2024
The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches
Barth K, Hiller D, Strobel S. The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches. Biochemistry 2024, 63: 487-497. PMID: 38329042, PMCID: PMC11306416, DOI: 10.1021/acs.biochem.3c00586.Peer-Reviewed Original ResearchCyclic di-GMPLigand specificityHigh-throughput mutational analysisLigand contactsRegulate downstream gene expressionDownstream gene expressionDistal nucleotidesTerminal helixSequence differencesChemically similar ligandsRiboswitchNucleotideLigand-binding pocketMutation analysisVariant familiesGene expressionSmall molecule ligandsBinding sitesBinding pocketStructural motifsCrystal structureMolecule ligandsLigandSequenceMotif
2001
Biochemical Detection of Monovalent Metal Ion Binding Sites within RNA
Basu S, Strobel S. Biochemical Detection of Monovalent Metal Ion Binding Sites within RNA. Methods 2001, 23: 264-275. PMID: 11243839, DOI: 10.1006/meth.2000.1137.Peer-Reviewed Original ResearchConceptsX-ray crystal structureMonovalent cationsMetal ion binding siteMetal ion bindingHeavy metal cationsIon binding siteMetal sitesMetal cationsSoft LewisCrystal structureIon bindingCationsChemical propertiesNucleotide analog interference mappingP4-P6 domainAzoarcus group I intronMetal potassiumSimilar binding sitesNucleic acidsBinding sitesBiochemical detectionTetrahymena group I intronLarge RNAsGroup I intronDistinct biochemical signatures