Transcription inhibition using modified pentanucleotides

Inhibition of gene expression was recently achieved by targeting the transcriptionally competent open complex using relatively short, pentameric modified oligonucleotides at ∼60 μM. Corroborative affinity cleavage experiments using the copper complex of a phenanthroline conjugate provided the impetus to synthesize additional analogues containing substituents at the 2′-position of uridine in a derivative of 5′-GUGGA (-4 to +1), with the purpose of inhibiting transcription at lower concentrations. Conjugates of 5′-GUGGA modified at the 2′-position of uridine were convergently synthesized using a recently reported method. Seven analogues based upon the 5′-GUGGA scaffold were tested for their ability to inhibit transcription of the lac UV-5 operon. The conjugate containing a tethered pyrene showed 70% inhibition at 20 μM, and modest inhibition at as low as 5 μM. This is a significant improvement over previously tested pentanucleotides and provides direction for the preparation of a next generation of inhibitors.