Orthogonal RNA imaging and simple RNA detection tools

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International interest in the regulatory role of RNA is rapidly growing. Genomic regions previously thought of as 'junk' DNA play complex roles in gene regulation and are typically transcribed into RNA. Stress granules and other dynamic cellular particles contain RNA and are being found to play important roles in gene regulation. Tools for the study of RNA however are still embryonic and the global market for RNA research tools (excluding RNA interference) is anticipated to reach nearly 1 billion US dollars by 2020 (BCC research). ****While the study of proteins was revolutionized by the development of multicolour fluorescent protein tags and orthogonal protein based affinity tags, RNA imaging and purification methods have not kept pace. The first generation of RNA Mango, holds much potential for RNA imaging and RNA protein complex purification, but currently does not allow multichannel imaging or orthogonal purifications. This NSERC CRD proposal aims to directly address these issues so as to continue the rapid commercialization of this Canadian technology together with Applied Biological Materials (Burnaby, BC).****The proposal has two specific aims: The first is to develop an orthogonal RNA Mango system capable of imaging two RNAs simultaneously. These new high affinity aptamers will allow the development of two colour imaging and orthogonal purification methodologies and will have many in vitro and in vivo applications. The second aim of this proposal will apply first generation Mango technology to the detect of low concentrations of RNA using isothermal methods. Together this proposal will generate a broad range of commercializable elements that will significantly extend the utility of first generation RNA Mango technology.