Abstract
The use of degenerate primers in the polymerase chain reaction (PCR) is an effective method for identifying related genes that share limited sequence similarity. Other methods, using oligonucleotide or heterologous probes, for example, may fail to identify genes that are not highly conserved, have diverged over evolutionary time, or share only short regions of structural similarity.
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References
Gould, S. J., Subramani, S., and Scheffler, I. E. (1989) Use of the DNA polymerase chain reaction for homology probing: isolation of partial cDNA or genomic clones encoding the iron-sulfur protein of succinate dehydrogenase from several species. Proc. Acad. Natl. Sci. USA 86, 1934–1938.
Bartl, S. and Weissman, I. L. (1994) Isolation and characterization of major histocompatibility complex class IIB genes from the nurse shark. Proc. Acad. Natl. Sci. USA 91, 262–266.
Bartl, S. and Weissman, I. L. (1994) PCR primers containing a inosine triplet to complement a variable codon within a conserved protein-coding region. BioTechniques 16(2), 246–250.
Huang, G. C., Page, M. J., Roberts, A. J., Malik, A. N., Spence, H., McGregor, A. M., and Banga, J. P. (1990) Molecular cloning of a human thyrotropin receptor cDNA fragment: use of highly degenerate, inosine containing primers derived from aligned amino acid sequences of a homologous family of glycoprotein hormone receptors. FEBS Lett. 264, 193–197.
Knoth, K., Roberds, S., Poteet, C., and Tamkin, M. (1988) Highly degenerate, inosine-containing primers specially amplify rare cDNA using the polymerase chain reaction. Nucleic Acids Res. 16, 10,932.
Patil, R. V. and Dekker, E. E. (1990) PCR-amplification of a Eschericha coli gene using mixed primers containing deoxyinosine at ambiguous positions in degenerate amino acid codons. Nucleic Acids Res. 18, 3080.
Ohtsuka, E., Matsuki, S., Ikehara, M., Takahashi, Y., and Matsubara, K. (1985) An alternative approach to deoxyoligonucleotides as hybridization probes by insertion of deoxyinosine at ambiguous codon positions. J. Biol. Chem. 260, 2605–2608.
Bartl, S. and Weissman, I. L. (1994) The isolation of putative major histocompatibility complex gene fragments from dogfish and nurse shark. Ann. NY Acad. Sci. 721, 346–349.
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© 1997 Humana Press Inc.
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Bartl, S. (1997). Amplification Using Degenerate Primers with Multiple Inosines to Isolate Genes with Minimal Sequence Similarity. In: White, B.A. (eds) PCR Cloning Protocols. Methods in Molecular Biology™, vol 67. Humana Press, Totowa, NJ. https://doi.org/10.1385/0-89603-483-6:451
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DOI: https://doi.org/10.1385/0-89603-483-6:451
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-0-89603-483-9
Online ISBN: 978-1-59259-553-2
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