2023
Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity
Focht C, Hiller D, Grunseich S, Strobel S. Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity. RNA 2023, 29: 1126-1139. PMID: 37130702, PMCID: PMC10351892, DOI: 10.1261/rna.079560.122.Peer-Reviewed Original Research
2009
Structural basis of ligand binding by a c-di-GMP riboswitch
Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA. Structural basis of ligand binding by a c-di-GMP riboswitch. Nature Structural & Molecular Biology 2009, 16: 1218-1223. PMID: 19898477, PMCID: PMC2850612, DOI: 10.1038/nsmb.1702.Peer-Reviewed Original ResearchStructural and Chemical Basis for Glucosamine 6-Phosphate Binding and Activation of the glmS Ribozyme
Cochrane JC, Lipchock SV, Smith KD, Strobel SA. Structural and Chemical Basis for Glucosamine 6-Phosphate Binding and Activation of the glmS Ribozyme. Biochemistry 2009, 48: 3239-3246. PMID: 19228039, PMCID: PMC2854835, DOI: 10.1021/bi802069p.Peer-Reviewed Original Research
2006
Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor
Cochrane JC, Lipchock SV, Strobel SA. Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor. Cell Chemical Biology 2006, 14: 97-105. PMID: 17196404, PMCID: PMC1847778, DOI: 10.1016/j.chembiol.2006.12.005.Peer-Reviewed Original Research
2001
SITE SPECIFIC INCORPORATION OF 6-AZAURIDINE INTO THE GENOMIC HDV RIBOZYME ACTIVE SITE
Oyelere A, Strobel S. SITE SPECIFIC INCORPORATION OF 6-AZAURIDINE INTO THE GENOMIC HDV RIBOZYME ACTIVE SITE. Nucleosides Nucleotides & Nucleic Acids 2001, 20: 1851-1858. PMID: 11719998, DOI: 10.1081/ncn-100107196.Peer-Reviewed Original ResearchAn efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5′- and 3′-termini
Jones F, Ryder S, Strobel S. An efficient ligation reaction promoted by a Varkud Satellite ribozyme with extended 5′- and 3′-termini. Nucleic Acids Research 2001, 29: 5115-5120. PMID: 11812844, PMCID: PMC97611, DOI: 10.1093/nar/29.24.5115.Peer-Reviewed Original ResearchpH-dependent conformational flexibility within the ribosomal peptidyl transferase center.
Muth G, Chen L, Kosek A, Strobel S. pH-dependent conformational flexibility within the ribosomal peptidyl transferase center. RNA 2001, 7: 1403-15. PMID: 11680845, PMCID: PMC1370184.Peer-Reviewed Original ResearchInvestigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping.
Ryder S, Oyelere A, Padilla J, Klostermeier D, Millar D, Strobel S. Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. RNA 2001, 7: 1454-63. PMID: 11680850, PMCID: PMC1370189.Peer-Reviewed Original ResearchAdenosineBase SequenceCatalysisNucleic Acid ConformationNucleotidesRNA, CatalyticTranscription, GeneticThe hairpin's turn
Strobel S, Ryder S. The hairpin's turn. Nature 2001, 410: 761-762. PMID: 11298426, DOI: 10.1038/35071209.Peer-Reviewed Original ResearchMeSH KeywordsCatalysisCatalytic DomainCrystallography, X-RayNucleic Acid ConformationOrganophosphatesRNA, CatalyticStructure-Activity RelationshipBiochemical 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 ResearchMeSH KeywordsBinding SitesCationsElectrophoresis, Polyacrylamide GelGuanosineIonsMetalsModels, MolecularNucleic Acid ConformationRNAThionucleosidesConceptsX-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 signaturesExploring the mechanism of the peptidyl transfer reaction by chemical footprinting.
Strobel S, Muth G, Chen L. Exploring the mechanism of the peptidyl transfer reaction by chemical footprinting. Cold Spring Harbor Symposia On Quantitative Biology 2001, 66: 109-17. PMID: 12762013, DOI: 10.1101/sqb.2001.66.109.Peer-Reviewed Original Research
2000
A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme11Edited by D. Draper
Strauss-Soukup J, Strobel S. A chemical phylogeny of group I introns based upon interference mapping of a bacterial ribozyme11Edited by D. Draper. Journal Of Molecular Biology 2000, 302: 339-358. PMID: 10970738, DOI: 10.1006/jmbi.2000.4056.Peer-Reviewed Original Research
1999
Nucleotide Analog Interference Mapping of the Hairpin Ribozyme: Implications for Secondary and Tertiary Structure Formation
Ryder S, Strobel S. Nucleotide Analog Interference Mapping of the Hairpin Ribozyme: Implications for Secondary and Tertiary Structure Formation. Journal Of Molecular Biology 1999, 291: 295-311. PMID: 10438622, DOI: 10.1006/jmbi.1999.2959.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBinding SitesMolecular Sequence DataNucleic Acid ConformationRibonucleotidesRNA, CatalyticConceptsNucleotide analog interference mappingLoop AMinor groove edgeTertiary structure formationProper foldingThree-dimensional structureHairpin ribozymeNucleotide conservationNMR structureLoop BInterference mappingTertiary interactionsLoop B.Purine nucleotidesBiochemical evidenceRibozymeIntact ribozymeA chemogenetic approach to RNA function/structure analysis
Strobel S. A chemogenetic approach to RNA function/structure analysis. Current Opinion In Structural Biology 1999, 9: 346-352. PMID: 10361087, DOI: 10.1016/s0959-440x(99)80046-3.Peer-Reviewed Original ResearchA hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme
Strobel S, Ortoleva-Donnelly L. A hydrogen-bonding triad stabilizes the chemical transition state of a group I ribozyme. Cell Chemical Biology 1999, 6: 153-165. PMID: 10074469, DOI: 10.1016/s1074-5521(99)89007-3.Peer-Reviewed Original Research
1998
A minor groove RNA triple helix within the catalytic core of a group I intron
Szewczak A, Ortoleva-Donnelly L, Ryder S, Moncoeur E, Strobel S. A minor groove RNA triple helix within the catalytic core of a group I intron. Nature Structural & Molecular Biology 1998, 5: 1037-1042. PMID: 9846872, DOI: 10.1038/4146.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCatalytic DomainIntronsModels, ChemicalModels, MolecularMolecular Sequence DataNucleic Acid ConformationRNA, CatalyticRNA, ProtozoanTetrahymenaA 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 ionsIdentifying RNA Minor Groove Tertiary Contacts by Nucleotide Analogue Interference Mapping with N 2-Methylguanosine †
Ortoleva-Donnelly L, Kronman M, Strobel S. Identifying RNA Minor Groove Tertiary Contacts by Nucleotide Analogue Interference Mapping with N 2-Methylguanosine †. Biochemistry 1998, 37: 12933-12942. PMID: 9737873, DOI: 10.1021/bi980723j.Peer-Reviewed Original ResearchN2-Methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops
Rife J, Cheng C, Moore P, Strobel S. N2-Methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops. Nucleic Acids Research 1998, 26: 3640-3644. PMID: 9685477, PMCID: PMC147776, DOI: 10.1093/nar/26.16.3640.Peer-Reviewed Original ResearchMeSH KeywordsBase CompositionBase SequenceGuanosineMagnetic Resonance SpectroscopyNucleic Acid ConformationNucleic Acid DenaturationRNAThermodynamicsConceptsM2GGNRA tetraloopRNA duplexesG substitutionSecondary structural stabilityHypermethylated regionsRNA structureNatural RNAPossible functionsRNAWatson-Crick pairsTetraloopNucleotidesN2-methylguanosineRibosomesRRNADuplexMethylationThermodynamic consequencesSubstitutionWide varietyDuplex stabilityPairsFunctionGuanosineThe chemical basis of adenosine conservation throughout the Tetrahymena ribozyme.
Ortoleva-Donnelly L, Szewczak A, Gutell R, Strobel S. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 1998, 4: 498-519. PMID: 9582093, PMCID: PMC1369635, DOI: 10.1017/s1355838298980086.Peer-Reviewed Original Research