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Nucleic Acids Research, 1995, Vol. 23, No. 13 2361-2366
© 1995

MOLECULAR BIOLOGY

3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR

David Loakes*, Daniel M. Brown, Solvita Linde1,+ and Fergal Hill

Medical Research Council, Laboratory of Molecular Biology Hills Road, Cambridge CB2 2h, UK 1Department of Haemotology, UNiversity of Cambridge Hills road, Cambridge, UK

*To whom corespondence should be addressed

Received April 28, 1995. Accepted May 19, 1995.

3-Nitropyrrole and 5-nitrolndole have been assessed as universal bases In primers for dideoxy DNA sequencing and In the polymerase chain reaction (PCR). In contrast to a previous report, we have found that the introduction of more than one 3-nitropyrrole residue at dispersed positions into primers significantly reduced their efficiency In PCR and sequencing reactions. Primers containing 5-nitroindole at multiple dispersed positions were similarly affected; for both bases only a small number of substitutions were tolerated. In PCR experiments neither base, when incorporated into primers in codon third positions, was as effective as hypoxanthine, which was incorporated In six codon third positions In a 20mer oligomer. However, primers containing up to four consecutive 5-nitroindole substitutions performed well in both PCR and sequencing actions.Consecutive 3-nitropyrrole substitutions were tolerated, but less well in comparable reactions.

+Present address: Biomedical Research and Study Centre, University if Lativia, Kirstenteina 1, Riga. Lativa LV-1067


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