtubules of graphitic carbon. Nature 354, 56–58.

    Article  CAS  Google Scholar 

  16. Ferrari, M. (2005) Cancer nanotechnology: opportunities and challenges. Nat. Rev. Cancer 5, 161–171.

    Article  CAS  Google Scholar 

  17. Silva, G. A. (2004) Introduction to nanotechnology and its applications to medicine. Surg. Neurol. 61, 216–220.

    Article  Google Scholar 

  18. Stix, G. (2001) Little big science. Scientific American 285, 32–37.

    Article  CAS  Google Scholar 

  19. Fortina, P., Kricka, L. J., Surrey, S., and Grodzinski, P. (2005) Nanobiotechnology: the promise and reality of new approaches to molecular recognition. Trends Biotechnol. 23, 168–173.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  21. Emerich, D. F. (2005) Nanomedicine—prospective therapeutic and diagnostic applications. Expert. Opin. Biol. Ther. 5, 1–5.

    Article  CAS  Google Scholar 

  22. Silva, G. A. (2005) Nanotechnology approaches for the regeneration and neuroprotection of the central nervous system. Surg. Neurol. 63, 301–306.

    Article  Google Scholar 

  23. Dresselhaus, M. S., Dresselhaus, G., and Eklund, P. C. (eds.) (1996) Science of Fullerenes and Carbon Nanotubes. Academic Press, New York.

    Google Scholar 

  24. Meyyappan, M. (ed.) (2004) Carbon Nanotubes: Science and Applications. CRC Press, Boca Raton, FL.

    Google Scholar 

  25. McCreery, R. L. (1991) Carbon electrodes: structural effects on electron transfer kinetics, in Electroanalytical Chemistry, vol. 1 (Bard, A. J., ed.), Marcel Dekker, New York, pp. 221–374.

    Google Scholar 

  26. Koehne, J., Li, J., Cassell, A. M., et al. (2004) The fabrication and electrochemical characterization of carbon nanotube nanoelectrode arrays. J. Matr. Chem. 14, 676–684.

    Article  CAS  Google Scholar 

  27. Bard, A. J. and Faulkner, L. R. (eds.) (2001) Electrochemical Methods: Fundamentals and Applications, 2nd ed. Wiley, New York.

    Google Scholar 

  28. Wightman, R. M. (1981) Microvoltammetric electrodes. Anal. Chem. 53, 1125A–1134A.

    Article  CAS  Google Scholar 

  29. Fan, F. R. F. and Bard, A. J. (1995) Electrochemical detection of single molecules. Science 267, 871.

    Article  CAS  Google Scholar 

  30. Menon, V. P. and Martin, C. R. (1995) Fabrication and evaluation of nanoelectrode ensemble. Anal. Chem. 67, 1920.

    Article  CAS  Google Scholar 

  31. Peterson, A. W., Heaton, R. J., and Georgiadis, R. M. (2001) The effect of surface probe density on DNA hybridization. Nucleic Acids Res. 29, 5163–5168.

    Article  CAS  Google Scholar 

  32. Peterson, A. W., Wolf, L. K., and Georgiadis, R. M. (2002) Hybridization of mismatched or partially matched DNA at surfaces. J. Am. Chem. Soc. 124, 14,601–14,607.

    Article  CAS  Google Scholar 

  33. Dorris, D. R., Nguyen, A., Gieser, L., et al. (2003) Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios. BMC Biotechnol. 3, 1472–1483.

    Article  Google Scholar 

  34. Yao, D., Kim, J., Yu, F., Nielsen, P. E., Sinner, E.-K., and Knoll, W. (2005) Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers. Biophys. J. 88, 2745–2751.

    Article  CAS  Google Scholar 

  35. Heaton, R. J., Peterson, A. W., and Georgiadis, R. M. (2001) Electrostatic surface plasmon resonance: direct electric field-induced hybridization and denaturation in monolayer nucleic acid films and label-free diacrimination of base mismatches. Proc. Natl. Acad. Sci. USA 98, 3701–3704.

    Article  CAS  Google Scholar 

  36. Sosnowski, R. G., Tu, E., Butler, W. F., O’Connell, J. P., and Heller, M. J. (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl. Acad. Sci. USA 94, 1119.

    Article  CAS  Google Scholar 

  37. Popovich, N. D. and Thorp, H. H. (2002) New strategies for electrochemical nucleic acid detection. Interface 11, 30.

    CAS  Google Scholar 

  38. Einstein, A. (1956) On the movement of small particles suspended in a stationary liquid demanded by the molecular kinetic theory of heat, in Investigations on the Theory of the Brownian Movement (Furth, R., and Cowper, A. D. eds.), Dover, New York, pp. 1–18.

    Google Scholar 

  39. Dresselhaus, M. S., Dresselhaus, G., and Eklund, P. C. (eds.) (1996) Science of Fullerenes and Carbon Nanotubes. Academic Press, New York.

    Google Scholar 

  40. Ebbesen, T. W. (ed.) (1996) Carbon Nanotubes: Preparation and Properties. CRC Press, Boca Raton, FL.

    Google Scholar 

  41. Saito, R., Dresselhaus, M. S., and Dresselhaus, G. (eds.) (1998) Physical Properties of Carbon Nanotubes. World Scientific, New York.

    Google Scholar 

  42. Tománek, D. and Enbody, R. (eds.) (2000) Science and Application of Nanotubes. Kluwer Academic, New York.

    Google Scholar 

  43. Collins, P. G., Arnold, M. S., and Avouris, P. (2001) Engineering carbon nanotubes and nanotube circuits using electrical breakdown. Science 292, 706–709.

    Article  CAS  Google Scholar 

  44. Tans, S. J., Verschueren, A. R. M., and Dekker, C. (1998) Room-temperature transistor based on a single carbon nanotube. Natur 393, 49–52.

    Article  CAS  Google Scholar 

  45. Fuhrer, M. S., Nygard, J., Shih, L., et al. (2000) Crossed nanotube junctions. Science 288, 494–497.

    Article  CAS  Google Scholar 

  46. Zhou, C. W., Kong, J., Yenilmez, E., and Dai, H. (2000) Modulated chemical do** of individual carbon nanotubes. Science 290, 1552–1555.

    Article  CAS  Google Scholar 

  47. Rueckes, T., Kim, K., Joselevich, E., Tseng, G. Y., Cheung, C. L., and Lieber, C. M. (2000) Carbon nanotube-based nonvolatile random access memory for molecular computing. Science 289, 94–97.

    Article  CAS  Google Scholar 

  48. Derycke, V., Martel, R., Appenzeller, J., and Avouris, Ph. (2001) Carbon Nanotube inter-and intramolecular logic gates. Nano Lett. 1, 453–456.

    Article  CAS  Google Scholar 

  49. Bachtold, A., Hadley, P., Nakanishi, T., and Dekker, C. (2001) Logic circuits with carbon nanotube transistors. Science 294, 1317–1320.

    Article  CAS  Google Scholar 

  50. Liu, X. L., Lee, C., Zhou, C. W., and Han, J. (2001) Carbon nanotube field-effect inverters. Appl. Phys. Lett. 79, 3329–3331.

    Article  CAS  Google Scholar 

  51. Rosenblatt, S., Yaish, Y., Park, J., Gore, J., Sazonova, V., and McEuen, P. L. (2002) High performance electrolyte gated carbon nanotube transistors. Nano Lett. 2, 869–872.

    Article  CAS  Google Scholar 

  52. Vigolo, B., Penicaud, A., Coulon, C., et al. (2000) Macroscopic fibers and ribbons of oriented carbon nanotubes. Science 290, 1331–1334.

    Article  CAS  Google Scholar 

  53. de Heer, W. A., Chatelain, A., and Ugarte, D. (1995) A carbon nanotube field-emission electron source. Science 270, 1179–1180.

    Article  Google Scholar 

  54. Rinzler, A. G., Hafner, J. H., Nikolaev, P., et al. (1995) Unraveling nanotubes: field emission from an atomic wire. Science 269, 1550–1553.

    Article  CAS  Google Scholar 

  55. Dai, H., Hafner, J. H., Rinzler, A. G., Colbert, D. T., and Smalley, R. E. (1996) Nanotubes as nanoprobes in scanning probe microscopy. Nature 384, 147–150.

    Article  CAS  Google Scholar 

  56. Wong, S., Joselevich, E., Woolley, A., Cheung, C., and Lieber, C. M. (1998) Covalently functionalized nanotubes as nanometer-sized probes in chemistry and biology. Nature 394, 52–55.

    Article  CAS  Google Scholar 

  57. Li, J., Cassell, A., and Dai, H. (1999) Carbon nanotubes as AFM tips: measuring DNA molecules at the liquid/solid interfaces. Surf. Interface Anal. 28, 8–11.

    Article  Google Scholar 

  58. Nguyen, C. V., Chao, K. J., Stevens, R. M. D., et al. (2001) Growth of carbon nanotubes by thermal and plasma chemical vapour deposition processes and applications in microscopy. Nanotechnology 12, 363–367.

    Article  CAS  Google Scholar 

  59. Liu, C. F., Fan, Y. Y., Liu, M., Cong, H. T., Chen, H. M., and Dresselhaus, M. S. (1999) Hydrogen storage in single-walled carbon nanotubes at room temperature. Science 286, 1127–1129.

    Article  CAS  Google Scholar 

  60. Che, G., Lakshmi, B. B., Fisher, E. R., and Martin, C. R. (1998) Carbon nanotubule membranes for electrochemical energy storage and production. Nature 393, 346–349.

    Article  CAS  Google Scholar 

  61. Kong, J., Franklin, N. R., Zhou, C. W., et al. (2000) Nanotube molecular wires as chemical sensors. Science 287, 622–625.

    Article  CAS  Google Scholar 

  62. Collins, P. G., Bradley, K., Ishigami, M., and Zettl, A. (2000) Extreme oxygen sensitivity of electronic properties of carbon nanotubes. Science 287, 1801–1804.

    Article  CAS  Google Scholar 

  63. Sumanasekera, G. U., Adu, C. K. W., Fang, S., and Eklund, P. C. (2000) Effects of gas adsorption and collisions on electrical transport in single-walled carbon nanotubes. Phys. Rev. Lett. 85, 1096–1099.

    Article  CAS  Google Scholar 

  64. Ng, H. T., Fang, A., Li, J., and Li, S. F. Y. (2001) Flexible carbon nanotube membrane sensory system: a generic platform. J. Nanosci. Nanotech. 1, 375–379.

    Article  CAS  Google Scholar 

  65. Li, J. and Ng, H. T. (2003) Carbon nanotube sensors, in Encyclopedia of Nanoscience and Nanotechnology, vol. 1 (Nalwa, H. S., ed.), American Scientific Publishers, Santa Barbar, CA, pp. 591–601.

    Google Scholar 

  66. Li, J., Ye, Q., Cassell, A., et al. (2003) Bottom-up approach for carbon nanotube interconnects. Appl. Phys. Lett. 82, 2491–2493.

    Article  CAS  Google Scholar 

  67. Ren, Z. F., Huang, Z. P., Xu, J. W., et al. (1998) Synthesis of large arrays of well-aligned carbon nanotubes on glass. Science 282, 1105–1107.

    Article  CAS  Google Scholar 

  68. Delzeit, L., McAninch, I., Cruden, B. A., et al. (2002) Growth of multiwall carbon nanotubes in an inductively coupled plasma reactor. J. Appl. Phys. 91, 6027–6033.

    Article  CAS  Google Scholar 

  69. Cassell, A. M., Ye, Q., Cruden, B. A., et al. (2004) Combinatorial chips for optimizing the growth and integration of carbon nanofibre based devices. Nanotechnology 15, 9–15.

    Article  CAS  Google Scholar 

  70. Cruden, B. A., Cassell, A. M., Ye, Q., and Meyyappan, M. (2003) Reactor design considerations in the hot filament/direct current plasma synthesis of carbon nanofibers. J. Appl. Phys. 94, 4070–4078.

    Article  CAS  Google Scholar 

  71. Staros, J. V. (1982) N-hydroxysulfosuccinimide active esters—bis(N-hydroxysulfosuccinimide) esters of 2 dicarboxylic-acids are hydrophilic, membrane-impermeant, protein cross-linkers. Biochemistry 21, 3950–3955.

    Article  CAS  Google Scholar 

  72. Miki, Y., Swensen, J., Shattuck-Eidens, D., et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266, 66–71.

    Article  CAS  Google Scholar 

  73. Staros, J. V. (1982) N-hydroxysulfosuccinimide active esters—bis(N-hydroxysulfosuccinimide) esters of 2 dicarboxylic-acids are hydrophilic, membrane-impermeant, protein cross-linkers. Biochemistry 21, 3950–3955.

    Article  CAS  Google Scholar 

  74. Popovich, N. D. and Thorp, H. H. (2002) New strategies for electrochemical nucleic acid detection. Interface 11, 30.

    CAS  Google Scholar 

  75. Cheng, J., Sheldon, E. L., Wu, L., et al. (1998) Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips. Nat. Biotechnol. 16, 541–546.

    Article  CAS  Google Scholar 

  76. Edman, C. F., Raymond, D. E., Wu, D. J., et al. (1997) Electric field directed nucleic acid hybridization on microchips. Nucleic Acids Res. 25, 4907–4914.

    Article  CAS  Google Scholar 

  77. Sosnowski, R. G., Tu, E., Butler, W. F., O’Connell, J. P., and Heller, M. J. (1997) Rapid determination of single base mismatch mutations in DNA hybrids by direct electric field control. Proc. Natl. Acad. Sci. USA 94, 1119.

    Article  CAS  Google Scholar 

  78. Gilles, P. N., Wu, D. J., Foster, C. B., Dillon, P. J., and Chanock, S. J. (1999) Single nucleotide polymorphoric discrimination by an electronic dot blot assay on semiconductor microchip. Nat. Biotechnol. 17, 365–370.

    Article  CAS  Google Scholar 

  79. Bertilsson, L. and Liedberg, B. (1993) Infrared study of thiol monolayer assemblies on gold: preparation, characterization and functionalization of mixed monolayers. Langmuir 9, 141–149.

    Article  CAS  Google Scholar 

  80. Nuzzo, R. G. and Allara, D. L. (1983) Adsorption of bifunctional organic disulfides on gold surfaces. J. Am. Chem. Soc. 105, 4481–4483.

    Article  CAS  Google Scholar 

  81. Porter, M. D., Bright, T. B., Allara, D. L., and Chidsey, C. D. (1987) Spontaneously organized molecular assemblies. 4. Structural characterization of n-Alkyl Thiol monolayers on gold by optical ellipsometry, infrared spectroscopy, and electrochemistry. J. Am. Chem. Soc. 109, 3559–3568.

    Article  CAS  Google Scholar 

  82. Whitesides, G. M. and Bain C. D. (1988) Molecular-level control over surface order in self-assembled monolayer films of thiols on gold. Science 240, 62–63.

    Article  Google Scholar 

  83. Strong, L. and Whitesides, G. M. (1988) The structures of self-assembled monolayer films of organosulfur compounds adsorbed on gold single crystals: electron diffraction studies. Langmuir 4, 546–558.

    Article  CAS  Google Scholar 

  84. Dubois, L. H., Zegarski, B. R., and Nuzzo, R. G. (1987) Fundamental studies of the interactions of adsorbates on organic surfaces. Proc. Natl. Acad. Sci. USA 84, 4739–4742.

    Article  CAS  Google Scholar 

  85. Bain, C. D. and Whitesides, G. M. (1988) Correlation between wettability and structure in monolayers in alkanethiols adsorbed on gold. J. Am. Chem. Soc. 110, 3665–3666.

    Article  CAS  Google Scholar 

  86. Springer, A. L., Gall, A. S., Hughes, K. A., Kaiser, R. J., Li, G. S., and Lund, K. P. (2003) Salicylhydroxamic acid functionalized affinity membranes for specific immobilization of proteins and oligonucleotides. J. Biomol. Tech. 14, 183–190.

    Google Scholar 

  87. Schaeferling, M., Stefan, S. S., Hubert, P. H., et al. (2002) Application of self-assembly techniques in the design of biocompatible protein microarray surfaces. Electrophoresis 23, 3097–3105.

    Article  CAS  Google Scholar 

  88. Kenseth, J. R., Harnisch, J. R., Vivian, W., Jones, V. W., and Porter, M. D. (2001) Investigation of approaches for the fabrication of protein patterns by scanning probe lithography. Langmuir 17, 4105–4112.

    Article  CAS  Google Scholar 

  89. Nakano, K., Taira, H., Maeda, M., and Takagi, M. (1993) New bifunctional dialkyl disulfide reagent for the fabrication of a gold surface with the bioaffinity ligand. Anal. Sci. 9, 133–136.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Humana Press Inc., Totowa, NJ

About this protocol

Cite this protocol

Chen, H., Li, J. (2007). Nanotechnology. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology™, vol 381. Humana Press. https://doi.org/10.1007/978-1-59745-303-5_22

Download citation

  • DOI: https://doi.org/10.1007/978-1-59745-303-5_22

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-589-7

  • Online ISBN: 978-1-59745-303-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Navigation