Sequence-specific inhibition of a transcription factor by circular dumbbell DNA oligonucleotides

The inhibition of specific transcription regulatory proteins is a new approach to control gene expression. The transcriptional activities of DNA-binding proteins can be inhibited by the use of double-stranded oligonucleotides that compete for the binding to their specific target sequences in promoters and enhancers. We used nicked (NDODN-kappa B) and circular (CDODN-kappa B) dumbbell DNA oligonucleotides containing a NF-kappa B binding site to analyze the inhibition of the NF-kappa B-dependent activation of the human immunodeficiency virus type-1 (HIV-1) enhancer, The dumbbell DIVA oligonucleotides are stable, short segments of double-stranded DNA with closed nucleotide loops on each end, which confer resistance to exonucleases, The dumbbell and other oligonucleotides (decoys) with the NF-kappa B sequence were found to compete with the native strand for NF-kappa B binding. The circular dumbbell and double-stranded phosphorothioate oligonucleotides competed with the native strand for binding to the NF-kappa B binding proteins, while the nicked NF-kappa B dumbbell was a less effective competitor. In Jurkat T-cells, the dumbbell and other oligonucleotides were tested for their ability to block the activation of the plasmid HIV-NL4-3 Luc, The CDODN-kappa B strongly inhibits the specific transcriptional regulatory proteins, as compared with the NDODN-kappa B and the double stranded phosphodiester oligonucleotides, On the other hand, the double stranded phosphorothioate oligonucleotides could also block this activation, but the effect was non-specific. The circular (CDODN) dumbbell oligonucleotides may efficiently compete for the binding of specific transcription factors within cells, thus providing anti-HIV-1 or other therapeutic effects, (C) 1999 Federation of European Biochemical Societies.