We propose developing a trans-molecular RNA-switch for scientists to negatively affect the activity of endogenous microRNA for use as a molecular tool or therapeutic, an anti-miR. Since the discovery of miRNA, the creation of effective anti-miRs has been important, first to study and verify miRNA interactions, and, secondly, as a therapeutic tool. But, creating an effective anti-miR is not straightforward. At firt glance, one would thing that a strand of RNA in matching length and perfectly complementary in sequence would be the ideal anti-miR to fight for the attention of a particular miRNA and effectively neutralize it. However, a perfectly complementary sequence would induce the RISC complex and get cleaved rendering that strategy alone ineffective. While the backbone of the anti-miR can be modified, those modifications do not completely resolve this trade-off in complementariness and cleavage and add hepatoxicity issues to any therapeutic use of anti-miRs. We have been studying what we call "structurally interacting RNA" (or sxRNA) and believe sxRNA to be a post-transcriptional regulatory mechanism that regulates RNA Binding Protein interactions with mRNA. This is essentially a novel trans-acting RNA-RNA interaction forming a three way junction. This approach has three advantages for use as an anti-miR: (1) the presence of a stem loop within the bounds of the miRNA interaction eliminates concerns about cleavage, (2) the flanks of the stem loop can be perfectly complementary to an miRNA to increase binding and (3) three way junctions appear to be very stable structures. Our goal with this proposal is optimize an anti-miR using sxRNA and test the best candidate against other commercially available anti-miRs. Success at the product level using sxRNA as a molecular tool should ideally position the technology for additional uses.
Anti-miRs, oligonucleotides that diminish or eliminate the effectiveness of endogenous microRNA, are important both as molecular tools to study microRNA activity and as therapeutics. To date, rationally designed anti-miRs have not achieved high efficiencies. We believe anti-miRs can be created consistent with a regulatory method naturally in use, called structurally interacting RNA or sxRNA. sxRNA based anti-miR have the potential to be more effective as molecular tools and reduce hepatotoxicity issues when used as therapeutics.