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Nucleic Acids Research, Vol 25, Issue 3 575-581, Copyright © 1997 by Oxford University Press

ARTICLES

Sequence-independent inhibition of RNA transcription by DNA dumbbells and other decoys

CS Lim, N Jabrane-Ferrat, JD Fontes, H Okamoto, MR Garovoy, BM Peterlin and CA Hunt
Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143-0446, USA. limc@dce41.nci.nih.gov

DNA dumbbells are stable, short segments of double-stranded DNA with closed nucleotide loops on each end, conferring resistance to exonucleases. Dumbbells may be designed to interact with transcription factors in a sequence-specific manner. The internal based paired sequence of DNA dumbbells in this study contains the X-box, a positive regulatory motif found in all MHC class II DRA promoters. In electrophoretic mobility shift assays (EMSAs), dumbbells and other oligonucleotides ('decoys') with the core X-box sequence were found to compete with the native strand for binding to X-box binding proteins (including RFX1). However, only the X-box dumbbell was capable of forming detectable complexes with such proteins using EMSA. In a model cell system, dumbbells were tested for their ability to block RFX1VP16 activation of a plasmid containing multiple repeats of the X-box linked to the CAT gene. While it appeared that dumbbells could block this activation, the effect was non-specific. This and further evidence suggests an inhibition of transcription, most likely via an interaction with the general transcriptional machinery.
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