2008
A relaxed active site after exon ligation by the group I intron
Lipchock SV, Strobel SA. A relaxed active site after exon ligation by the group I intron. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 5699-5704. PMID: 18408159, PMCID: PMC2311373, DOI: 10.1073/pnas.0712016105.Peer-Reviewed Original ResearchConceptsActive siteMetal ionsRelaxed active siteActive site metal ionScissile phosphateDirect metal coordinationHydrogen bonding contactsMetal coordinationBonding contactsTransition stateCrystal structureThermodynamic measurementsIonsGround stateStructureCoordinationStructural observationsTertiary interactionsIntron releaseExon ligationGroup I intronPhosphateComplexesReactionSecond step
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 ResearchRegiospecificity of the Peptidyl tRNA Ester within the Ribosomal P Site
Huang KS, Weinger JS, Butler EB, Strobel SA. Regiospecificity of the Peptidyl tRNA Ester within the Ribosomal P Site. Journal Of The American Chemical Society 2006, 128: 3108-3109. PMID: 16522067, DOI: 10.1021/ja0554099.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 ResearchBiochemical 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
2000
A Single Adenosine with a Neutral pKa in the Ribosomal Peptidyl Transferase Center
Muth G, Ortoleva-Donnelly L, Strobel S. A Single Adenosine with a Neutral pKa in the Ribosomal Peptidyl Transferase Center. Science 2000, 289: 947-950. PMID: 10937997, DOI: 10.1126/science.289.5481.947.Peer-Reviewed Original Research
1999
An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site
Szewczak A, Ortoleva-Donnelly L, Zivarts M, Oyelere A, Kazantsev A, Strobel S. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 11183-11188. PMID: 10500151, PMCID: PMC18008, DOI: 10.1073/pnas.96.20.11183.Peer-Reviewed Original ResearchConceptsHelix dockingBase triplesRecognition surfaceGroup I intronActive siteNetwork of interactionsTetrahymena group IP3 helixStructural biologySubstrate bindingI intronCatalytic RNAProduct bindingSuppression analysisFunctional importanceRNA foldingRNA constructsSubstrate helixBiochemical evidenceMutant ribozymesRibozyme active siteSubstantial rearrangementHelixCrystallographic modelRibozymeNucleotide 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 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 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 ionsComplementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site
Strobel S, Ortoleva-Donnelly L, Ryder S, Cate J, Moncoeur E. Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site. Nature Structural & Molecular Biology 1998, 5: 60-66. PMID: 9437431, DOI: 10.1038/nsb0198-60.Peer-Reviewed Original Research
1996
Exocyclic Amine of the Conserved G·U Pair at the Cleavage Site of the Tetrahymena Ribozyme Contributes to 5‘-Splice Site Selection and Transition State Stabilization †
Strobel S, Cech T. Exocyclic Amine of the Conserved G·U Pair at the Cleavage Site of the Tetrahymena Ribozyme Contributes to 5‘-Splice Site Selection and Transition State Stabilization †. Biochemistry 1996, 35: 1201-1211. PMID: 8573575, DOI: 10.1021/bi952244f.Peer-Reviewed Original Research
1995
Minor Groove Recognition of the Conserved G⋅U Pair at the Tetrahymena ribozyme Reaction Site
Strobel S, Cech T. Minor Groove Recognition of the Conserved G⋅U Pair at the Tetrahymena ribozyme Reaction Site. Science 1995, 267: 675-679. PMID: 7839142, DOI: 10.1126/science.7839142.Peer-Reviewed Original ResearchThe branch site adenosine is recognized differently for the two steps of pre-mRNA splicing.
Query C, Strobel S, Sharp P. The branch site adenosine is recognized differently for the two steps of pre-mRNA splicing. Nucleic Acids Symposium Series 1995, 224-5. PMID: 8643377.Peer-Reviewed Original Research
1994
Translocation of an RNA duplex on a ribozyme
Strobel S, Cech T. Translocation of an RNA duplex on a ribozyme. Nature Structural & Molecular Biology 1994, 1: 13-17. PMID: 7544680, DOI: 10.1038/nsb0194-13.Peer-Reviewed Original Research
1993
Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme.
Strobel S, Cech T. Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme. Biochemistry 1993, 32: 13593-604. PMID: 7504953, DOI: 10.1021/bi00212a027.Peer-Reviewed Original Research
1990
Site-Specific Cleavage of a Yeast Chromosome by Oligonucleotide-Directed Triple-Helix Formation
Strobel S, Dervan P. Site-Specific Cleavage of a Yeast Chromosome by Oligonucleotide-Directed Triple-Helix Formation. Science 1990, 249: 73-75. PMID: 2195655, DOI: 10.1126/science.2195655.Peer-Reviewed Original Research