Antisense Gene Inhibition by Oligonucleotides Containing C-5 Propyne Pyrimidines

Abstract

Phosphorothioate oligodeoxynucleotides containing the C-5 propyne analogs of uridine and cytidine bind RNA with high affinity and are potent antisense inhibitors of gene expression. In a cellular assay, gene-specific antisense inhibition occurred at nanomolar concentrations of oligonucleotide, was dose-dependent and exquisitely sensitive to sequence mismatches, and was correlated with the melting temperature and length of oligonucleotide. Activity was independent of RNA target site and cell type but was detectable only when the oligonucleotides were microinjected or delivered with cell-permeabilizing agents. These oligonucleotides may have important applications in therapy and in studies of gene function.

Antisense Inhibition of Silica-induced Tumor Necrosis Factor in Alveolar Macrophages

“…Several research groups (23,33,34) also observed that in the absence of appropriate delivery systems ONs exhibited no antisense activity, whereas in the presence of these delivery systems, i.e. liposomes, ONs showed strong activity.…”

Antisense oligonucleotide-based therapeutics for cancer

“…The scope of heterocyclic modifications is somewhat limited as they provide the recognition points for the Watson-Crick base pairing. Modifications to pyrmidine bases such as a methyl group, propyne or G-clamp (Figure 3) have been shown to increase the binding affinity for both DNA and RNA (Wagner et al, 1993;Flanagan et al, 1999). The 5-propynyl modification has proven to enhance the potency of phosphorothioate oligodeoxynucleotides in cell culture assays, but profound hepatoxicity limits their utility for in vivo application and human therapeutics (Shen et al, 2003).…”

Preorganization of DNA: Design Principles for Improving Nucleic Acid Recognition by Synthetic Oligonucleotides

“…A high affinity often means slow dissociation from the target and therefore a long lifetime for detection or for inhibition of biological processes. 43 It also implies being able to bind even when present at very low concentrations. Thus, a high affinity is desirable in many if not most of our current applications.…”