title: Sequence-independent inhibition of RNA transcription by DNA dumbbells and other decoys.
abstract: 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.
authors.affiliation: Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143-0446, USA. limc@dce41.nci.nih.gov
authors.forename: C S
authors.initials: CS
authors.lastname: Lim
authors.forename: N
authors.initials: N
authors.lastname: Jabrane-Ferrat
authors.forename: J D
authors.initials: JD
authors.lastname: Fontes
authors.forename: H
authors.initials: H
authors.lastname: Okamoto
authors.forename: M R
authors.initials: MR
authors.lastname: Garovoy
authors.forename: B M
authors.initials: BM
authors.lastname: Peterlin
authors.forename: C A
authors.initials: CA
authors.lastname: Hunt
mesh_terms: D000818:Animals; D001667:Binding, Competitive; D019556:COS Cells; D004247:DNA; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D005802:Genes, MHC Class II; D017930:Genes, Reporter; D009838:Oligodeoxyribonucleotides / Q000378:metabolism; D010957:Plasmids; D012313:RNA; D012333:RNA, Messenger; D000071701:Regulatory Factor X Transcription Factors; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D015533:Transcriptional Activation; D014162:Transfection; D014407:Tumor Cells, Cultured
chemical_list: D004268:DNA-Binding Proteins; D009838:Oligodeoxyribonucleotides; D012333:RNA, Messenger; D000071701:Regulatory Factor X Transcription Factors; D014157:Transcription Factors; D012313:RNA; D004247:DNA