Summary
A strategy employing the polymerase chain reaction to synthesize gene-specific probes suitable for genomic Southern analyses and for screening genomic libraries is described. The method utilizes partial amino acid sequence data from the protein of interest, genomic DNA and inosine-containing oligonucleotide primers. An example of its application for the isolation of plant gene sequences encoding saporin, a ribosome inactivating protein, is described.
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References
Barbieri L, Stirpe F (1982) Ribosome-inactivating proteins from plants: Properties and possible uses. Cancer Surv 1:489–520
Barbieri L, Zamboni M, Montanaro L, Sperti S, Stirpe F (1980a) Inhibition of protein synthesis in vitro by proteins from the seeds of Momordica charantia (bitter pear melon). Biochem J 186:443–452
Barbieri L, Zamboni M, Montanaro L, Sperti S, Stirpe F (1980b) Purification and properties of different forms of modeccin, the toxin of Adenia digitata. Separation of subunits with inhibitory and lectin activity. Biochem J 185:203–210
Endo Y, Tsurugi K (1987) RNA N-glycosidase activity of ricin A-chain. J Biol Chem 262:8128–8130
Endo Y, Mitsui K, Motizuki M, Tsurugi K (1987) The mechanism of action of ricin and related toxic iectins on eukaryotic ribosomes. J Biol Chem 262:8128–8130
Frischauf AM, Lehrach H, Poutska A, Murray N (1983) Lambda replacement vectors carrying polylinker sequences. J Mol Biol 170:827–842
Girgis SI, Alevizaki M, Denny P, Ferrier GJM, Legon S (1988) Generation of DNA probes for peptides with highly degenerate codons using mixed primer PCR. Nucleic Acids Res 26:10371
Gould SJ, Subramani S, Schefler IE (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 Natl Acad Sci USA 86:1934–1938
Graham DE (1978) The isolation of high molecular weight DNA from whole organisms or large tissue masses. Anal Biochem 85:609–613
Halling KC, Halling AC, Murray EE, Ladin BF, Houston LL, Weaver RF (1985) Genomic cloning and characterization of a ricin gene from Ricinus communis. Nucleic Acids Res 13:8019–8033
Lamb FI, Roberts LM, Lord JM (1985) Nucleotide sequence of cloned cDNA coding for preproricin. Eur J Biochem 148:265–270
Lappi DA, Esch FS, Barbieri L, Stirpe F, Soria M (1985) Characterization of a Saponaria officinalis seed ribosome-inactivating protein: immunoreactivity and sequence homologies. Biochem Biophys Res Commun 129:934–942
Lee CC, Wu X, Gibbs RA, Cook RG, Muzny DM, Caskey TC (1988) Generation of cDNA probes directed by amino acid sequence: Cloning of urate oxidase. Science 239:1288–1291
Lewis RM (1986) Probfind: a computer program for selecting oligonucleotides from peptide sequences. Nucleic Acids Res 14:567–570
Maniatis T, Fritschf EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Nordmann PL, Makris CJ, Reznikoff WS (1988) Inosine induced mutations. Mol Gen Genet 214:62–67
Ohtsuka E, Matsuki S, Ikehara M, Takahashi Y, Matsubara K (1985) An alternative approach to deoxyoligonucleotides as hybridisation probes by insertion of deoxyinosine at ambiguous codnn positions. J Biol Chem 260:2605–2608
Olsnes S, Pihl A (1976) Abrin, ricin and their associated agglutinins. The specificity of action of animal, bacterial and plant toxins. In: Cuatrecasas P (ed) Receptors and recognition, Series B, vol 1. Chapman and Hall, London, pp 129–173
Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5468
Shuldiner AR, Nirula A, Roth J (1989) Hybrid DNA artifact from PCR of closely related target sequences. Nucleic Acids Res 17:4409
Stirpe F, Barbieri L (1986) Ribosome-inactivating proteins up to date. FEBS Lett 195:1–8
Stirpe F, Olsnes S, Pihl A (1980) Gelonin, a new inhibitor of protein synthesis, non toxic to intact cells. Isolation, characterization and preparation of cytotoxic conjugates with concanavalin A. J Biol Chem 255:6947–6955
Stirpe F, Williams DG, Onyon LJ, Legg RF, Stevens WA (1981) Dianthins, ribosome-damaging proteins with antiviral properties from Dianthus caryophyllus L. (carnation). Biochem J 195:399–405
Stirpe F, Gasperi-Campani A, Barbieri L, Falasca A, Abbondanza A, Stevens WA (1983) Ribosome-inactivating proteins from the seeds of Saponaria officinalis L. (soapwort), of Agrostemma githago L. (corncockle) and of Asparagus officinalis L. (asparagus), and from the latex of Hura crepitans L. (sandbox tree). Biochem J 216:617–625
Stirpe F, Bailey S, Miller SP, Bodley JW (1988) Modification of ribosomal RNA by ribosome-inactivating proteins from plants. Nucleic Acids Res 16:1349–1357
Yarwood A (1989) Manual methods of protein sequencing. In: Findlay JBC, Geisow MJ (eds) Protein sequencing. Practical Approach Series. IRL Press at Oxford University Press, Oxford, pp 119–145
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Fordham-Skelton, A.P., Yarwood, A. & Croy, R.R.D. Synthesis of saporin gene probes from partial protein sequence data Use of inosine-oligonucleotides, genomic DNA and the polymerase chain reaction. Molec. Gen. Genet. 221, 134–138 (1990). https://doi.org/10.1007/BF00280379
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DOI: https://doi.org/10.1007/BF00280379