{"doi":"10.1101/2024.07.07.602435","title":"Fluorogenic Aptamer Optimizations on a Massively Parallel Sequencing Platform","abstract":"F luorogenic ap tamers (FAPs) have become an increasingly important tool in cellular sensing and pathogen diagnostics. However, fine-tuning FAPs for enhanced performance remains challenging even with the structural details provided by X-ray crystallography. Here we present a novel approach to optimize a DNA-based FAP (D-FAP), Lettuce, on repurposed Illumina next-generation sequencing (NGS) chips. When substituting its cognate chromophore, DFHBI-1T, with TO1-biotin, Lettuce not only shows a red-shifted emission peak by 53 nm (from 505 to 558 nm), but also a 4-fold bulk fluorescence enhancement. After screening 8,821 Lettuce variants complexed with TO1-biotin, the C14T mutation is found to exhibit an improved apparent dissociated constant ( vs. 0.82 µM), an increased quantum yield (QY: 0.62 vs. 0.59) and an elongated fluorescence lifetime (τ: 6.00 vs. 5.77 ns), giving 45% more ensemble fluorescence than the canonical Lettuce/TO1-biotin complex. Molecular dynamic simulations further indicate that the π-π stacking interaction is key to determining the coordination structure of TO1-biotin in Lettuce. Our screening-and-simulation pipeline can effectively optimize FAPs without any prior structural knowledge of the canonical FAP/chromophore complexes, providing not only improved molecular probes for fluorescence sensing but also insights into aptamer-chromophore interactions.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":488712,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1229861,"name":"Yuan-I Chen","orcid":null,"position":1,"is_corresponding":false},{"id":946224,"name":"Yanxing Wang","orcid":"0000-0001-7239-8482","position":2,"is_corresponding":false},{"id":1333662,"name":"Zeynep Korkmaz","orcid":null,"position":3,"is_corresponding":false},{"id":1333663,"name":"Siem Yonas","orcid":null,"position":4,"is_corresponding":false},{"id":1208341,"name":"Yujie He","orcid":"0000-0002-6984-3052","position":5,"is_corresponding":false},{"id":568662,"name":"Trung D. Nguyen","orcid":"0009-0005-7838-3317","position":6,"is_corresponding":false},{"id":568663,"name":"Soonwoo Hong","orcid":"0000-0002-7618-9052","position":7,"is_corresponding":false},{"id":1333664,"name":"Anh-Thu Nguyen","orcid":null,"position":8,"is_corresponding":false},{"id":1333298,"name":"Sohyun Kim","orcid":"0009-0004-7345-3331","position":9,"is_corresponding":false},{"id":1333299,"name":"Saeed Seifi","orcid":"0000-0003-1245-9671","position":10,"is_corresponding":false},{"id":1079202,"name":"Po‐Hsun Fan","orcid":null,"position":11,"is_corresponding":false},{"id":734009,"name":"Yuting Wu","orcid":"0000-0003-3196-5916","position":12,"is_corresponding":false},{"id":689038,"name":"Zhenglin Yang","orcid":"0000-0003-2743-5779","position":13,"is_corresponding":false},{"id":419939,"name":"Hung‐wen Liu","orcid":"0000-0001-8953-4794","position":14,"is_corresponding":false},{"id":1333300,"name":"Yi Lu","orcid":"0000-0002-6768-7893","position":15,"is_corresponding":false},{"id":381570,"name":"Pengyu Ren","orcid":"0000-0002-5613-1910","position":16,"is_corresponding":false},{"id":1035349,"name":"Hsin-Chih Yeh","orcid":null,"position":17,"is_corresponding":false},{"id":569384,"name":"Yu-An Kuo","orcid":null,"position":0,"is_corresponding":true}],"reference_count":40,"raw_metadata":null,"created_at":"2026-07-19T02:08:19.655720Z","pmid":"39026723","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":[]}