{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T03:22:55Z","timestamp":1792120975938,"version":"4.4.0"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,1,23]],"date-time":"2025-01-23T00:00:00Z","timestamp":1737590400000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/Y009703\/1"],"award-info":[{"award-number":["MR\/Y009703\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100003914","name":"Kennedy\u2019s Disease Association","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100003914","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005202","name":"Muscular Dystrophy Association","doi-asserted-by":"publisher","award":["578222"],"award-info":[{"award-number":["578222"]}],"id":[{"id":"10.13039\/100005202","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/N024850\/1"],"award-info":[{"award-number":["MR\/N024850\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Marie Curie Initial Training Network EScoDNA","award":["317110"],"award-info":[{"award-number":["317110"]}]},{"name":"xford University Press John Fell Fund"},{"name":"La Caixa Foundation Fellowship","award":["LCF\/BQ\/EU16\/11560044"],"award-info":[{"award-number":["LCF\/BQ\/EU16\/11560044"]}]},{"DOI":"10.13039\/501100000769","name":"University of Oxford","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Nucleic acid nanostructures offer unique opportunities for biomedical applications due to their sequence-programmable structures and functions, which enable the design of complex responses to molecular cues. Control of the biological activity of therapeutic cargoes based on endogenous molecular signatures holds the potential to overcome major hurdles in translational research: cell specificity and off-target effects. Endogenous microRNAs (miRNAs) can be used to profile cell type and cell state, and are ideal inputs for RNA nanodevices. Here, we present CRISPR MiRAGE (miRNA-activated genome editing), a tool comprising a dynamic single-guide RNA that senses miRNA complexed with Argonaute proteins and controls downstream CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) activity based on the detected miRNA signature. We study the operation of the miRNA-sensing single-guide RNA and attain muscle-specific activation of gene editing through CRISPR MiRAGE in models of Duchenne muscular dystrophy. By enabling RNA-controlled gene editing activity, this technology creates opportunities to advance tissue-specific CRISPR treatments for human diseases.<\/jats:p>","DOI":"10.1093\/nar\/gkaf016","type":"journal-article","created":{"date-parts":[[2025,1,8]],"date-time":"2025-01-08T07:16:23Z","timestamp":1736320583000},"source":"Crossref","is-referenced-by-count":15,"title":["Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs"],"prefix":"10.1093","volume":"53","author":[{"given":"Antonio","family":"Garcia-Guerra","sequence":"first","affiliation":[{"name":"Department of Physics, University of Oxford , OX1 3PU\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Department of Paediatrics, University of Oxford , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Kavli Institute for Nanoscience Discovery, University of Oxford , OX1 3QU\u00a0Dorothy Crowfoot Hodgkin Building, Oxford ,","place":["United Kingdom"]},{"name":"Institute of Developmental and Regenerative Medicine (IDRM), IMS-Tetsuya Nakamura Building, Old Road Campus , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaitra","family":"Sathyaprakash","sequence":"additional","affiliation":[{"name":"Department of Molecular Therapy, National Institute of Neuroscience , National Centre of Neurology and Psychiatry, 187-8551\u00a0 Tokyo ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier\u00a0G","family":"de\u00a0Jong","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutics, Utrecht Institute of Pharmaceutical Sciences, Utrecht University , 3584 CG\u00a0 Utrecht ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wooi\u00a0F","family":"Lim","sequence":"additional","affiliation":[{"name":"Department of Paediatrics, University of Oxford , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Institute of Developmental and Regenerative Medicine (IDRM), IMS-Tetsuya Nakamura Building, Old Road Campus , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7059-8920","authenticated-orcid":false,"given":"Pieter","family":"Vader","sequence":"additional","affiliation":[{"name":"CDL Research, University Medical Center Utrecht , 3584 CX\u00a0 Utrecht ,","place":["The Netherlands"]},{"name":"Department of Experimental Cardiology, University Medical Center Utrecht , 3584 CX\u00a0 Utrecht ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samir","family":"El\u00a0Andaloussi","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, TRACK, Karolinska Institutet , 141 52\u00a0Huddinge,","place":["Sweden"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Bath","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Oxford , OX1 3PU\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Kavli Institute for Nanoscience Discovery, University of Oxford , OX1 3QU\u00a0Dorothy Crowfoot Hodgkin Building, Oxford ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jesus","family":"Reine","sequence":"additional","affiliation":[{"name":"Oxford Vaccine Group, University of Oxford , OX3 7LE\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Clinical Sciences, Liverpool School of Tropical Medicine , L3 5QA\u00a0 Liverpool ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshitsugu","family":"Aoki","sequence":"additional","affiliation":[{"name":"Department of Molecular Therapy, National Institute of Neuroscience , National Centre of Neurology and Psychiatry, 187-8551\u00a0 Tokyo ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew\u00a0J","family":"Turberfield","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Oxford , OX1 3PU\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Kavli Institute for Nanoscience Discovery, University of Oxford , OX1 3QU\u00a0Dorothy Crowfoot Hodgkin Building, Oxford ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew\u00a0J A","family":"Wood","sequence":"additional","affiliation":[{"name":"Department of Paediatrics, University of Oxford , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Institute of Developmental and Regenerative Medicine (IDRM), IMS-Tetsuya Nakamura Building, Old Road Campus , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8307-6638","authenticated-orcid":false,"given":"Carlo","family":"Rinaldi","sequence":"additional","affiliation":[{"name":"Department of Paediatrics, University of Oxford , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]},{"name":"Institute of Developmental and Regenerative Medicine (IDRM), IMS-Tetsuya Nakamura Building, Old Road Campus , OX3 7TY\u00a0 Oxford ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,22]]},"reference":[{"key":"2025012305302296500_B1","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1126\/science.1225829","article-title":"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity","volume":"337","author":"Jinek","year":"2012","journal-title":"Science"},{"key":"2025012305302296500_B2","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1038\/s41587-020-0561-9","article-title":"Genome editing with CRISPR\u2013Cas nucleases, base editors, transposases and prime editors","volume":"38","author":"Anzalone","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2025012305302296500_B3","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1056\/NEJMoa2107454","article-title":"CRISPR\u2013Cas9 in vivo gene editing for transthyretin amyloidosis","volume":"385","author":"Gillmore","year":"2021","journal-title":"N Engl J Med"},{"key":"2025012305302296500_B4","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1056\/NEJMoa2031054","article-title":"CRISPR\u2013Cas9 gene editing for sickle cell disease and \u03b2-thalassemia","volume":"384","author":"Frangoul","year":"2021","journal-title":"N Engl J Med"},{"key":"2025012305302296500_B5","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/s41392-021-00645-w","article-title":"Spatiotemporal control of CRISPR\/Cas9 gene editing","volume":"6","author":"Zhuo","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"2025012305302296500_B6","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1021\/acs.accounts.9b00106","article-title":"Delivery aspects of CRISPR\/Cas for in vivo genome editing","volume":"52","author":"Wilbie","year":"2019","journal-title":"Acc Chem Res"},{"key":"2025012305302296500_B7","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/j.omtn.2018.05.006","article-title":"One-vector system for multiplexed CRISPR\/Cas9 against Hepatitis B virus cccDNA utilizing high-capacity adenoviral vectors","volume":"12","author":"Schiwon","year":"2018","journal-title":"Mol Ther Nucleic Acids"},{"key":"2025012305302296500_B8","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1021\/acssynbio.7b00246","article-title":"Control of adipogenic differentiation in mesenchymal stem cells via endogenous gene activation using CRISPR\u2013Cas9","volume":"6","author":"Furuhata","year":"2017","journal-title":"ACS Synth Biol"},{"key":"2025012305302296500_B9","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.ymeth.2015.10.014","article-title":"Controlling transcription in human pluripotent stem cells using CRISPR-effectors","volume":"101","author":"Genga","year":"2016","journal-title":"Methods"},{"key":"2025012305302296500_B10","doi-asserted-by":"crossref","first-page":"1715","DOI":"10.1021\/jacs.9b11638","article-title":"Cell-type-specific CRISPR\/Cas9 delivery by biomimetic metal organic frameworks","volume":"142","author":"Alyami","year":"2020","journal-title":"J Am Chem Soc"},{"key":"2025012305302296500_B11","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1073\/pnas.1912220117","article-title":"Near-infrared optogenetic engineering of photothermal nanoCRISPR for programmable genome editing","volume":"117","author":"Chen","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025012305302296500_B12","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1126\/sciadv.abb1777","article-title":"Engineering a far-red light-activated split-Cas9 system for remote-controlled genome editing of internal organs and tumors","volume":"6","author":"Yu","year":"2020","journal-title":"Sci Adv"},{"key":"2025012305302296500_B13","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/nature04586","article-title":"Folding DNA to create nanoscale shapes and patterns","volume":"440","author":"Rothemund","year":"2006","journal-title":"Nature"},{"key":"2025012305302296500_B14","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/s41557-021-00679-1","article-title":"RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds","volume":"13","author":"Geary","year":"2021","journal-title":"Nat Chem"},{"key":"2025012305302296500_B15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-09985-2","article-title":"Controlling CRISPR\u2013Cas9 with ligand-activated and ligand-deactivated sgRNAs","volume":"10","author":"Kundert","year":"2019","journal-title":"Nat Commun"},{"key":"2025012305302296500_B16","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/s41556-019-0292-7","article-title":"A microRNA-inducible CRISPR\u2013Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool","volume":"21","author":"Wang","year":"2019","journal-title":"Nat Cell Biol"},{"key":"2025012305302296500_B17","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1021\/acssynbio.9b00073","article-title":"Cell-type-specific CRISPR activation with microRNA-responsive AcrllA4 switch","volume":"8","author":"Hirosawa","year":"2019","journal-title":"ACS Synth Biol"},{"key":"2025012305302296500_B18","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1146\/annurev-micro-020518-120107","article-title":"Structures and strategies of anti-CRISPR-mediated immune suppression","volume":"74","author":"Wiegand","year":"2020","journal-title":"Annu Rev Microbiol"},{"key":"2025012305302296500_B19","doi-asserted-by":"crossref","first-page":"e118","DOI":"10.1093\/nar\/gkx309","article-title":"Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch","volume":"45","author":"Hirosawa","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025012305302296500_B20","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1261\/rna.071704.119","article-title":"Tissue-restricted genome editing in vivo specified by microRNA-repressible anti-CRISPR proteins","volume":"25","author":"Lee","year":"2019","journal-title":"RNA"},{"key":"2025012305302296500_B21","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1021\/acscentsci.9b00340","article-title":"Conditional guide RNAs: programmable conditional regulation of CRISPR\/Cas function in bacterial and mammalian cells via dynamic RNA nanotechnology","volume":"5","author":"Hanewich-Hollatz","year":"2019","journal-title":"ACS Cent Sci"},{"key":"2025012305302296500_B22","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1021\/acssynbio.1c00037","article-title":"High-performance allosteric conditional guide RNAs for mammalian cell-selective regulation of CRISPR\/Cas","volume":"10","author":"Hochrein","year":"2021","journal-title":"ACS Synth Biol"},{"key":"2025012305302296500_B23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms14633","article-title":"Rational design of inducible CRISPR guide RNAs for de novoassembly of transcriptional programs","volume":"8","author":"Ferry","year":"2017","journal-title":"Nat Commun"},{"key":"2025012305302296500_B24","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1038\/nmeth.3994","article-title":"Directing cellular information flow via CRISPR signal conductors","volume":"13","author":"Liu","year":"2016","journal-title":"Nat Methods"},{"key":"2025012305302296500_B25","doi-asserted-by":"crossref","first-page":"15939","DOI":"10.1038\/ncomms15939","article-title":"Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation","volume":"8","author":"Tang","year":"2017","journal-title":"Nat Commun"},{"key":"2025012305302296500_B26","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1038\/s41467-017-02265-x","article-title":"Engineering cell signaling using tunable CRISPR\u2013Cpf1-based transcription factors","volume":"8","author":"Liu","year":"2017","journal-title":"Nat Commun"},{"key":"2025012305302296500_B27","doi-asserted-by":"crossref","first-page":"23894","DOI":"10.1002\/anie.202107258","article-title":"Controlling gene expression in mammalian cells using multiplexed conditional guide RNAs for Cas12a","volume":"60","author":"Oesinghaus","year":"2021","journal-title":"Angew Chem Int Ed"},{"key":"2025012305302296500_B28","doi-asserted-by":"crossref","first-page":"18599","DOI":"10.1002\/anie.202004751","article-title":"Activatable CRISPR transcriptional circuits generate functional RNA for mRNA sensing and silencing","volume":"59","author":"Ying","year":"2020","journal-title":"Angew Chem Int Ed"},{"key":"2025012305302296500_B29","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/s41589-018-0186-1","article-title":"Riboregulated toehold-gated gRNA for programmable CRISPR\u2013Cas9 function","volume":"15","author":"Siu","year":"2019","journal-title":"Nat Chem Biol"},{"key":"2025012305302296500_B30","doi-asserted-by":"crossref","first-page":"11773","DOI":"10.1093\/nar\/gkaa842","article-title":"Conditional guide RNA through two intermediate hairpins for programmable CRISPR\/Cas9 function: building regulatory connections between endogenous RNA expressions","volume":"48","author":"Lin","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025012305302296500_B31","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1089\/crispr.2020.0029","article-title":"Engineered RNA-interacting CRISPR guide RNAs for genetic sensing and diagnostics","volume":"3","author":"Galizi","year":"2020","journal-title":"CRISPR J"},{"key":"2025012305302296500_B32","doi-asserted-by":"crossref","article-title":"ssRNA\/DNA-sensors via embedded strand-displacement programs in CRISPR\/Cas9 guides","author":"Jakimo","DOI":"10.1101\/264424"},{"key":"2025012305302296500_B33","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1021\/acssynbio.9b00141","article-title":"Programmable CRISPR\u2013Cas repression, activation, and computation with sequence-independent targets and triggers","volume":"8","author":"Jin","year":"2019","journal-title":"ACS Synth Biol"},{"key":"2025012305302296500_B34","doi-asserted-by":"crossref","first-page":"6215","DOI":"10.1039\/D2CC01478E","article-title":"A microRNA-gated thgRNA platform for multiplexed activation of gene expression in mammalian cells","volume":"58","author":"Hunt","year":"2022","journal-title":"Chem Commun"},{"key":"2025012305302296500_B35","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1021\/acssynbio.1c00479","article-title":"Deciphering the design rules of toehold-gated sgRNA for conditional activation of gene expression and protein degradation in mammalian cells","volume":"11","author":"Hunt","year":"2022","journal-title":"ACS Synth Biol"},{"key":"2025012305302296500_B36","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1002\/jcc.21600","article-title":"Gabedit\u2014a graphical user interface for computational chemistry softwares","volume":"32","author":"Allouche","year":"2011","journal-title":"J Comput Chem"},{"key":"2025012305302296500_B37","doi-asserted-by":"crossref","first-page":"3865","DOI":"10.1093\/nar\/gkw116","article-title":"Distribution of miRNA expression across human tissues","volume":"44","author":"Ludwig","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025012305302296500_B38","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1016\/j.cell.2012.10.036","article-title":"Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties","volume":"151","author":"Wee","year":"2012","journal-title":"Cell"},{"key":"2025012305302296500_B39","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.cell.2015.06.032","article-title":"A dynamic search process underlies microRNA targeting","volume":"162","author":"Chandradoss","year":"2015","journal-title":"Cell"},{"key":"2025012305302296500_B40","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.cell.2015.06.029","article-title":"Single-molecule imaging reveals that argonaute reshapes the binding properties of its nucleic acid guides","volume":"162","author":"Salomon","year":"2015","journal-title":"Cell"},{"key":"2025012305302296500_B41","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1146\/annurev-genom-090314-025003","article-title":"The pathogenesis and therapy of muscular dystrophies","volume":"16","author":"Guiraud","year":"2015","journal-title":"Annu Rev Genom Hum Genet"},{"key":"2025012305302296500_B42","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/s41467-020-14977-8","article-title":"A CRISPR\u2013Cas9-based reporter system for single-cell detection of extracellular vesicle-mediated functional transfer of RNA","volume":"11","author":"de\u00a0Jong","year":"2020","journal-title":"Nat Commun"},{"key":"2025012305302296500_B43","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/j.omtn.2022.10.010","article-title":"Non-uniform dystrophin re-expression after CRISPR-mediated exon excision in the dystrophin\/utrophin double-knockout mouse model of DMD","volume":"30","author":"Hanson","year":"2022","journal-title":"Mol Ther Nucleic Acids"},{"key":"2025012305302296500_B44","doi-asserted-by":"crossref","first-page":"2044","DOI":"10.1016\/j.ymthe.2020.05.024","article-title":"Correction of three prominent mutations in mouse and human models of duchenne muscular dystrophy by single-cut genome editing","volume":"28","author":"Min","year":"2020","journal-title":"Mol Ther"},{"key":"2025012305302296500_B45","doi-asserted-by":"crossref","first-page":"eabi6896","DOI":"10.1126\/sciadv.abi6896","article-title":"Gene therapy with AR isoform 2 rescues spinal and bulbar muscular atrophy phenotype by modulating AR transcriptional activity","volume":"7","author":"Lim","year":"2021","journal-title":"Sci Adv"},{"key":"2025012305302296500_B46","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1002\/jcc.21596","article-title":"NUPACK: analysis and design of nucleic acid systems","volume":"32","author":"Zadeh","year":"2011","journal-title":"J Comput Chem"},{"key":"2025012305302296500_B47","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/0076-6879(95)59047-1","article-title":"Predicting thermodynamic properties of RNA","volume":"259","author":"Serra","year":"1995","journal-title":"Methods Enzymol"},{"key":"2025012305302296500_B48","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1093\/nar\/gkt174","article-title":"CoFold: an RNA secondary structure prediction method that takes co-transcriptional folding into account","volume":"41","author":"Proctor","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2025012305302296500_B49","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","article-title":"Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure","volume":"288","author":"Mathews","year":"1999","journal-title":"J Mol Biol"},{"key":"2025012305302296500_B50","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1089\/crispr.2020.0022","article-title":"Deconvolution of complex DNA repair (DECODR): establishing a novel deconvolution algorithm for comprehensive analysis of CRISPR-edited sanger sequencing data","volume":"4","author":"Bloh","year":"2021","journal-title":"CRISPR J"},{"key":"2025012305302296500_B51","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1126\/science.1225829","article-title":"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity","volume":"337","author":"Jinek","year":"2012","journal-title":"Science"},{"key":"2025012305302296500_B52","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1016\/j.cell.2014.02.001","article-title":"Crystal structure of Cas9 in complex with guide RNA and target DNA","volume":"156","author":"Nishimasu","year":"2014","journal-title":"Cell"},{"key":"2025012305302296500_B53","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1038\/s41580-019-0136-0","article-title":"The roles of structural dynamics in the cellular functions of RNAs","volume":"20","author":"Ganser","year":"2019","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025012305302296500_B54","doi-asserted-by":"crossref","first-page":"102344","DOI":"10.1016\/j.omtn.2024.102344","article-title":"CRISPR\u2013Cas9-mediated homology-directed repair for precise gene editing","volume":"35","author":"Liao","year":"2024","journal-title":"Mol Ther Nucleic Acids"},{"key":"2025012305302296500_B55","doi-asserted-by":"crossref","first-page":"e29551","DOI":"10.1371\/journal.pone.0029551","article-title":"High-throughput functional microRNAs profiling by recombinant AAV-based microRNA sensor arrays","volume":"7","author":"Tian","year":"2012","journal-title":"PLoS One"},{"key":"2025012305302296500_B56","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1089\/adt.2006.053","article-title":"Bioluminescent assays for high-throughput screening","volume":"5","author":"Fan","year":"2007","journal-title":"Assay Drug Dev Technol"},{"key":"2025012305302296500_B57","doi-asserted-by":"crossref","first-page":"e62","DOI":"10.1093\/nar\/gks1439","article-title":"Widespread inference of weighted microRNA-mediated gene regulation in cancer transcriptome analysis","volume":"41","author":"Suzuki","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2025012305302296500_B58","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.cell.2007.04.037","article-title":"Molecular basis for target RNA recognition and cleavage by human RISC","volume":"130","author":"Ameres","year":"2007","journal-title":"Cell"},{"key":"2025012305302296500_B59","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/nar\/gkl1036","article-title":"Encoding folding paths of RNA switches","volume":"35","author":"Xayaphoummine","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2025012305302296500_B60","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/35020524","article-title":"A DNA-fuelled molecular machine made of DNA","volume":"406","author":"Bernard","year":"2000","journal-title":"Nature"},{"key":"2025012305302296500_B61","doi-asserted-by":"crossref","first-page":"17303","DOI":"10.1021\/ja906987s","article-title":"Control of DNA strand displacement kinetics using toehold exchange","volume":"131","author":"Zhang","year":"2009","journal-title":"J Am Chem Soc"},{"key":"2025012305302296500_B62","doi-asserted-by":"crossref","first-page":"10098","DOI":"10.1073\/pnas.1104144108","article-title":"Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence","volume":"108","author":"Semenova","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025012305302296500_B63","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1186\/s13059-015-0846-3","article-title":"Optimizing sgRNA structure to improve CRISPR\u2013Cas9 knockout efficiency","volume":"16","author":"Dang","year":"2015","journal-title":"Genome Biol"},{"key":"2025012305302296500_B64","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1056\/NEJMoa1716153","article-title":"Patisiran, an RNAi therapeutic, for hereditary transthyretin amyloidosis","volume":"379","author":"Adams","year":"2018","journal-title":"N Engl J Med"},{"key":"2025012305302296500_B65","doi-asserted-by":"crossref","first-page":"2603","DOI":"10.1056\/NEJMoa2034577","article-title":"Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine","volume":"383","author":"Polack","year":"2020","journal-title":"N Engl J Med"},{"key":"2025012305302296500_B66","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1261\/rna.037390.112","article-title":"On the importance of cotranscriptional RNA structure formation","volume":"19","author":"Lai","year":"2013","journal-title":"RNA"},{"key":"2025012305302296500_B67","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1038\/s41565-023-01321-6","article-title":"Structure, folding and flexibility of co-transcriptional RNA origami","volume":"18","author":"McRae","year":"2023","journal-title":"Nat Nanotechnol"},{"key":"2025012305302296500_B68","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1016\/S1474-4422(21)00001-6","article-title":"Onasemnogene abeparvovec gene therapy for symptomatic infantile-onset spinal muscular atrophy in patients with two copies of SMN2 (STR1VE): an open-label, single-arm, multicentre, phase 3 trial","volume":"20","author":"Day","year":"2021","journal-title":"Lancet Neurol."},{"key":"2025012305302296500_B69","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1038\/nbt.4005","article-title":"Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing","volume":"35","author":"Yin","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2025012305302296500_B70","doi-asserted-by":"crossref","first-page":"7214","DOI":"10.1073\/pnas.1821740116","article-title":"A CRISPR\/Cas9-based central processing unit to program complex logic computation in human cells","volume":"116","author":"Kim","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"key":"2025012305302296500_B71","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1038\/nmeth.4042","article-title":"Complex transcriptional modulation with orthogonal and inducible dCas9 regulators","volume":"13","author":"Gao","year":"2016","journal-title":"Nat Methods"},{"key":"2025012305302296500_B72","doi-asserted-by":"crossref","first-page":"2092","DOI":"10.1038\/s41467-019-09953-w","article-title":"Switching the activity of Cas12a using guide RNA strand displacement circuits","volume":"10","author":"Oesinghaus","year":"2019","journal-title":"Nat Commun"},{"key":"2025012305302296500_B73","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1038\/s41576-020-00300-0","article-title":"The epigenetic basis of cellular heterogeneity","volume":"22","author":"Carter","year":"2021","journal-title":"Nat Rev Genet"},{"key":"2025012305302296500_B74","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1016\/j.omtm.2020.05.006","article-title":"Variability in cardiac miRNA-122 level determines therapeutic potential of miRNA-regulated AAV vectors","volume":"17","author":"Kraszewska","year":"2020","journal-title":"Mol Ther Methods Clin Dev"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/2\/gkaf016\/61573134\/gkaf016.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/2\/gkaf016\/61573134\/gkaf016.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,23]],"date-time":"2025-01-23T00:31:08Z","timestamp":1737592268000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf016\/7973898"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,11]]},"references-count":74,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025,1,11]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf016","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.08.09.605335","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1,27]]},"published":{"date-parts":[[2025,1,11]]},"article-number":"gkaf016"}}