Developing RNA based RNA sensors

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William Rostain

Institute of Systems and Synthetic biology, France

In the last few years, new types of structures and roles for RNA molecules have been constantly discovered: sRNAs, microRNAs, siRNA are just a few amongst an ever growing catalogue of RNA types, with the latest addition to the collection being circular RNAs (circRNA). There is therefore an urgent need for reliable and robust methods for in vivo visualisation and quantification of this type of molecule. Our team has recently created an RNA design software based on first principles, RNAdes, which uses in silico evolution to automatically design small RNAs capable of allosteric interactions with other RNAs in vivo. Using this software, we are designing and implementing various small sensors. By using fluorophore binding aptamers such as the malachite green aptamer within these designs, we have created artificial scaffolds which stabilise these fluorescent aptamers, allowing in vivo visualisation of RNA. We are developing methods to automatically design allosteric RNA sensors using these fluorescent RNAs and/or genetically encoded reporters. These will expand the toolbox for researchers in RNA biology, as well as aid in the construction of more advanced synthetic RNA circuits.