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
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 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
[6] Chemical probing of RNA by nucleotide analog interference mapping
Ryder S, Ortoleva-Donnelly L, Kosek A, Strobel S. [6] Chemical probing of RNA by nucleotide analog interference mapping. Methods In Enzymology 2000, 317: 92-109. PMID: 10829274, DOI: 10.1016/s0076-6879(00)17008-9.Peer-Reviewed Original Research
1999
A 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 ResearchNucleotide Analog Interference Mapping
Ryder S, Strobel S. Nucleotide Analog Interference Mapping. Methods 1999, 18: 38-50. PMID: 10208815, DOI: 10.1006/meth.1999.0755.Peer-Reviewed Original ResearchConceptsFunctional groupsActive moleculesGroup substitutionNucleotide analog interference mappingIncorporation propertiesIndividual analoguesMoleculesSeries 5AnaloguesSubstitution experimentsGel electrophoresisInterference mappingUnique biochemical signatureSubstitutionSynthesisNucleoside analog triphosphatesActivity assaysBiochemical informationReactionAnalog substitutionsAssayable functionChemogenetic approachRNA structureNucleotide analoguesIodine
1998
N2-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 ResearchConceptsM2GGNRA tetraloopRNA duplexesG substitutionSecondary structural stabilityHypermethylated regionsRNA structureNatural RNAPossible functionsRNAWatson-Crick pairsTetraloopNucleotidesN2-methylguanosineRibosomesRRNADuplexMethylationThermodynamic consequencesSubstitutionWide varietyDuplex stabilityPairsFunctionGuanosine
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
1994
The 2,6-diaminopurine riboside.5-methylisocytidine wobble base pair: an isoenergetic substitution for the study of G.U pairs in RNA.
Strobel S, Cech T, Usman N, Beigelman L. The 2,6-diaminopurine riboside.5-methylisocytidine wobble base pair: an isoenergetic substitution for the study of G.U pairs in RNA. Biochemistry 1994, 33: 13824-35. PMID: 7524665, DOI: 10.1021/bi00250a037.Peer-Reviewed Original ResearchTranslocation 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