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Biochips: Focusing on Surfaces and Surface Modification

  • Conference paper
Biomaterials

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 553))

Abstract

Thousands of genes and their products (i.e., proteins) in a given living organism function in a complicated and orchestrated way that creates the mystery of life. In “genomics”, briefly genes of organisms, their functions and activities are investigated. Genomics is naturally linked to “proteomics” — large scale study of all proteins encoded by an organism’s genome. Genomics’ combination with proteomics resulted with a fascinating growth in the biomedical research and in the field of large scale and high throughput biology.1,2

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References

  1. Eing, A., and Vaupel, M., 2002, Imaging Ellipsometry in Biotechnology. Scientific Series, pp 1–10.

    Google Scholar 

  2. Zhu, H., and Snyder, M., 2003, Protein chip technology, Curr. Opin. in Chem. Biol., 7, 55–63.

    Article  Google Scholar 

  3. Zammatteo, N., Jeanmart, L., Hamels, S., Courtois, S., Loutte, P., Hevest, L., and Remacle, J., 2000, Comprasion between Different Strategies of Covalnet Attachment of DNA to Glass Surfaces to Build DNA Microarray. Anal. Biochem., 248, 143–150.

    Article  Google Scholar 

  4. Dolan, P. L., Wu, Y., Ista, K. L., Metzenberg, L. R., Nelson, M.A., and Lopez, G.P., 2001, Robust and efficient synthetic method for forming DNA microarrays. Nucleic Acids Res. , 21, e 107.

    Article  Google Scholar 

  5. Habb, BB., 2001, Advances in protein microarray technology for protein expression and interaction profiling. Curr. Opin. in Drug Disc., 4, 116–123.

    Google Scholar 

  6. Cahill, DJ., 2001, Protein and antibody arrays and thier medical applications. J. of Immunol. Methods. 250. 81–91.

    Article  Google Scholar 

  7. Stoll, D., Templin, MF., Schrenk, M., Traub, PC, Vohringer, CF., and Joos, TO., 2002, Protein Microarray Technology. Front Biosci., 7:c, 13-c32.

    Article  Google Scholar 

  8. Zhu, H., and Snyder, M., 2002, Omic approaches for unravelling signalling networks. Curr. Opin. in Cell. Biol. , 14, 173–179.

    Article  Google Scholar 

  9. Lueking, A., Horn, M., Eickhoff, H., Bussow, K., Lehrach, H., and Walter, G., 1999, Protein microarrays for gene expression and antibody screening. Anal. Biochem., 270, 103–111

    Article  Google Scholar 

  10. McGall, G.H., Barone, A.D., Diggelmann, M., Fodor, S.P.A., Gentalen, E., Ngo, N, 1997, The efficiency of light directed synthesis of DNA arrays on glass substrates,. J. Am. Chem. Soc., 119, 5081–5090.

    Article  Google Scholar 

  11. Southern, E.M., Case-Green, S.C., Elder, J.K., Johnson, M., Mir, K.U., Wang, L., and Williams, J.C., 1994, Arrays of complementary olionucleotides for analysing the hybridization behaviour of nucleic acids. Nucleic Acids Res., 22, 1368–1373.

    Article  Google Scholar 

  12. Fodor, S. P. A. 1997, DNA SEQUENCING: Massively Parallel Genomics. Science, 277, 393–395.

    Article  Google Scholar 

  13. Podyminogin, M.A., Lukhtanov, E.A., and Reed, M.W., 2001, Attachment of benzaldehyde-modifiied oligodeoxynucleotide probes to semicarbazide-coated glass. Nucleic Acids Res., 29, 5090–5098.

    Article  Google Scholar 

  14. Charles, P.T., Vora, G.J., Andreadis, J.D., Fortney, A.J., Meador, C.E., Dulsey, C.S., and Stenger, D.A., 2003, Fabrication and Surface Characterization of DNA Microarrays Using Amine- and Thiol-Terminated Oligonucleotide Probes. Langmuir, 19, 1586–159.

    Article  Google Scholar 

  15. Houseman, B. T., Gawalt, E. S., and Mrksich, M., 2003, Maleimide-Functionalized SelfAssembled Monolayers for the Preparation of Peptide and Carbohydrate Biochips. Langmuir, 19, 1522–1531.

    Article  Google Scholar 

  16. Lipshutz, R. J., Fodor, S. P. A., Gingeras, T. R., and Lockhart, D. J., 1999, High density synthetic oligonucleotide arrays. Nat. Genet., 21, 20–24

    Article  Google Scholar 

  17. Guschin, D., Yershov, G., Zaslaysky, A., Gemmell, A., Shick, V., Proudnikov, D., Arenkov, P., and Mirzabekov, A. 1997, Manual manufacturing of oligonucleotide, DNA, and protein microchips. Anal. Biochem. 250, 203–211.

    Article  Google Scholar 

  18. Benters, R., Niemeyer, C. M., and Wohrle, D. 2001, Dendrimer-activated solid supports for nucleic acid- and protein-microarrays. Chem.Biol. Chem., 2, 686–694.

    Article  Google Scholar 

  19. Andreadis, J. D.; and Chrisey, L. A. 2000, Use of immobilized PCR primers to generate covalently immobilized DNAs for in vitro transcription/translation reactions. Nucleic Acids Res., 28, e5.

    Google Scholar 

  20. Lenigk, R., Cartes, M., Ip, N. Y., and Sucher, N. J., 2001, Surface Characterization of a Silicon-Chin-Based DNA Microarray. Langmuir, 17, 2497–2501.

    Article  Google Scholar 

  21. Chrisey, L. A., Lee, G. U., and O’Ferrall, E., 1996, Covalent attachment of synthetic DNA to self-assembled monolayer films. Nucleic Acids Res., 24, 3031–3039.

    Article  Google Scholar 

  22. Chrisey, L. A., O’Ferrall, E., Spargo, B. J., Dulcey, C. S., Calvert, J. M., 1996, Nucleic Acids Res., 24, 3040–3047.

    Article  Google Scholar 

  23. Oh, S. J., Cho, S. J., Kim, C. O., and Park, J. W., 2002, Characteristics of DNA Microarrays Fabricated on Various Aminosilane Layers, Langmuir, 18, 1764–1769.

    Article  Google Scholar 

  24. Westphal, P., and Bornmann, A., 2002, Biomolecular detection by surface plasmon enhanced ellipsometry. Sens. Actuators B, 84, 278–282.

    Article  Google Scholar 

  25. Bassil, N., Maillart, E., Canva, M., Levya, Y., Millot, MC., Pissard, S., Narwa, R., and Goossens, M., 2003, One hundred spots parallel monitoring of DNA interactions by SPR imaging of polymer-functionalized surfaces applied to the detection of cystic fibrosis mutations. Sens. Actuators B, 94, 313–323.

    Article  Google Scholar 

  26. Zhu-, X.M., Lin, P.H., Ao, P., and Sorensen, LB., 2002, Surface treatments for surface plasmon resonance biosensors. Sens. Actuators B, 84, 106–112.

    Article  Google Scholar 

  27. Rich, R., and Myszka, D.G., 2000, Survey of the 1999 surface plasmon resonance biosensor literature. J. Mol. Recognition, 13, 388–407.

    Article  Google Scholar 

  28. Green, R.J., Fraizer, R.A., Shakesheff, K.M., Davies, M.C., Roberts, C.J., and Tendler, S.J.B., 2000, Surface plasmon resonance analysis of dynamic biological interactions with biomaterials. Biomaterials. 21, 1823–1835.

    Article  Google Scholar 

  29. Southern, E., Mir, K., and Shchepinov, M., 1999, Molecular interactions on microarrays. Nature Genetics (Suppl.), 21, 5–9.

    Article  Google Scholar 

  30. Lamture, J.B., Beattie, K.L., Burke, B.E., Eggers, M.D., Ehrlich, D.J., Fowler, R., Hollis, M.A., Kosicki, B.B., Reich, R.K., and Smith, S.R., 1994, Direct detection of nucleic acid hybridization on the surface of a charge coupled device. Nucleic Acids Res., 22, 2121–2125.

    Article  Google Scholar 

  31. Chen, D., Yan, Z., Cole, D.L. and Srivatsa, G.S., 1999, Analysis of internal (n-1)mer deletion sequences in synthetic oligodeoxyribonucleotides by hybridization to an immobilized probe array. Nucleic Acids Res., 27, 389–395.

    Article  Google Scholar 

  32. Guo, Z., Guilfoyle, R.A., Thiel, A.J., Wang, R. and Smith, L.M., 1994, Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports. Nucleic Acids Res., 22, 5456–5465.

    Article  Google Scholar 

  33. Beier, M., and Hoheisel, J.D., 1999, Versatile derivatisation of solid support media for covalent bonding on DNA-microchips. Nucleic Acids Res., 27, 1970–1977.

    Article  Google Scholar 

  34. Cohen, G., Deutsch, J., Fineberg, J., and Levine, A., 1997, Covalent attachment of DNA oligonucleotides to glass. Nucl. Acids. Res., 25, 911–912.

    Article  Google Scholar 

  35. Kumar, A., Larsson, O., Parodi, D., and Linag, Z., 2001, Silanized nucleic acids: a general platform for DNA immobilization. Nucl. Acids. Res., 28, e71.

    Google Scholar 

  36. Tomalia, D.A., Naylor, A.M. and Goddard, W.A., 1990, Starburst dendrimers: molecular-level control of size, shape, surface chemistry, topology and flexibility from atoms to macroscopic matter. Angew. Chem. Int. Ed. Engl., 29, 138–175.

    Article  Google Scholar 

  37. Benters, R., Niemeyer, C.M., Drutschmann, D., Blohm, D., and Wöhrle, D., 2002, DNA microarrays with PAMAM dendritic linker systems. Nucleic Acids Res., 30, e10.

    Article  Google Scholar 

  38. Lee, P. H., Sawan, S. P., Modrusan, Z., Arnold, L. J., Jr., and Reynolds, M. A., 2002, An Efficient Binding Chemistry for Glass Polynucleotide Microarrays. Bioconjugate Chem., 13, 97–103.

    Article  Google Scholar 

  39. Wiese, R., 2001, Simultaneous multianalyte ELISA performed on a microarray platform. Clin. Chem., 47, 1451–1457.

    Google Scholar 

  40. Haab, B.B., 2001, Protein microarrays for highly parallel detection and quantification of specific proteins and antibodies in complex solutions. Genome Biology, 2, 0004.1–0004.13.

    Google Scholar 

  41. MacBeath, G. and Schreiber, S.L., 2000, Printing proteins as microarrays for high-throughput function determination. Science, 289, 1760–1762.

    Google Scholar 

  42. Arenkov, P., 2000, Protein microchips: use of immunoassay and enzymatic reactions. Anal. Biochem., 278, 123–131.

    Article  Google Scholar 

  43. Afanassiev, V., 2000, Preparation of DNA and protein micro arrays on glass slides with an agarose film. Nucleic Acids Res., 28, e66.

    Google Scholar 

  44. Rowe, C.A., 1998, An array immunosensor for simultaneous detection of clinical analytes. Anal. Chem, 71, 433–439.

    Article  Google Scholar 

  45. Strother, T., Hamers, R.J., and Smith, L.M., 2000, Covalent attachment of oligodeoxyribonucleotides to amine-modified Si (001) surfaces. Nucleic Acids Res., 28, 3535–3541.

    Article  Google Scholar 

  46. Waddell, T.G., Leyden, D.E. and DeBello, M.T., 1981, The nature of organosilane to silica-surface bonding. J. Am. Chem. Soc., 103, 5303–5307.

    Article  Google Scholar 

  47. Linford, M.R., Fenter, P., Eisenberger, P.M. and Chidsey, C.E.D., 1995, Alkyl Monolayers on Silicon Prepared from 1-Alkenes and Hydrogen-Terminated Silicon. J. Am. Chem. Soc., 117, 3145–3155.

    Article  Google Scholar 

  48. Mullet, W.M., Lai, E.P.C., and Yeung, J.M., 2000, Surface plasmon resonance based immunoassays. Methods, 22, 77–91.

    Article  Google Scholar 

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

    Article  Google Scholar 

  50. Nuzzo, R. G., Dubois, L. H., and Allara, D. L., 1990, Fundamental studies of microscopic wetting on organic surfaces. 1. Formation and structural characterization of a self-consistent series of polyfunctional organic monolayers. J. Am. Chem. Soc., 112, 558–569.

    Article  Google Scholar 

  51. 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  Google Scholar 

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

    Article  Google Scholar 

  53. Arnold, R., Terfort, A., and Woll, C., 2001, Determination of Molecular Orientation in Self-Assembled Monolayers Using IR Absorption Intensities: The Importance of Grinding Effects. Langmuir, 17, 4980–4989.

    Article  Google Scholar 

  54. Houssiau, L., Graupe, M., Colorado, R., Kim, H. I., Lee, T. R., Perry, S. S., and Rabalais, J. W., 1998, Characterization of the surface structure of CH 3and CF 3terminated n-alkanethiol monolayers self assembled on Au 111 . J. Chem. Phys., 109, 9134–9147.

    Article  Google Scholar 

  55. Buscher, C. T., McBranch, D., and Li, D. Q., 1996, Understanding the Relationship between Surface Coverage and Molecular Orientation in Polar Self-Assembled Monolayers. J. Am. Chem. Soc., 118, 2950–2953.

    Article  Google Scholar 

  56. Riepl, M., Enander, K., Liedberg, B., Schaferling, M., Kruschina, M., and Ortigao, F., 2002, Functionalized Surfaces of Mixed Alkanethiols on Gold as a Platform for Oligonucleotide Microarrays. Langmuir, 18, 7016–7023.

    Article  Google Scholar 

  57. Duschl, C., Sevin-Landais, A., and Vogel, H. 1996, Surface engineering: optimization of antigen presentation in self- assembled monolayers. Biophys. J., 70, 1985–1995.

    Article  Google Scholar 

  58. Peterlinz, K. A., and Georgiadis, R., 1996, In Situ Kinetics of Self-Assembly by Surface Plasmon Resonance Spectroscopy, Langmuir, 12, 4731–4740.

    Article  Google Scholar 

  59. Schlenoff, J. B., Li, M., and Ly, H., 1995, Stability and Self-Exchange in Alkanethiol Monolayers. J. Am. Chem. Soc., 117, 12528–12536.

    Article  Google Scholar 

  60. Bain, C. D., Troughton, E. B., Tao, Y. T., Evall, J., Whitesides, G. M., and Nuzzo, R. G., 1989, Formation of monolayer films by the spontaneous assembly of organic thiols from solution onto gold. J. Am. Chem. Soc., 111, 321–335.

    Article  Google Scholar 

  61. Sasaki, S., Nagata, R., Hock, B., and Karube, I., 1998, Novel surface plasmon resonance sensor chip functionalized with organic silica compounds for antibody attachment Anal. Chim. Acta, 368, 71–76.

    Article  Google Scholar 

  62. Lu, Y. J., Zhang, F., and Sui, S. F., 2002, Specific Binding of Integrin alphambeta3 to RGD Peptide Immobilized on a Nitrilotriacetic Acid Chip: a Surface Plasmon Resonance Study. Biochemistry (Mosc), 67, 933–939.

    Article  Google Scholar 

  63. Zhu, H., Bilgin, M., Bangham, R., and Hall, D., 2001, Global Analysis of Protein Activities Using Proteome Chips. Science, 293, 2101–2105.

    Article  Google Scholar 

  64. Seong, Y.S., and Choi, C.Y., 2003, Current status of protein chip development in terms of fabrication and application. Proteomics, 3, 2176–2189.

    Article  Google Scholar 

  65. Brockman, J.M., Nelson, B.P., and Corn, R.M., 2001, Surface plasmon reosonace imaging measurements of ultrathin organic films. Annu. Rev. Phys. Chem., 51, 41–63.

    Article  Google Scholar 

  66. Kremsky, J.N., Wooters, J.L., Dougherty, J.P., Meyers, R.E., Collins, M. and Brown, E.L., 1987, Immobilization of DNA via oligonucleotides containing an aldehyde or carboxylic acid group at the 5’ terminus. Nucleic Acids Res., 15, 2891–2909.

    Article  Google Scholar 

  67. VanNess, J., Kalbfleisch, S., Petrie, C.R., Reed, M.W., Tabone, J.C. and Vermeulen, N.M.J., 1991, A versatile solid support system for oligodeoxynucleotide probe-based hybridization assays. Nucleic Acids Res., 19, 3345–3350.

    Article  Google Scholar 

  68. Hauser, N.C., Vingron, M., Scheideler, M., Krems, B., Hellmuth, K., Entian, K.-D. and Hoheisel, J.D., 1998, Yeast, 14, 1209–1221.

    Article  Google Scholar 

  69. Predki, P.F., (Article in press), Functional protein microarrays: ripe for discovery. Curr. Opin. Chem. Biol.

    Google Scholar 

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Authors and Affiliations

  1. Center of Bioengineering and Bioengineering Division, and TÜBİTAK: Center of Excellence-BİYOMÜH, Hacettepe University, Beytepe, Ankara, Turkey

    Erhan Pişkin & Bora Garipcan

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  1. Erhan Pişkin
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  2. Bora Garipcan
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  1. Biomaterials Research Labs, Middle East Technical University, Ankara, Turkey

    Nesrin Hasirci  & Vasif Hasirci  & 

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Pişkin, E., Garipcan, B. (2004). Biochips: Focusing on Surfaces and Surface Modification. In: Hasirci, N., Hasirci, V. (eds) Biomaterials. Advances in Experimental Medicine and Biology, vol 553. Springer, Boston, MA. https://doi.org/10.1007/978-0-306-48584-8_12

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  • DOI: https://doi.org/10.1007/978-0-306-48584-8_12

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