Enhanced and synergistic downregulation of oncogenic miRNAs by self-assembled branched DNA

Abstract

miRNAs, a group of small non-coding RNA molecules, regulate the expression of many genes involved in various cellular processes. Acute evidence suggests that one miRNA can regulate many genes as its targets, while one gene can be targeted by many miRNAs that co-operatively regulate the gene. Thus, targeting a single miRNA is not sufficient enough to rescue the disease phenotype but it is also essential to target multiple miRNAs simultaneously. This inspired us to design a novel DNA nanostructure that can concurrently downregulate multiple oncomiRNAs. Here we designed a programmable antimiR branched DNA (antimiR-bDNA) nanostructure having antimiRNAs for selective binding to oncomiRNAs miRNA-27a, 96 and 182 which collectively downregulate FOXO1a expression. The antimiR-bDNAs show enhanced stability compared to naked antimiRNAs in serum and are able to knockdown these miRNAs with up to similar to 50% greater repression as compared to antimiRNAs. This synergistic miRNA repression leads to the restoration of FOXO1a protein levels which in turn inhibit G1-S traversion in cancer cells. To the best of our knowledge, this is the first study harnessing the ability of bDNA structures to silence multiple miRNAs simultaneously.