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
1998
A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor
Basu S, P. Rambo R, Strauss-Soukup J, H.Cate J, R. Ferré-D´Amaré A, Strobel S, Doudna J. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nature Structural & Molecular Biology 1998, 5: 986-992. PMID: 9808044, DOI: 10.1038/2960.Peer-Reviewed Original ResearchConceptsP4-P6 domainTetraloop receptorCatalytic RNALarge catalytic RNAsGroup I intronRNA tertiary structure formationTertiary structure formationTertiary structural motifsI intronRNAWide diversityFoldingStructural motifsDivalent metal ionsPotassium ionsReceptorsIntronsAzoarcusDomainDiversityMotifSitesActivityMonovalent ions
1997
RNA seeing double: Close-packing of helices in RNA tertiary structure
Strobel S, Doudna J. RNA seeing double: Close-packing of helices in RNA tertiary structure. Trends In Biochemical Sciences 1997, 22: 262-266. PMID: 9255068, DOI: 10.1016/s0968-0004(97)01056-6.Peer-Reviewed Original ResearchConceptsHigher-order structure formationPacking of helicesChromosome maintenanceNoncanonical base pairsRNA processingDouble-helical segmentsRNA tertiary structureProtein biosynthesisRecognition motifRNA moleculesTertiary structureBase pairsHelical packingRNAEssential roleProteinActive siteBiosynthesisComplex architectureFoldingMotifHelixAssemblyDifferent strategies