Computational Design of an RNA Nanoparticle Consisting of a Three-Way Junction and pre-miRNAs

Abstract

Recent research on RNA-based regulation, RNAi, and development of human diseases has shed light on the huge potential of miRNAs as novel therapeutic agents for medicine. It has been suggested that a successful tissue-targetable nucleic acid delivery system has to overcome the problem of poor stability of nucleic acids in biological media. To solve this problem we rationally designed a pre-miRNA-nanoparticle-mediated RNA delivery system by integrating computer modeling, miRNA regulatory function and RNA structure versatility. It has been well documented that the initial product of a miRNA, the pri-miRNA, is transcribed in the nucleus. It forms a highly stable stem-loop structure that is processed to form the pre-miRNA by the RNase III enzyme, Drosha. The stable pre-miRNA stem-loop structure of 60-70 nt is transported to the cytoplasm and is then processed into a short double stranded fragment by dicer. Finally the miRNA duplex is unwound to form a ∼22-nt single stranded mature miRNA which is associated with the RISC complex. In this study, we present a computational design of a synthetic, highly stable superstructure made from an RNA junction that can accommodate multiple pre-miRNAs. A three-way junction building block, which was obtained from the RNAjunction database, was attached to three human let-7 pre-miRNAs. This highly stable RNA nanoparticle is expected to enable the binding of the dicer protein for the efficient cleavage of the pre-miRNA in the cytoplasm. As a result, the mature let-7 miRNAs can enter into the targeted cell cytosol, and be protected from degrading interactions while performing its specific regulatory functions.