Abstract
Major uses of oligodeoxyribonucleotides are as hybridization probes, sequencing primers, and, more recently, as primers for the polymerization chain reaction. When a protein sequence or part thereof is known, the construction of oligomer probes and primers is complicated by the codon degeneracy. The chain multiplicity in such probes or primers may reach very large numbers, leading to often ineffective reagents or poor signals. A number of ways of mitigating this general problem have been devised (1); among these is the use of hypoxanthine I as a base that may be inserted at positions of degeneracy. Although it forms basepairs with C, A, G, and T of weak and varying stabilities (in that order), its ability to sustain the dissociation temperatures of DNA duplexes containing it above those with mismatches has led to its use first in probes and more recently in primers (2–6). We discuss I later, but here we describe the synthesis of monomers and oligomers containing the pyrimidine, 6H,8H-3,4-dihydropyrimido[4,5-c][l,2]oxazin-7-one, P (showing C, T degeneracy) and 2-amino-6-methoxyaminopurine, K (showing A,G degeneracy) (Fig. 1) (7,8). These bases were chosen on the grounds that their amino-imino tautomeric constants were much nearer to unity than the normal bases and that, for example, the P base could form Watson-Crick basepairs with both A and G as shown in Fig. 1 (a,b).
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References
Lathe, R. (1985) Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations. J. Mol. Biol. 183, 1–12.
Compton, T. (1990) Degenerate primers for DNA amplification, in PCR Protocols, A Guide to Methods and Their Applications, Chapter 5. (Innis, M. A., Gelfand, D. H., Sninsky, J. J., and White, T J., eds.), Academic, New York, pp. 39–45.
Bej, A. K., Mahbubani, M. H., and Atlas, R. M. (1991) Amplification of nucleic acids by polymerase chain reaction (PCR) and other methods and their applications, in Critical Reviews in Biochemistry and Molecular Biology (Fasman, G. D., ed.), 26, 301–344
Ohtsuka, E., Matsuki, S., Ikehara, M., Takahashi, Y., and Matsubara, K. (1985) An alternative approach to deoxyoligonucleotides as hybridisation probes by insertion of deoxyinosine at ambiguous codon positions. J. Biol. Chem. 260, 2605–2608.
Martin, F. H., Castro, M. M., Abou-Ela, F., and Tinoco, I. (1985) Basepairing involving deoxyinosine: implications for probe design Nucleic Acids Res. 13, 8927–8938.
Knoth, K., Roberds, S, Potect, C, and Tamkun, M. (1988) Highly degenerate inosine-containing primers specifically amplifying rare cDNA using polymerase chain reaction. Nucleic Acids Res. 16, 10932.
Kong Thoo Lin, P. and Brown, D. M. (1989) Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues. Nucleic Acids Res. 17, 10373–10383.
Brown, D M. and Kong Thoo Lin, P. (1991) Synthesis and duplex stability of oligonucleotides containing adenine-guanine analogues. Carbohydrate Res. 216, 129–139.
Nederman, A. N. R, Stone, M J., Kong Thoo Lin, P., Brown, D. M., and Williams, D H (1991) Basepairing of cytosine analogues with adenine and guanine in oligonucleotide duplexes: evidence for exchange between Watson-Crick and Wobble basepairs using 1H NMR spectroscopy. J. Chem. Soc, Chem Commun. 19, 1357–1359.
Kong Thoo Lin, P. and Brown, D. M. (1991) Synthesis of oligodeoxy-nbonucleotides containing degenerate bases and their use as primers in the polymerase chain reaction Nucleic Acids Res. 20, 5149–5152.
Fissekis, J. D and Sweet, F. (1973) The chemistry of some 5-(2-hydroxyalkyl) uracil derivatives and a synthesis of 5-vinyl uracil J Org. Chem 28, 264–269.
Hoffer, M. (1960) α-Thymidine. Chem. Ber. 93, 2777–2781.
Jones, L. W and Major, R T. (1927) Substituted O-alkyl hydroxylamines chemically related to medicinally valuable amines J. Am. Chem Soc 49, 1527–1540.
Griengl, H., Bodenteich, M., Hayden, W., Wanek, E., Streicher, W., Stutz, P., Bachmayer, H., Ghazzouh, I, and Rosenwirth, B (1985) 5-Haloalkyl-2′-deoxyuridines: a novel type of potent antiviral nucleoside analogue. J. Med. Chem. 28, 1679–1684.
Reese, C. B. and Skone, P A (1984) The protection of thymine and guanine residues in oligodeoxynucleotide synthesis. J Chem Soc, Perkin Trans. 11263–1271
Seela, F., Westermann, B., and Bindig, U. (1988) Liquid-liquid and solid-liquid phase-transfer glycosylation of pyrrolo [2,3-cO-pyrimidines-stereospecific synthesis of 2-deoxy-P-D-ribofuranosides related to 2′-deoxy-7-carboguanosine. J Chem. Soc, Perkin Trans. 1697–1702.
Giner-Sorolla, A, O’Bryant, S. A,, Nanos, C, Dolhnger, M. R., Bendich, A., and Burchenal, J H. (1968) The synthesis and biological properties of hydroxylaminopurines and related derivatives. J. Med. Chem. 11, 521–523.
Zemlicka, J., Chladek, S., Holy, A, and Smrt, J. (1966) Oligonucleotide compounds XIV Synthesis of some diribonucleoside phosphates using the dimethylaminomethylene derivatives of 2′, 3′-0-ethoxymethylene nbonucleo-sides Collect. Czech Chem. Commun. 31, 3198–3211
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© 1994 Humana Press Inc., Totowa, NJ
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Lin, P.K.T., Brown, D.M. (1994). Oligonucleotides Containing Degenerate Bases. In: Protocols for Oligonucleotide Conjugates. Methods in Molecular Biology, vol 26. Humana Press. https://doi.org/10.1007/978-1-59259-513-6_7
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DOI: https://doi.org/10.1007/978-1-59259-513-6_7
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