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Microarrays pp 227-246 | Cite as

Construction of In Situ Oligonucleotide Arrays on Plastic

  • Jang B. Rampal
  • Peter J. Coassin
  • Robert S. Matson
Part of the Methods in Molecular Biology™ book series (MIMB, volume 381)

Abstract

The concept of DNA arrays was first introduced in the early 1980s, by Sir Edwin Southern. Since then, many research institutions and biotechnology companies have investigated the potential use of arrays in fields ranging from genetic diagnostics to forensics investigations. A 64-channel automated chemical delivery system, known as the Southern Array Maker, which synthesizes oligonucleotides directly onto an aminated polypropylene substrate has been constructed. Many different arrays have been synthesized for the purpose of detecting single point mutations, which might be either indicators of, or directly responsible for, many different types of genetic diseases and cancers. These include cystic fibrosis, H-ras, K-ras, and other mutations. In addition to the synthesized arrays, we are also looking into various alternative methods of producing both highand low-density DNA arrays. This chapter is intended to demonstrate the synthesis of oligoarrays by in situ method using standard phosphoramidite chemistry. Phosphoramidate linkage to the aminated polypropylene is quite stable under oligo cleavage and deprotection conditions. Oligonucleotide density is approx 3 pmole or 1012 molecules/mm2.

Key Words

DNA microarrays oligoarrays phosphoramidite chemistry probe density solid-phase synthesis hybridization 

References

  1. 1.
    Southern, E. M., Maskos, U., and Elder, J. K. (1992) Analyzing and comparing nucleic acid sequences by hybridization to arrays of oliogonucleotide: evaluation using experimental models. Genomics 13, 1008–1017.CrossRefGoogle Scholar
  2. 2.
    Roger, Y. H., Baucom, P. J., Huang, Z. J., Bogdanov, V., Anderson, S., and Jacino, M. T. B. (1999) Immobilization of oligonucleotides onto glass support via disulfide bonds: a method for preparation of DNA microarrays. Anal. Biochem. 266, 23–30.CrossRefGoogle Scholar
  3. 3.
    Chrisey, L. A., Lee, G. U., and O’Ferrall, C. E. (1996) Covalent attachment of synthetic DNA to self-assembled monolayer films. Nucleic Acids Res. 24, 3031–3039.CrossRefGoogle Scholar
  4. 4.
    Lamture, J. B., Beattie, K. L., Burke, B. E., et al. (1994) Direct detection of nucleic acid hybridization on surface of a charge coupled device. Nucleic Acid Res. 22, 2121–2125.CrossRefGoogle Scholar
  5. 5.
    Nikiforov, T. T. and Rogers, Y. H. (1995) The use of 96-well polystyrene plates for DNA hybridization-based assays: an evaluation of different approaches to oligonucleotide immobilization. Anal. Biochem. 227, 201–209.CrossRefGoogle Scholar
  6. 6.
    Matson, R. S. and Rampal, J. B. (2003) DNA arrays: past, present, and future. Am. Genomic/Proteomic Technol. April/May Issue, 37–44.Google Scholar
  7. 7.
    Khrapko, K. R., Lysov, Y. P., Khorlin, A. A., et al. (1991) A method for DNA sequencing by hybridization with oligonucleotide matrix. J. DNA Sequencing Mapping 1, 375–388.CrossRefGoogle Scholar
  8. 8.
    Fodor, S. P. A., Read, J. L., Pirrung, M. C., Stryer, L., Lu, A. T., and Solas, D. (1991) Light-directed, spatially addressable parallel chemical synthesis. Science 251, 767–773.CrossRefGoogle Scholar
  9. 9.
    Pirrung, M. C., Fallon, L., and McGall, G. (1998) Proofing of photolithographic DNA synthesis and 3′,5′-dimethoxybenzoinyloxycarbonyl-protected deoxynucleoside phosphoramidities. J. Org. Chem. 63, 241–246CrossRefGoogle Scholar
  10. 10.
    Pease, A. C., Solas, D., Sullivan, E. J., Cronin, M. T., Holmes, C. P., and Fodor, S. P. A. (1994) Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91, 5022–5026.CrossRefGoogle Scholar
  11. 11.
    Matson, R. S., Rampal, J. B., and Coassin, P. J. (1994) Biopolymer synthesis on polypropylene supports. 1. Oligonucleotide. Anal. Biochem. 217, 306–310.CrossRefGoogle Scholar
  12. 12.
    Koester, H. and Coull, J. M. (1990) Membranes with bound oligonucleotides and peptides. US Patent No. 4,923,901.Google Scholar
  13. 13.
    Rampal, J. B. (2000) Covalent attachment of biomolecules to derivatized polypropylene supports. US Patent No. 6,013,789.Google Scholar
  14. 14.
    Wehnert, M. S., Matson, R. S., Rampal, J. B., Coassin, P. J., and Caskey, C. T. (1994) A rapid scanning strip for tri-and dinucleotide short tandem repeats. Nucleic Acids Res. 22, 1701–1704.CrossRefGoogle Scholar
  15. 15.
    Hollahan, J. R. and Stafford, B. B. (1969) Attachment of amino groups to polymer surfaces by radiofrequency plasmas. J. Appl. Polymer Sci. 13, 807–816.CrossRefGoogle Scholar
  16. 16.
    Matson, R. S., Rampal, J., Pentoney, S. L., Anderson, P. D., and Coassin, P. (1995) Biopolymer synthesis on polypropylene supports: oligonucleotide arrays. Anal. Biochem. 224, 110–116.CrossRefGoogle Scholar
  17. 17.
    Weiler, J. and Hoheisel, J. D. (1996) Combining the preparation of oligonucleotide arrays and synthesis of high-quality primers. Anal. Biochem. 243, 218–227.CrossRefGoogle Scholar
  18. 18.
    Reddy, M. P., Rampal, J. B., and Beaucage, S. L. (1987) An efficient procedure for the solid phase tritylation of nucleosides and nucleotides. Tetrahedron Lett. 28, 23–26.CrossRefGoogle Scholar
  19. 19.
    The evaluation and purification of synthetic oligonucleotides (1987) DNA Synthesis User Bulletin by Applied Biosystems no. 13.Google Scholar
  20. 20.
    Warren, W. J. and Vella, G. (1994) Analysis and purification of synthetic oligonucleotides by high-performance liquid chromatography, in Protocols for Oligonucleotide Conjugates, (Agrawal, S., ed.), Humana, Totowa, NJ, pp. 233–264.CrossRefGoogle Scholar
  21. 21.
    Matteucci, M. D. and Caruthers, M. H. (1981) Synthesis of deoxyoligonucleotides on polymer support. J. Am. Chem. Soc. 103, 3185–3191.CrossRefGoogle Scholar
  22. 22.
    Rampal, J. B. (1999) Hybridization detection by pretreating bound singlestranded probes. US Patent No. 5,985,567.Google Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Jang B. Rampal
    • 1
  • Peter J. Coassin
    • 2
  • Robert S. Matson
    • 3
  1. 1.Beckman Coulter, Inc.Brea
  2. 2.Aurora BioSciences DiscoverySan Diego
  3. 3.Beckman Coulter, Inc.Fullerton

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