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Nucleic Acids Research, 1994, Vol. 22, No. 20 4039-4043
© 1994

RNA

5-Nitroindole as an universal base analogue

D. Loakes and D.M. Brown*

Medical Research Council, Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK

*To whom correspondence should be addressed

Received August 16, 1994. Revised September 5, 1994. Accepted September 5, 1994.

4-, 5- and 6-Nitroindole have been investigated and compared with 3-nitropyrrole as universal bases in oligodeoxynucleotides. Of these the 5-nitroindole derivative was found to be superior giving higher duplex stability, and behaving indiscriminately towards each of the four natural bases in duplex melting experiments. 3-Nitropyrrole, whilst not discriminating between the natural bases, was found to lead to considerable destabilisation of the duplexes, particularly when multiple substitutions were made, in contrast to the 5-nitroindole nucleoside.


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