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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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.
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.
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.
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.
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.
Matson, R. S. and Rampal, J. B. (2003) DNA arrays: past, present, and future. Am. Genomic/Proteomic Technol. April/May Issue, 37–44.
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.
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.
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, 241–246
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.
Matson, R. S., Rampal, J. B., and Coassin, P. J. (1994) Biopolymer synthesis on polypropylene supports. 1. Oligonucleotide. Anal. Biochem. 217, 306–310.
Koester, H. and Coull, J. M. (1990) Membranes with bound oligonucleotides and peptides. US Patent No. 4,923,901.
Rampal, J. B. (2000) Covalent attachment of biomolecules to derivatized polypropylene supports. US Patent No. 6,013,789.
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.
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.
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.
Weiler, J. and Hoheisel, J. D. (1996) Combining the preparation of oligonucleotide arrays and synthesis of high-quality primers. Anal. Biochem. 243, 218–227.
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.
The evaluation and purification of synthetic oligonucleotides (1987) DNA Synthesis User Bulletin by Applied Biosystems no. 13.
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.
Matteucci, M. D. and Caruthers, M. H. (1981) Synthesis of deoxyoligonucleotides on polymer support. J. Am. Chem. Soc. 103, 3185–3191.
Rampal, J. B. (1999) Hybridization detection by pretreating bound singlestranded probes. US Patent No. 5,985,567.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Rampal, J.B., Coassin, P.J., Matson, R.S. (2007). Construction of In Situ Oligonucleotide Arrays on Plastic. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology™, vol 381. Humana Press. https://doi.org/10.1007/978-1-59745-303-5_11
Download citation
DOI: https://doi.org/10.1007/978-1-59745-303-5_11
Publisher Name: Humana Press
Print ISBN: 978-1-58829-589-7
Online ISBN: 978-1-59745-303-5
eBook Packages: Springer Protocols