{"doi":"10.1101/2023.06.02.23290873","title":"Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches","abstract":"ABSTRACT Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. Here, we describe a class of aptamer-based RNA switches called aptaswitches that recognize specific target nucleic acid molecules and respond by initiating folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide a fast and intense fluorescent readout, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. We demonstrate that aptaswitches can be used to regulate folding of six different fluorescent aptamer/fluorogen pairs, providing a general means of controlling aptamer activity and an array of different reporter colors for multiplexing. By coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/µL in one-pot reactions. Application of multiplexed one-pot reactions against RNA extracted from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that can be readily integrated into rapid diagnostic assays.","journal":"medRxiv","year":2023,"id":392421,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":5,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.943,"is_data_producer":false,"deposit_databanks":null,"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":857243,"name":"Anli A. Tang","orcid":null,"position":1,"is_corresponding":false},{"id":1019925,"name":"Amit Eshed","orcid":"0000-0001-7172-6579","position":2,"is_corresponding":false},{"id":1166494,"name":"Zackary M. Ticktin","orcid":null,"position":3,"is_corresponding":false},{"id":857244,"name":"Soma Chaudhary","orcid":null,"position":4,"is_corresponding":false},{"id":276709,"name":"Duo Ma","orcid":null,"position":5,"is_corresponding":false},{"id":1166495,"name":"Griffin McCutcheon","orcid":null,"position":6,"is_corresponding":false},{"id":1165973,"name":"Yongdan Li","orcid":"0000-0002-0430-9879","position":7,"is_corresponding":false},{"id":275747,"name":"Kaiyue Wu","orcid":"0000-0002-2009-6287","position":8,"is_corresponding":false},{"id":1166496,"name":"Sanchari Saha","orcid":null,"position":9,"is_corresponding":false},{"id":856618,"name":"Jonathan Alcántar‐Fernández","orcid":"0000-0001-5302-4223","position":10,"is_corresponding":false},{"id":857245,"name":"José L. Moreno-Camacho","orcid":null,"position":11,"is_corresponding":false},{"id":856619,"name":"Abraham Campos‐Romero","orcid":"0000-0002-4982-9528","position":12,"is_corresponding":false},{"id":31916,"name":"James J. Collins","orcid":"0000-0002-5560-8246","position":13,"is_corresponding":false},{"id":44857,"name":"Peng Yin","orcid":"0000-0002-2769-6357","position":14,"is_corresponding":false},{"id":275750,"name":"Alexander A. Green","orcid":"0000-0003-2058-1204","position":15,"is_corresponding":false},{"id":856616,"name":"Zhaoqing Yan","orcid":"0000-0002-5023-605X","position":0,"is_corresponding":true}],"reference_count":54,"raw_metadata":null,"created_at":"2026-07-19T01:18:56.730121Z","pmid":"37333364","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":[]}