{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Hoeher JE"],"funding":["National Institutes of Health","NIGMS NIH HHS","NIH HHS"],"pagination":["419-433"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10950518"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["100(2)"],"pubmed_abstract":["Riboswitches are mRNA segments that regulate gene expression in response to ligand binding. The Class I preQ<sub>1</sub> 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<sub>1</sub> . 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<sub>1</sub> at all labeling positions tested, although modified and unmodified variants undergo the same global conformational changes at sufficiently high preQ<sub>1</sub> 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<sub>1</sub> riboswitch and that 2-AP substitution exerts complex and varied impacts on this riboswitch."],"journal":["Photochemistry and photobiology"],"pubmed_title":["Probing and perturbing riboswitch folding using a fluorescent base analogue."],"pmcid":["PMC10950518"],"funding_grant_id":["R00 GM120457"],"pubmed_authors":["Sande NE","Hoeher JE","Widom JR"],"additional_accession":[]},"is_claimable":false,"name":"Probing and perturbing riboswitch folding using a fluorescent base analogue.","description":"Riboswitches are mRNA segments that regulate gene expression in response to ligand binding. The Class I preQ<sub>1</sub> 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<sub>1</sub> . 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<sub>1</sub> at all labeling positions tested, although modified and unmodified variants undergo the same global conformational changes at sufficiently high preQ<sub>1</sub> 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<sub>1</sub> riboswitch and that 2-AP substitution exerts complex and varied impacts on this riboswitch.","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Mar-Apr","modification":"2026-06-02T10:23:20.464Z","creation":"2025-04-06T08:32:32.53Z"},"accession":"S-EPMC10950518","cross_references":{"pubmed":["38098287"],"doi":["10.1111/php.13896"]}}