Innovations in the use of antisense oligonucleotides

Approaches for the sequence-specific knockdown of mRNA

Over the past 25 years there have been thousands of published reports describing applications of antisense nucleic acid derivatives for targeted inhibition of gene function. The major classes of antisense agents currently used by investigators for sequence-specific mRNA knockdowns are antisense oligonucleotides (ODNs), ribozymes, DNAzymes and RNA interference (RNAi). Whatever the method, the problems for effective application are remarkably similar: efficient delivery, enhanced stability, minimization of off-target effects and identification of sensitive sites in the target RNAs. These challenges have been in existence from the first attempts to use antisense research tools, and need to be met before any antisense molecule can become widely accepted as a therapeutic agent.

Reversible permeabilization. A novel technique for the intracellular introduction of antisense oligodeoxynucleotides into intact smooth muscle

Antisense oligodeoxynucleotides (ODNs) have been used to modify gene expression in vitro and are also promising therapeutic agents. Although there are numerous reports of antisense ODN-mediated changes in protein expression of cultured cells, use of these compounds to achieve antisense regulation of specific proteins in intact tissue has been limited. The aims of this study were (1) to define organ culture conditions for ileum smooth muscle that would permit long-term maintenance of force-generating capabilities and normal ultrastructure and (2) to develop a method for efficient introduction of antisense ODNs into intact tissue. Sheets of ODN-containing, reversibly permeabilized rat outer longitudinal ileum were maintained in a serum-free organ culture medium for 1 week without significant decreases in tension response to membrane depolarization or carbachol stimulation; the G protein-coupled calcium sensitization pathway was also intact after 7 days. Reversible permeabilization, a method previously used to load smooth and cardiac muscle with aequorin and heparin, was effective for loading > 95% of ileum smooth muscle cells with a fluorescein-conjugated antisense ODN (5'-AAGGGCCATTTTGTT-FITC-3'). Confocal microscopy of reversibly permeabilized smooth muscle loaded with fluorescent antisense ODNs revealed intense nuclear fluorescence and less intense, homogeneous, cytoplasmic fluorescence. Internally radiolabeled ODNs (homologous to the above sequence) showed complete degradation between 4 and 16 hours after introduction into the cells. In summary, we have demonstrated methods for long-term organ culture and high-efficiency introduction of antisense ODNs into intact smooth muscle sheets. Such methods have broad potential utility for investigating many questions in smooth muscle biology. At present, however, a major limitation of this approach is the short half-life of phosphorothioated ODNs.

Inhibition of dengue virus by novel, modified antisense oligonucleotides

Five different target regions along the length of the dengue virus type 2 genome were compared for inhibition of the virus following intracellular injection of the cognate antisense oligonucleotides and their analogs. Unmodified phosphodiester oligonucleotides as well as the corresponding phosphorothioate oligonucleotides were ineffective in bringing about a significant inhibition of the virus. Novel modified phosphorothioate oligonucleotides in which the C-5 atoms of uridines and cytidines were replaced by propynyl groups caused a significant inhibition of the virus. Antisense oligonucleotide directed against the target region near the translation initiation site of dengue virus RNA was the most effective, followed by antisense oligonucleotide directed against a target in the 3' untranslated region of the virus RNA. It is suggested that the inhibitory effect of these novel modified oligonucleotides is due to their increased affinity for the target sequences and that they probably function via an RNase H cleavage of the oligonucleotide:RNA heteroduplex.

Selection of antisense oligonucleotides on the basis of genomic frequency of the target sequence

Antisense oligonucleotides (ASOs) are capable of blocking the expression of targeted genes and are potential antitumor and antiviral therapeutic agents. The specificity of ASO gene inhibition is compromised when homology to other sequences allows the selected ASO to bind to nontargeted mRNAs. To reduce this nonspecific activity, an ASO should target a sequence that is predicted to be unlikely to occur in other mRNAs. The probability of a sequence being unique can be predicted by determining the genomic frequency of short stretches of sequences contained within the target sequence. Two computer programs, OLIGOMER and HEXAGRAPH, were developed for this analysis. OLIGOMER was used to analyze the genomic frequencies of di-, tri-, and hexamers in more than 24 million nucleotides from 8 different genomes in GenBank. A mathematical model was developed that predicts the genomic frequency of longer oligomers on the basis of the observed frequencies of shorter oligomers. The second program, HEXAGRAPH, was used to graphically display the genomic frequency data of a selected target gene. The computational tools developed in this study may help to design more efficient ASOs by decreasing their nonspecific binding activity.

Quantitative evaluation of intracellular sense: antisense RNA hybrid duplexes

Previous studies have demonstrated that for an antisense RNA to be effective in attenuating gene expression, a large but indeterminate excess of antisense RNA is required. To quantitatively evaluate RNA hybrid duplex formation, expression vectors containing antisense dihydrofolate reductase (DHFR) cDNAs were transfected into KB and KB-1BT (a DHFR overexpressing variant) cells and transfectants expressing antisense transcripts of exon 1 through intron I (ex1-I) or exons 1 through 4 (ex1-4) were analyzed for hybrid duplex formation. Stable duplexes were detectable in KB-1BT but not in KB cells. Approximately 5-9% of antisense ex1-I RNA and 20-37% of antisense ex1-4 RNA were found in duplexes. The amount of each hybrid duplex RNA was found to be a linear function of intracellular single-stranded antisense RNA levels and a hybrid index, Hs:as, was devised to describe this relationship. Based upon the value of Hs:as for each antisense RNA:mRNA duplex, it is calculated that an approximate 2,800- and 600-fold excess of ex1-I and ex1-4 antisense RNA are respectively required for 50% of DHFR mRNA to be present in duplexes. Results support the hypothesis that intracellular sense:antisense RNA hybrid duplex formation is inefficient and dependent upon the levels, lengths and possibly the structures of the RNAs involved.