{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T18:42:48Z","timestamp":1791830568658,"version":"4.3.4"},"reference-count":45,"publisher":"American Chemical Society (ACS)","issue":"19","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009790","name":"University at Albany","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009790","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM156250"],"award-info":[{"award-number":["R35GM156250"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Rapid and accessible detection of pathogens through diverse detection modalities remains highly desirable. Most current pathogen detection assays rely on a single detection modality. Here, we have used the same RNA switch-CRISPR platform for detection of multiple pathogenic genomes through three different detection modalities. In this study, the RNA switch is repurposed as a reprogrammable platform for genome detection, enabling three orthogonal signal outputs: glucometer-based, fluorescence, and visual. Target pathogen genomes selectively regulate cell-free in vitro translation of \u03b2-galactosidase through the RNA switch, producing several hundred-fold increases in glucose following lactose hydrolysis while simultaneously generating fluorescence and colorimetric signals. The platform is readily reprogrammed to recognize conserved genomic regions from five distinct pathogens, with specificity dictated by CRISPR\u2013Cas12a-mediated processing of a DNA regulator that controls RNA switch activation and initiates the downstream cell-free translation cascade. Glucometer-based, fluorescence, and paper-based colorimetric outputs each enabled selective detection of Salmonella typhi, Salmonella enterica, Listeria monocytogenes, Shiga toxin-producing Escherichia coli (STEC), and Campylobacter jejuni. Fluorescence and colorimetric responses were analyzed both qualitatively and quantitatively using image processing and showed strong agreement with glucometer measurements obtained using a handheld glucometer, providing a simple and accessible quantitative readout. The platform was further validated using the complete Listeria monocytogenes genome, achieving a detection sensitivity approaching a single genome copy per microliter. Together, this reprogrammable CRISPR-RNA switch platform enables the same detection setup to be programmed for multiple targets and readouts through three different detection modalities, some of which are well suited for resource-limited environments.<\/jats:p>","DOI":"10.1021\/acs.biochem.6c00564","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T01:02:13Z","timestamp":1789606933000},"page":"2972-2985","source":"Crossref","is-referenced-by-count":1,"title":["Programmable\nGenome Sensing with Visual, Fluorescence,\nand Glucometer Readings: Cell-Free\n                    <i>In Vitro<\/i>\n                    Translation\nApproach Using RNA Switch-CRISPR"],"prefix":"10.1021","volume":"65","author":[{"given":"Mahla","family":"Lashkari","sequence":"first","affiliation":[{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]},{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie E.","family":"Connell","sequence":"additional","affiliation":[{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmett","family":"Hanson","sequence":"additional","affiliation":[{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel E.","family":"Adade","sequence":"additional","affiliation":[{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ram J.","family":"Tharu","sequence":"additional","affiliation":[{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4349-3701","authenticated-orcid":true,"given":"Mehmet V.","family":"Yigit","sequence":"additional","affiliation":[{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]},{"name":"University at Albany, State University of New York , , 1400 Washington Avenue , , ,","place":["Albany, New York, United States, 12222"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"issue":"1","key":"2026100608071787200_cit1","doi-asserted-by":"publisher","first-page":"5425","DOI":"10.1038\/s41467-024-49626-x","article-title":"Deconstructing Synthetic Biology across Scales:\nA Conceptual Approach for Training Synthetic Biologists","volume":"15","author":"Karim","year":"2024","journal-title":"Nat. Commun"},{"issue":"1","key":"2026100608071787200_cit2","doi-asserted-by":"publisher","first-page":"3347","DOI":"10.1038\/s41467-018-05864-4","article-title":"A Low-Cost Paper-Based\nSynthetic Biology Platform for Analyzing Gut Microbiota and Host Biomarkers","volume":"9","author":"Takahashi","year":"2018","journal-title":"Nat. Commun."},{"key":"2026100608071787200_cit3","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adu7366","article-title":"Counterions Influence the Isothermal Self-Assembly\nof DNA Nanostructures","volume":"11","author":"Rodriguez","year":"2025","journal-title":"Sci. Adv."},{"issue":"7963","key":"2026100608071787200_cit4","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/s41586-023-06091-8","article-title":"Programming Inactive\nRNA-Binding Small Molecules into Bioactive Degraders","volume":"618","author":"Tong","year":"2023","journal-title":"Nature"},{"issue":"12","key":"2026100608071787200_cit5","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/nnano.2010.231","article-title":"The Emerging\nField of RNA Nanotechnology","volume":"5","author":"Guo","year":"2010","journal-title":"Nat. Nanotechnol."},{"issue":"12","key":"2026100608071787200_cit6","doi-asserted-by":"publisher","first-page":"1578","DOI":"10.1038\/s41592-022-01684-z","article-title":"Quantification\nof Extracellular Proteins,\nProtein Complexes and MRNAs in Single Cells by Proximity Sequencing","volume":"19","author":"Vistain","year":"2022","journal-title":"Nat. Methods"},{"issue":"5","key":"2026100608071787200_cit7","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1016\/j.cell.2016.04.059","article-title":"Rapid,Low-Cost Detection\nof Zika Virus Using Programmable\nBiomolecular Components","volume":"165","author":"Pardee","year":"2016","journal-title":"Cell"},{"issue":"4","key":"2026100608071787200_cit8","doi-asserted-by":"publisher","first-page":"940","DOI":"10.1016\/j.cell.2014.10.004","article-title":"Paper-Based\nSynthetic Gene Networks","volume":"159","author":"Pardee","year":"2014","journal-title":"Cell"},{"key":"2026100608071787200_cit9","doi-asserted-by":"publisher","first-page":"45393","DOI":"10.1038\/srep45393","article-title":"Engineering\nStructurally Interacting RNA (SxRNA)","volume":"7","author":"Doyle","year":"2017","journal-title":"Sci. Rep."},{"issue":"12","key":"2026100608071787200_cit10","doi-asserted-by":"publisher","first-page":"1276","DOI":"10.1038\/nbt.3053","article-title":"Tunable Protein Degradation in Bacteria","volume":"32","author":"Cameron","year":"2014","journal-title":"Nat. Biotechnol."},{"issue":"22","key":"2026100608071787200_cit11","doi-asserted-by":"publisher","first-page":"2400508","DOI":"10.1002\/adhm.202400508","article-title":"Universal CRISPR-Cas12a and Toehold\nRNA Cascade Reaction on Paper Substrate for Visual Salmonella Genome\nDetection","volume":"13","author":"Kachwala","year":"2024","journal-title":"Adv. Healthcare Mater"},{"issue":"15","key":"2026100608071787200_cit12","doi-asserted-by":"publisher","first-page":"2500784","DOI":"10.1002\/smll.202500784","article-title":"CRISPR-Responsive\nReprogrammable\nLabel-Free Fluorescent Nanoclusters for ML-Assisted Pathogenic Genome\nDetection on Solid Substrates","volume":"21","author":"Hanson","year":"2025","journal-title":"Small"},{"issue":"6387","key":"2026100608071787200_cit13","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1126\/science.aaq0179","article-title":"Multiplexed and Portable Nucleic\nAcid Detection Platform with Cas13,\nCas12a and Csm6","volume":"360","author":"Gootenberg","year":"2018","journal-title":"Science"},{"issue":"6387","key":"2026100608071787200_cit14","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1126\/science.aar6245","article-title":"CRISPR-Cas12a\nTarget Binding Unleashes\nIndiscriminate Single-Stranded DNase Activity","volume":"360","author":"Chen","year":"2018","journal-title":"Science"},{"issue":"10","key":"2026100608071787200_cit15","doi-asserted-by":"publisher","first-page":"2986","DOI":"10.1038\/s41596-019-0210-2","article-title":"SHERLOCK: Nucleic Acid Detection\nwith CRISPR Nucleases","volume":"14","author":"Kellner","year":"2019","journal-title":"Nat. Protoc."},{"issue":"38","key":"2026100608071787200_cit16","doi-asserted-by":"publisher","first-page":"21098","DOI":"10.1021\/acs.analchem.5c04448","article-title":"An RCA-CRISPR-Enhanced\nSERS Platform for Ultrasensitive\nand Single-Nucleotide-Resolved Detection of Exosomal MiRNA-21 in Early\nLung Cancer","volume":"97","author":"Teng","year":"2025","journal-title":"Anal. Chem."},{"issue":"4","key":"2026100608071787200_cit17","doi-asserted-by":"publisher","first-page":"1934","DOI":"10.1021\/acs.analchem.0c04949","article-title":"Reprogrammable Gel\nElectrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization\nChain Reaction","volume":"93","author":"Kachwala","year":"2021","journal-title":"Anal. Chem."},{"issue":"37","key":"2026100608071787200_cit18","doi-asserted-by":"publisher","first-page":"13500","DOI":"10.1039\/D2NR03590A","article-title":"Recombinase Amplified\nCRISPR Enhanced Chain Reaction (RACECAR) for Viral Genome Detection","volume":"14","author":"Kachwala","year":"2022","journal-title":"Nanoscale"},{"issue":"1","key":"2026100608071787200_cit19","doi-asserted-by":"publisher","first-page":"5409","DOI":"10.1038\/s41467-023-41006-1","article-title":"Programmable\nRNA Detection with CRISPR-Cas12a","volume":"14","author":"Rananaware","year":"2023","journal-title":"Nat. Commun."},{"issue":"1","key":"2026100608071787200_cit20","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1089\/fpd.2023.0157","article-title":"Economic\nBurden of Foodborne Illnesses Acquired in\nthe United States","volume":"22","author":"Hoffmann","year":"2025","journal-title":"Foodborne Pathog. 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Microbiol."},{"key":"2026100608071787200_cit27","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268822000929","article-title":"Outbreak of STEC O157: H7 Linked to a Milk Pasteurisation\nFailure at a Dairy Farm in England, 2019","volume":"150","author":"Jenkins","year":"2022","journal-title":"Epidemiol.\nInfect."},{"issue":"4","key":"2026100608071787200_cit28","doi-asserted-by":"publisher","first-page":"2231","DOI":"10.1007\/s00248-023-02269-9","article-title":"Listeria Monocytogenes\nan Emerging Pathogen: A Comprehensive\nOverview on Listeriosis, Virulence Determinants, Detection, and Anti-Listerial\nInterventions","volume":"86","author":"Ravindhiran","year":"2023","journal-title":"Microb. Ecol."},{"issue":"31","key":"2026100608071787200_cit29","doi-asserted-by":"publisher","first-page":"9702","DOI":"10.1002\/anie.201804292","article-title":"Biocomputing for Portable,\nResettable, and Quantitative Point-of-Care\nDiagnostics: Making the Glucose Meter a Logic-Gate Responsive Device\nfor Measuring Many Clinically Relevant Targets","volume":"57","author":"Zhang","year":"2018","journal-title":"Angew. Chem. Int. Ed."},{"issue":"6","key":"2026100608071787200_cit30","doi-asserted-by":"publisher","first-page":"705","DOI":"10.2174\/1573411017666210804105750","article-title":"Recent Advances\nof Using Personal Glucose Meter as a Biosensor Readout for Non-Glucose\nTargets","volume":"18","author":"Zhang","year":"2022","journal-title":"Curr. Anal. Chem."},{"issue":"9","key":"2026100608071787200_cit31","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1038\/nchem.1092","article-title":"Using Personal Glucose\nMeters and Functional DNA Sensors to Quantify\na Variety of Analytical Targets","volume":"3","author":"Xiang","year":"2011","journal-title":"Nat. Chem."},{"issue":"1","key":"2026100608071787200_cit32","doi-asserted-by":"publisher","first-page":"724","DOI":"10.1038\/s41467-020-20639-6","article-title":"A Glucose Meter Interface\nfor Point-of-Care Gene Circuit-Based\nDiagnostics","volume":"12","author":"Amalfitano","year":"2021","journal-title":"Nat. Commun."},{"issue":"36","key":"2026100608071787200_cit33","doi-asserted-by":"publisher","first-page":"14283","DOI":"10.1073\/pnas.0703961104","article-title":"A Modular and Extensible RNA-Based\nGene-Regulatory\nPlatform for Engineering Cellular Function","volume":"104","author":"Maung","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026100608071787200_cit34","first-page":"5900","article-title":"Higher-Order Cellular Information\nProcessing with Synthetic\nRNA Devices","volume":"322","author":"Maung","year":"2008","journal-title":"Science"},{"issue":"6","key":"2026100608071787200_cit35","doi-asserted-by":"publisher","first-page":"3486","DOI":"10.1021\/acs.analchem.4c05808","article-title":"Development of a Cell-Free, Toehold Switch-Based Biosensor for Rapid\nand Sensitive Zika Virus Detection","volume":"97","author":"Chen","year":"2025","journal-title":"Anal. Chem."},{"issue":"43","key":"2026100608071787200_cit36","doi-asserted-by":"publisher","first-page":"5813","DOI":"10.1039\/d3ay01408h","article-title":"Development\nof a Cell-Free Toehold Switch for Hepatitis A Virus Type\nI on-Site Detection","volume":"15","author":"Kang","year":"2023","journal-title":"Anal. Methods"},{"issue":"3","key":"2026100608071787200_cit37","doi-asserted-by":"publisher","first-page":"2774","DOI":"10.1021\/acssensors.5c04848","article-title":"Cas12a-Programmed\nModular CRISPR Cascade Reaction on Paper Supports for Dual-Mode Detection\nof Pathogenic Genomes","volume":"11","author":"Hanson","year":"2026","journal-title":"ACS Sens."},{"key":"2026100608071787200_cit38","unstructured":"National Library of Medicine (NLM).\n          \n          Genome assembly\nASM19603v1; National Library of Medicine: 2026. https:\/\/www.ncbi.nlm.nih.gov\/datasets\/genome\/GCA_000196035.1\/."},{"issue":"1","key":"2026100608071787200_cit39","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1038\/s41597-024-03440-8","article-title":"Complete\nGenome of the Listeria Monocytogenes Strain AUF, Used as a Live Listeriosis\nVeterinary Vaccine","volume":"11","author":"Feodorova","year":"2024","journal-title":"Sci. Data"},{"issue":"24","key":"2026100608071787200_cit40","doi-asserted-by":"publisher","first-page":"6507","DOI":"10.1039\/c6an01409g","article-title":"Image Analysis for\na Microfluidic\nPaper-Based Analytical Device Using the CIE: L \u2217 a \u2217\nb \u2217 Color System","volume":"141","author":"Komatsu","year":"2016","journal-title":"Analyst"},{"key":"2026100608071787200_cit41","doi-asserted-by":"publisher","first-page":"107465","DOI":"10.1016\/j.biotechadv.2019.107465","article-title":"\u03b2-Galactosidases:\nA Great Tool for Synthesizing Galactose-Containing Carbohydrates","volume":"39","author":"Lu","year":"2020","journal-title":"Biotechnol. Adv."},{"key":"2026100608071787200_cit42","unstructured":"National Center for Biotechnology Information.\n          \n          PubChem\nCompound Summary for CID 9894651, Chlorophenol Red-beta-D-galactopyranoside.; 2026. https:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/Chlorophenol-Red-beta-D-galactopyranoside."},{"key":"2026100608071787200_cit43","unstructured":"National Center for Biotechnology Information.\n          \n          PubChem\nCompound Summary for CID 129844748, Fluorescein di-(beta-d-galactopyranoside); 2026. https:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/Fluorescein-di-_beta-d-galactopyranoside."},{"issue":"7","key":"2026100608071787200_cit44","doi-asserted-by":"publisher","first-page":"1785","DOI":"10.1021\/acssynbio.1c00204","article-title":"Recognition of DNA\nTarget Formulations by CRISPR-Cas12a Using a DsDNA Reporter","volume":"10","author":"Smith","year":"2021","journal-title":"ACS Synth. Biol."},{"issue":"15","key":"2026100608071787200_cit45","doi-asserted-by":"publisher","first-page":"1474","DOI":"10.1021\/acs.biochem.0c00140","article-title":"Probing CRISPR-Cas12a\nNuclease Activity Using Double-Stranded\nDNA-Templated Fluorescent Substrates","volume":"59","author":"Smith","year":"2020","journal-title":"Biochemistry"}],"container-title":["Biochemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.biochem.6c00564","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/19\/2972\/68538928\/acs.biochem.6c00564.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/bichaw\/article-pdf\/65\/19\/2972\/68538928\/acs.biochem.6c00564.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T12:29:32Z","timestamp":1791289772000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/bichaw\/article\/65\/19\/2972\/5431725\/Programmable-Genome-Sensing-with-Visual"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":45,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,9,16]]},"published-print":{"date-parts":[[2026,10,6]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.biochem.6c00564","relation":{},"ISSN":["0006-2960","1520-4995"],"issn-type":[{"value":"0006-2960","type":"print"},{"value":"1520-4995","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]}}}