Abstract
Alu PCR is a rapid and easy-to-perform “DNA fingerprinting” technique based on the simultaneous analysis of many genomic loci flanked by Alu repetitive elements, which allows the detection of genetic polymorphisms and mutations in human and primate genomes. In the protocol described in the present chapter, two fluorochrome-labelled primers complementary to Alu sequences are used to perform the PCR, and the amplification products are then analysed by capillary electrophoresis. The resulting complex electrophoretic pattern may show sample-to-sample variability due to insertion, deletion, or sequence change of Alu retrotransposons, or caused by length variation of the sequence interposed between two Alus.
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Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., et al. (2001) Initial sequencing and analysis of the human genome. Nature. 409, 860–921.
Cardelli, M., Marchegiani, F., Cavallone, L., Olivieri, F., Giovagnetti, S., Mugianesi, E., et al. (2006) A polymorphism of the YTHDF2 gene (1p35) located in an Alu-rich genomic domain is associated with human longevity. J Gerontol A Biol Sci Med Sci. 61, 547–56.
Moyzis, R.K., Torney, D.C., Meyne, J., Buckingham, J.M., Wu, J.-R., Burks, C., et al. (1989) The distribution of interspersed repetitive DNA sequences in the human genome. Genomics. 4, 273–89.
Jarnik, M., Tang, J.Q., Korab-Laskowska, M., Zietkiewicz, E., Cardinal, G., Gorska-Flipot, I., et al. (1996) Overall informativity, OI, in DNA polymorphisms revealed by inter-Alu PCR: detection of genomic rearrangements. Genomics. 36, 388–98.
Nelson, D.L., Ledbetter, S.A., Corbo, L., Victoria, M.F., Ramírez-Solis, R., Webster, T.D., Ledbetter, D.H., and Caskey, C.T. (1989) Alu polymerase chain reaction: a method for rapid isolation of human-specific sequences from complex DNA sources. Proc Natl Acad Sci U S A. 86, 6686–90.
Krajinovic, M., Richer, C., Labuda, D., and Sinnett, D. (1996) Detection of a mutator phenotype in cancer cells by inter-Alu polymerase chain reaction. Cancer Res. 56, 2733–7.
Furmaga, W.B., Cole, S.R., and Tsongalis, G.J. (2004) The use of Alu PCR to distinguish between typical pulmonary carcinoids versus classic midgut carcinoids. Int J Oncol. 24, 223–6.
Srivastava, T., Seth, A., Datta, K., Chosdol, K., Chattopadhyay, P., and Sinha, S. (2005) Inter-alu PCR detects high frequency of genetic alterations in glioma cells exposed to sub-lethal cisplatin. Int J Cancer. 117, 683–9.
McKie, A.B., Iwamura, T., Leung, H.Y., Hollingsworth, M.A., and Lemoine, N.R. (1997) Alu-polymerase chain reaction genomic fingerprinting technique identifies multiple genetic loci associated with pancreatic tumourigenesis. Genes Chromosomes Cancer. 18, 30–41.
Charlieu, J.P., Laurent, A.M., Carter, D.A., Bellis, M., and Roizès, G. (1992) 3′ Alu PCR: a simple and rapid method to isolate human polymorphic markers. Nucleic Acids Res. 20, 1333–7.
Bonafè, M., Cardelli, M., Marchegiani, F., Cavallone, L., Giovagnetti, S., Olivieri, F., et al. (2001) Increase of homozygosity in centenarians revealed by a new inter-Alu PCR technique. Exp Gerontol. 36, 1063–73.
Sinnett, D., Deragon, J.M., Simard, L.R., and Labuda, D. (1990) Alumorphs-human DNA polymorphisms detected by polymerase chain reaction using Alu-specific primers. Genomics. 7, 331–4.
Zietkiewicz, E., Labuda, M., Sinnett, D., Glorieux, F.H., and Labuda, D. (1992) Linkage mapping by simultaneous screening of multiple polymorphic loci using Alu oligonucleotide-directed PCR. Proc Natl Acad Sci U S A. 89, 8448–51.
Mighell, A.J., Markham, A.F., and Robinson, P.A. (1997) Alu sequences. FEBS Lett. 417, 1–5.
Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110, 462–7.
Blanco, L., Bernad, A., Lazaro, J.M., Martin, G., Garmendia, C., and Salas, M. (1989) Highly efficient DNA synthesis by the phage ϕ 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem. 264, 8935–40.
Acknowledgements
The author would like to thank I.N.R.C.A. (Italian National Research Center on Aging), Polo Scientifico e Tecnologico, Ancona, for having supported the development of this analytical method.
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© 2011 Humana Press
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Cardelli, M. (2011). Alu PCR. In: Park, D. (eds) PCR Protocols. Methods in Molecular Biology, vol 687. Humana Press. https://doi.org/10.1007/978-1-60761-944-4_15
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DOI: https://doi.org/10.1007/978-1-60761-944-4_15
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