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Sci Rep. 2017 Mar 28;7:45393. doi: 10.1038/srep45393.

Engineering Structurally Interacting RNA (sxRNA).

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Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA.
Department of Pediatrics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA.
HocusLocus, LLC, 253 Fuller Road, Nanofab North, Albany NY 12203, USA.
Pediatric Infectious Diseases, Departments of Pediatrics and Molecular Genetics and Microbiology, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA.


RNA-based three-way junctions (3WJs) are naturally occurring structures found in many functional RNA molecules including rRNA, tRNA, snRNA and ribozymes. 3WJs are typically characterized as resulting from an RNA molecule folding back on itself in cis but could also form in trans when one RNA, for instance a microRNA binds to a second structured RNA, such as a mRNA. Trans-3WJs can influence the final shape of one or both of the RNA molecules and can thus provide a means for modulating the availability of regulatory motifs including potential protein or microRNA binding sites. Regulatory 3WJs generated in trans represent a newly identified regulatory category that we call structurally interacting RNA or sxRNA for convenience. Here we show that they can be rationally designed using familiar cis-3WJ examples as a guide. We demonstrate that an sxRNA "bait" sequence can be designed to interact with a specific microRNA "trigger" sequence, creating a regulatable RNA-binding protein motif that retains its functional activity. Further, we show that when placed downstream of a coding sequence, sxRNA can be used to switch "ON" translation of that sequence in the presence of the trigger microRNA and the amount of translation corresponded with the amount of microRNA present.

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