Abstract
Heptadecaoligodeoxyribonucleotides containing one or more of the bases, 6H,8H-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-one (P), 2-amino-6-methoxyaminopurine (K), and hypoxanthine (I) and combinations of P with K and I have been synthesised on a DNA synthesiser. The stability of duplexes containing these basemodified oligomers with P/A, P/G, K/C and K/T; P/A, P/G, I/C, I/T and I/A, I/G, I/C, I/T base pairs were compared by measuring their melting transition (Tm) values. Oligomers containing both P and K and P and I were more stable than those with I alone or with mismatches. These oligomers together with one with a P base at the 3'-end were used as primers in polymerase chain reaction (PCR) experiments. They were all effective primers except one with I alone and a triple mismatch. Thus the use of the degenerate bases P and K in primer design is established.
Full text
PDF



Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Brown D. M., Lin P. K. Synthesis and duplex stability of oligonucleotides containing adenine-guanine analogues. Carbohydr Res. 1991 Sep 2;216:129–139. doi: 10.1016/0008-6215(92)84156-m. [DOI] [PubMed] [Google Scholar]
- Corfield P. W., Hunter W. N., Brown T., Robinson P., Kennard O. Inosine.adenine base pairs in a B-DNA duplex. Nucleic Acids Res. 1987 Oct 12;15(19):7935–7949. doi: 10.1093/nar/15.19.7935. [DOI] [PMC free article] [PubMed] [Google Scholar]
- D'Onofrio M., Starr C. M., Park M. K., Holt G. D., Haltiwanger R. S., Hart G. W., Hanover J. A. Partial cDNA sequence encoding a nuclear pore protein modified by O-linked N-acetylglucosamine. Proc Natl Acad Sci U S A. 1988 Dec;85(24):9595–9599. doi: 10.1073/pnas.85.24.9595. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ehlen T., Dubeau L. Detection of ras point mutations by polymerase chain reaction using mutation-specific, inosine-containing oligonucleotide primers. Biochem Biophys Res Commun. 1989 Apr 28;160(2):441–447. doi: 10.1016/0006-291x(89)92452-2. [DOI] [PubMed] [Google Scholar]
- Kawase Y., Iwai S., Inoue H., Miura K., Ohtsuka E. Studies on nucleic acid interactions. I. Stabilities of mini-duplexes (dG2A4XA4G2-dC2T4YT4C2) and self-complementary d(GGGAAXYTTCCC) containing deoxyinosine and other mismatched bases. Nucleic Acids Res. 1986 Oct 10;14(19):7727–7736. doi: 10.1093/nar/14.19.7727. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kennedy T. E., Wager-Smith K., Barzilai A., Kandel E. R., Sweatt J. D. Sequencing proteins from acrylamide gels. Nature. 1988 Dec 1;336(6198):499–500. doi: 10.1038/336499a0. [DOI] [PubMed] [Google Scholar]
- Lin P. K., Brown D. M. Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues. Nucleic Acids Res. 1989 Dec 25;17(24):10373–10383. doi: 10.1093/nar/17.24.10373. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Martin F. H., Castro M. M., Aboul-ela F., Tinoco I., Jr Base pairing involving deoxyinosine: implications for probe design. Nucleic Acids Res. 1985 Dec 20;13(24):8927–8938. doi: 10.1093/nar/13.24.8927. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Newton C. R., Graham A., Heptinstall L. E., Powell S. J., Summers C., Kalsheker N., Smith J. C., Markham A. F. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 1989 Apr 11;17(7):2503–2516. doi: 10.1093/nar/17.7.2503. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ohkawa J., Okada N., Shinmyo A., Takano M. Primary structure of cucumber (Cucumis sativus) ascorbate oxidase deduced from cDNA sequence: homology with blue copper proteins and tissue-specific expression. Proc Natl Acad Sci U S A. 1989 Feb;86(4):1239–1243. doi: 10.1073/pnas.86.4.1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ohtsuka E., Matsuki S., Ikehara M., Takahashi Y., Matsubara K. An alternative approach to deoxyoligonucleotides as hybridization probes by insertion of deoxyinosine at ambiguous codon positions. J Biol Chem. 1985 Mar 10;260(5):2605–2608. [PubMed] [Google Scholar]
- Okada N., Koizumi N., Tanaka T., Ohkubo H., Nakanishi S., Yamada Y. Isolation, sequence, and bacterial expression of a cDNA for (S)-tetrahydroberberine oxidase from cultured berberine-producing Coptis japonica cells. Proc Natl Acad Sci U S A. 1989 Jan;86(2):534–538. doi: 10.1073/pnas.86.2.534. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stone M. J., Nedderman A. N., Williams D. H., Lin P. K., Brown D. M. Molecular basis for methoxyamine initiated mutagenesis. 1H nuclear magnetic resonance studies of base-modified oligodeoxynucleotides. J Mol Biol. 1991 Dec 5;222(3):711–723. doi: 10.1016/0022-2836(91)90507-3. [DOI] [PubMed] [Google Scholar]
- Walker J. E., Arizmendi J. M., Dupuis A., Fearnley I. M., Finel M., Medd S. M., Pilkington S. J., Runswick M. J., Skehel J. M. Sequences of 20 subunits of NADH:ubiquinone oxidoreductase from bovine heart mitochondria. Application of a novel strategy for sequencing proteins using the polymerase chain reaction. J Mol Biol. 1992 Aug 20;226(4):1051–1072. doi: 10.1016/0022-2836(92)91052-q. [DOI] [PubMed] [Google Scholar]
- Winter G., Koch G. L., Hartley B. S., Barker D. G. The amino acid sequence of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus. Eur J Biochem. 1983 May 2;132(2):383–387. doi: 10.1111/j.1432-1033.1983.tb07374.x. [DOI] [PubMed] [Google Scholar]