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Nucleic Acids Research, 1992, Vol. 20, No. 19 5149-5152
© 1992

CHEMISTRY

Synthesis of oligodeoxyribonucleotides containing degenerate bases and their use as primers in the polymerase chain reaction

Paul Kong Thoo and Daniel M. Brown

MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK

Received June 2, 1992. Revised September 11, 1992. Accepted September 11, 1992.

Heptadecaoligodeoxyribonudeotides 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 base-modified 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.


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