{"doi":"10.1093/nar/gkad1127","title":"Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a","abstract":"Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. It utilizes a CRISPR RNA (crRNA) to target RNA sequences and trigger a composite active site formed by two 'Higher Eukaryotes and Prokaryotes Nucleotide' (HEPN) domains, cleaving any solvent-exposed RNA. In this system, an intriguing form of allosteric communication controls the RNA cleavage activity, yet its molecular details are unknown. Here, multiple-microsecond molecular dynamics simulations are combined with graph theory to decipher this intricate activation mechanism. We show that the binding of a target RNA acts as an allosteric effector, by amplifying the communication signals over the dynamical noise through interactions of the crRNA at the buried HEPN1-2 interface. By introducing a novel Signal-to-Noise Ratio (SNR) of communication efficiency, we reveal critical allosteric residues-R377, N378, and R973-that rearrange their interactions upon target RNA binding. Alanine mutation of these residues is shown to select target RNA over an extended complementary sequence beyond guide-target duplex for RNA cleavage, establishing the functional significance of these hotspots. Collectively our findings offer a fundamental understanding of the Cas13a mechanism of action and pave new avenues for the development of highly selective RNA-based cleavage and detection tools.","journal":"Nucleic Acids Research","year":2023,"id":323527,"datarank":0.8681822444316579,"base_score":3.6375861597263857,"endowment":3.6375861597263857,"self_citation_contribution":0.5456379239589579,"citation_network_contribution":0.3225443204727,"self_endowment_contribution":0.5456379239589579,"citer_contribution":0.3225443204727,"corpus_percentile":null,"corpus_rank":null,"citation_count":37,"citer_count":18,"citers_with_citation_signal":12,"citers_with_endowment":12,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9457,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.24498937"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":832410,"name":"Adrian M. Molina Vargas","orcid":"0000-0003-4090-1180","position":1,"is_corresponding":false},{"id":618883,"name":"Pablo Arantes","orcid":"0000-0001-9707-8493","position":2,"is_corresponding":false},{"id":882027,"name":"Amun C. Patel","orcid":"0000-0002-7119-2973","position":3,"is_corresponding":false},{"id":422293,"name":"Mitchell R. O’Connell","orcid":"0000-0002-8642-3973","position":4,"is_corresponding":false},{"id":316869,"name":"Giulia Palermo","orcid":"0000-0003-1404-8737","position":5,"is_corresponding":false},{"id":911575,"name":"Souvik Sinha","orcid":"0000-0003-4964-7713","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":null,"created_at":"2026-07-19T01:07:52.377944Z","pmid":"38033317","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}