2014
Principles of ion recognition in RNA: insights from the group II intron structures
Marcia M, Pyle AM. Principles of ion recognition in RNA: insights from the group II intron structures. RNA 2014, 20: 516-527. PMID: 24570483, PMCID: PMC3964913, DOI: 10.1261/rna.043414.113.Peer-Reviewed Original ResearchConceptsActive siteSite-bound ionsIon recognitionMetal ionsOrganic ionsLatter ionIon-binding sitesCatalytic ionsCrystal structureGU wobble pairsMonovalent ionsLarge RNA moleculesIonsStructural ionsBiophysical methodsGroup II intron structureGA mismatchesLong-range tertiary contactsRNA structureRNA foldingTertiary contactsWobble pairStructureCatalysisHeteronuclear
2004
Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif
Sigel RK, Sashital DG, Abramovitz DL, Palmer AG, Butcher SE, Pyle AM. Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif. Nature Structural & Molecular Biology 2004, 11: 187-192. PMID: 14745440, DOI: 10.1038/nsmb717.Peer-Reviewed Original ResearchConceptsGroup II intron ribozymeMetal ion titrationsSolution structureMetal ion bindingDivalent metal ionsMetal ion-binding sitesRibozyme active siteBackbone substituentsMetal ionsMajor groove faceIon-binding sitesIon titrationActive siteIon bindingSyn conformationIntron ribozymesMinor groove sideAGC triadNew RNA motifMajor grooveGroove faceStrong Mg2Catalytic triadGroove sideCentral core
2003
An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron Ribozyme
Su LJ, Brenowitz M, Pyle AM. An Alternative Route for the Folding of Large RNAs: Apparent Two-state Folding by a Group II Intron Ribozyme. Journal Of Molecular Biology 2003, 334: 639-652. PMID: 14636593, DOI: 10.1016/j.jmb.2003.09.071.Peer-Reviewed Original ResearchDomains 2 and 3 Interact to Form Critical Elements of the Group II Intron Active Site
Fedorova O, Mitros T, Pyle AM. Domains 2 and 3 Interact to Form Critical Elements of the Group II Intron Active Site. Journal Of Molecular Biology 2003, 330: 197-209. PMID: 12823961, DOI: 10.1016/s0022-2836(03)00594-1.Peer-Reviewed Original ResearchA Group II Intron Inserted into a Bacterial Heat-Shock Operon Shows Autocatalytic Activity and Unusual Thermostability †
Adamidi C, Fedorova O, Pyle AM. A Group II Intron Inserted into a Bacterial Heat-Shock Operon Shows Autocatalytic Activity and Unusual Thermostability †. Biochemistry 2003, 42: 3409-3418. PMID: 12653544, DOI: 10.1021/bi027330b.Peer-Reviewed Original ResearchLanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes.
Sigel RK, Pyle AM. Lanthanide ions as probes for metal ions in the structure and catalytic mechanism of ribozymes. 2003, 40: 477-512. PMID: 12723158.Peer-Reviewed Original Research
2002
Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions
Fedorova O, Su LJ, Pyle AM. Group II introns: highly specific endonucleases with modular structures and diverse catalytic functions. Methods 2002, 28: 323-335. PMID: 12431436, DOI: 10.1016/s1046-2023(02)00239-6.Peer-Reviewed Original ResearchProductive folding to the native state by a group II intron ribozyme11Edited by D. Draper
Swisher JF, Su LJ, Brenowitz M, Anderson VE, Pyle AM. Productive folding to the native state by a group II intron ribozyme11Edited by D. Draper. Journal Of Molecular Biology 2002, 315: 297-310. PMID: 11786013, DOI: 10.1006/jmbi.2001.5233.Peer-Reviewed Original Research
1996
Role of metal ions in ribozymes.
Pyle AM. Role of metal ions in ribozymes. 1996, 32: 479-520. PMID: 8640529.Peer-Reviewed Original Research
1995
Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection.
Chin K, Pyle AM. Branch-point attack in group II introns is a highly reversible transesterification, providing a potential proofreading mechanism for 5'-splice site selection. RNA 1995, 1: 391-406. PMID: 7493317, PMCID: PMC1482411.Peer-Reviewed Original ResearchConversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships.
Michels WJ, Pyle AM. Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: elucidation of reaction mechanism and structure/function relationships. Biochemistry 1995, 34: 2965-77. PMID: 7893710, DOI: 10.1021/bi00009a028.Peer-Reviewed Original Research
1994
Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity.
Pyle AM, Moran S, Strobel SA, Chapman T, Turner DH, Cech TR. Replacement of the conserved G.U with a G-C pair at the cleavage site of the Tetrahymena ribozyme decreases binding, reactivity, and fidelity. Biochemistry 1994, 33: 13856-63. PMID: 7947794, DOI: 10.1021/bi00250a040.Peer-Reviewed Original ResearchBuilding a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate.
Pyle AM, Green JB. Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate. Biochemistry 1994, 33: 2716-25. PMID: 8117737, DOI: 10.1021/bi00175a047.Peer-Reviewed Original ResearchConceptsGeneral base catalysisChemical stepLinear rangeMichaelis-Menten mechanismSplice-site hydrolysisMultiple-turnover kinetic analysesPH/rate profileEnergetic stabilizationBase catalysisActive siteGel filtration chromatographyRibozyme kineticsReaction rateFiltration chromatographySpecific hydrolysisKinetic frameworkKinetic analysisHydrolysisReactionLower Km valuesBase pairingRibozyme activityKcat
1992
RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization.
Cech TR, Herschlag D, Piccirilli JA, Pyle AM. RNA catalysis by a group I ribozyme. Developing a model for transition state stabilization. Journal Of Biological Chemistry 1992, 267: 17479-17482. PMID: 1381347, DOI: 10.1016/s0021-9258(19)37064-4.Peer-Reviewed Original Research
1990
Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena.
Pyle AM, McSwiggen JA, Cech TR. Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena. Proceedings Of The National Academy Of Sciences Of The United States Of America 1990, 87: 8187-8191. PMID: 2236030, PMCID: PMC54920, DOI: 10.1073/pnas.87.21.8187.Peer-Reviewed Original ResearchConceptsSingle base changeBase-pairing interactionsGuanosine-binding siteRNA substratesSubstrate bindingRNA cleavageOligonucleotide substratesEfficient RNA cleavageTertiary interactionsBase changesRibozyme variantsTetrahymena ribozymeWeak substrateMutant ribozymesRibozymePolyacrylamide gelsEquilibrium dissociation constantsDeoxyribose sugarCatalytic activityDivalent cationsEnergetic stabilizationMutagenesisDissociation constantsTetrahymenaLow Mg2