{"doi":"10.1111/php.13896","title":"Probing and perturbing riboswitch folding using a fluorescent base analogue","abstract":"Abstract Riboswitches are mRNA segments that regulate gene expression in response to ligand binding. The Class I preQ 1 riboswitch consists of a stem‐loop and an adenine‐rich single‐stranded tail (“L3”), which adopt a pseudoknot structure upon binding of the ligand preQ 1 . We inserted 2‐aminopurine (2‐AP), a fluorescent analogue of adenine (A), into the riboswitch at six different positions within L3. Here, 2‐AP functions both as a spectroscopic probe and as a “mutation” that reveals how alteration of specific A residues impacts the riboswitch. Using fluorescence and circular dichroism spectroscopy, we found that 2‐AP decreases the affinity of the riboswitch for preQ 1 at all labeling positions tested, although modified and unmodified variants undergo the same global conformational changes at sufficiently high preQ 1 concentration. 2‐AP substitution is most detrimental to ligand binding at sites proximal to the ligand‐binding pocket, while distal labeling sites exhibit the largest impacts on the stability of the L3 domain in the absence of ligand. Insertion of multiple 2‐AP residues does not induce significant additional disruptions. Our results show that interactions involving the A residues in L3 play a critical role in ligand recognition by the preQ 1 riboswitch and that 2‐AP substitution exerts complex and varied impacts on this riboswitch.","journal":"Photochemistry and Photobiology","year":2023,"id":350604,"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":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9597,"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":1095443,"name":"Natalie E. Sande","orcid":null,"position":1,"is_corresponding":false},{"id":816823,"name":"Julia R. Widom","orcid":"0000-0002-6357-2749","position":2,"is_corresponding":false},{"id":923876,"name":"Janson E. Hoeher","orcid":"0000-0001-9492-8771","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-07-19T01:12:37.409066Z","pmid":"38098287","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":[]}