Stable DNA triple helix formation using oligonucleotides containing 2'-aminoethoxy,5-propargylamino-U

Sollogoub, Matthieu, Darby, Richard A.J., Cuenoud, Bernard, Brown, Tom and Fox, Keith R. (2002) Stable DNA triple helix formation using oligonucleotides containing 2'-aminoethoxy,5-propargylamino-U. Biochemistry, 41 (23), 7224-7231. (doi:10.1021/bi020164n).

Abstract

We have prepared oligonucleotides containing the novel base analogue 2'-aminoethoxy,5-proparaylamino-U in place of thymidine and examined their ability to form intermolecular and intramolecular triple helices by DNase I footprinting and thermal melting studies. The results were compared with those for oligonucleotides containing 5-propargylamino-dU and 2'-aminoethoxy-T. We find that the bis-substituted derivative produces a large increase in triplex stability, much greater than that produced by either of the monosubstituted analogues, which are roughly equipotent with each other. Intermolecular triplexes with 9-mer oligonucleotides containing three or four base modifications generate footprints at submicromolar concentrations even at pH 7.5, in contrast to the unmodified oligonucleotide, which failed to produce a footprint at pH 5.0, even at 30 muM. UV- and fluorescence melting studies with intramolecular triplexes confirmed that the bis-modified base produces a much greater increase in T-m than either modification alone.

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Contributors

Author: Keith R. Fox

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