2004
Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase
Serebrov V, Pyle AM. Periodic cycles of RNA unwinding and pausing by hepatitis C virus NS3 helicase. Nature 2004, 430: 476-480. PMID: 15269774, DOI: 10.1038/nature02704.Peer-Reviewed Original ResearchBackbone tracking by the SF2 helicase NPH-II
Kawaoka J, Jankowsky E, Pyle AM. Backbone tracking by the SF2 helicase NPH-II. Nature Structural & Molecular Biology 2004, 11: 526-530. PMID: 15146171, DOI: 10.1038/nsmb771.Peer-Reviewed Original Research
2003
Domains 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 ResearchThe Pathway for DNA Recognition and RNA Integration by a Group II Intron Retrotransposon
Aizawa Y, Xiang Q, Lambowitz AM, Pyle AM. The Pathway for DNA Recognition and RNA Integration by a Group II Intron Retrotransposon. Molecular Cell 2003, 11: 795-805. PMID: 12667460, DOI: 10.1016/s1097-2765(03)00069-8.Peer-Reviewed Original ResearchConceptsGroup II intron RNPsIntron-encoded proteinTarget site specificityMobile genetic elementsIntron invasionDNA recognitionDNA bindingGenetic elementsConformational changesDuplex DNADNA targetsSite specificityDNAStrand DNAComplex cascadeReverse transcriptionRNPInvasionRetrotransposonsSplicingTranscriptionProteinKinetic frameworkPathwayCascade
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
1998
More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns.
Chu VT, Liu Q, Podar M, Perlman PS, Pyle AM. More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns. RNA 1998, 4: 1186-202. PMID: 9769094, PMCID: PMC1369692, DOI: 10.1017/s1355838298980724.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
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