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Although tracrRNAs are diverse in sequence and structure across type II CRISPR systems, the programmability of crRNA-tracrRNA hybridization for Cas9 is not fully understood. Here, we reveal the programmability of crRNA-tracrRNA hybridization for\n                    <jats:italic>Streptococcus pyogenes<\/jats:italic>\n                    Cas9, and in doing so, redefine the capabilities of Cas9 proteins and the sources of crRNAs, providing new biosensing applications for type II CRISPR systems. By reprogramming the crRNA-tracrRNA hybridized sequence, we show that engineered crRNA-tracrRNA interactions can not only enable the design of orthogonal cellular computing devices but also facilitate the hijacking of endogenous small RNAs\/mRNAs as crRNAs. We subsequently describe how these re-engineered gRNA pairings can be implemented as RNA sensors, capable of monitoring the transcriptional activity of various environment-responsive genomic genes, or detecting SARS-CoV-2 RNA in vitro, as an\n                    <jats:underline>A<\/jats:underline>\n                    typical\n                    <jats:underline>g<\/jats:underline>\n                    RNA-\n                    <jats:underline>a<\/jats:underline>\n                    ctivated\n                    <jats:underline>T<\/jats:underline>\n                    ranscription\n                    <jats:underline>H<\/jats:underline>\n                    alting\n                    <jats:underline>A<\/jats:underline>\n                    larm (AGATHA) biosensor.\n                  <\/jats:p>","DOI":"10.1038\/s41467-022-29604-x","type":"journal-article","created":{"date-parts":[[2022,4,11]],"date-time":"2022-04-11T06:04:03Z","timestamp":1649657043000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":53,"title":["Reprogrammed tracrRNAs enable repurposing of RNAs as crRNAs and sequence-specific RNA biosensors"],"prefix":"10.1038","volume":"13","author":[{"given":"Yang","family":"Liu","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8554-6648","authenticated-orcid":false,"given":"Filipe","family":"Pinto","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5250-9277","authenticated-orcid":false,"given":"Xinyi","family":"Wan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4183-8160","authenticated-orcid":false,"given":"Zhugen","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Shuguang","family":"Peng","sequence":"additional","affiliation":[]},{"given":"Mengxi","family":"Li","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2358-1050","authenticated-orcid":false,"given":"Jonathan M.","family":"Cooper","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8798-9592","authenticated-orcid":false,"given":"Zhen","family":"Xie","sequence":"additional","affiliation":[]},{"given":"Christopher E.","family":"French","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4858-8937","authenticated-orcid":false,"given":"Baojun","family":"Wang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,4,11]]},"reference":[{"key":"29604_CR1","doi-asserted-by":"publisher","first-page":"1247997","DOI":"10.1126\/science.1247997","volume":"343","author":"M Jinek","year":"2014","unstructured":"Jinek, M. et al. 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