SEQUENCE-INDEPENDENT INHIBITION OF RNA-TRANSCRIPTION BY DNA DUMBBELLSAND OTHER DECOYS

DNA dumbbells are stable, short segments of double-stranded DNA with c losed nucleotide loops on each end, conferring resistance to exonuclea ses, Dumbbells may be designed to interact with transcription factors in a sequence-specific manner, The internal based paired sequence of D NA dumbbells in this study contains the X-box, a positive regulatory m otif found in all MHC class II DRA promoters, In electrophoretic mobil ity shift assays (EMSAs), dumbbells and other oligonucleotides ('decoy s') with the core X-box sequence were found to compete with the native strand for binding to X-box binding proteins (including RFX1), Howeve r, 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 co ntaining multiple repeats of the X-box linked to the CAT gene, While i t appeared that dumbbells could block this activation, the effect was non-specific, This and further evidence suggests an inhibition of tran scription, most likely via an interaction with the general transcripti onal machinery.