2022
Chapter Three Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study
Guo R, Pyle AM. Chapter Three Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study. Methods In Enzymology 2022, 673: 39-52. PMID: 35965013, DOI: 10.1016/bs.mie.2022.03.064.Peer-Reviewed Original ResearchConceptsEnzymatic ATPase activitySuperfamily 1Nucleic acid-dependent ATPasesATPase activityRNA-dependent ATPaseSimple reporter systemNucleic acid bindingNucleic acid ligandsNucleic acidsATPase enzymeSF2 helicaseAcid ligandsKinetic parametersRNA associationSF2 helicasesRNA bindingMultitude of processesMotor proteinsBiological functionsSF1 helicasesReporter systemFunctional bindingConformational changesDirect binding assaysAcid binding
2020
Visualizing group II intron dynamics between the first and second steps of splicing
Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M. Visualizing group II intron dynamics between the first and second steps of splicing. Nature Communications 2020, 11: 2837. PMID: 32503992, PMCID: PMC7275048, DOI: 10.1038/s41467-020-16741-4.Peer-Reviewed Original ResearchConceptsGroup II intron splicingGroup II intronsSelf-splicing ribozymesGene-editing toolsIntron dynamicsEukaryotic spliceosomeActive site dynamicsIntron splicingRetrotransposable elementsCatalytic triadSplicingMolecular machinesConformational changesFirst residueMultiple conformationsSite dynamicsSpliceosomeIntronsStructural rearrangementsX-ray crystallographyEnzymatic assayStructural dataEnzymatic strategyFunctional dataActive site
2003
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space
Duarte CM, Wadley LM, Pyle AM. RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Research 2003, 31: 4755-4761. PMID: 12907716, PMCID: PMC169959, DOI: 10.1093/nar/gkg682.Peer-Reviewed Original ResearchConceptsRNA structureRepertoire of RNANovel RNA structuresNew RNA structuresStructural genomicsRNA functionRNA conformational spaceRibosomal subunitRNA researchRNA moleculesRNA motifsRNA structure comparisonMotif searchTertiary structureConformational changesStructure comparisonNew motifMotifReduced representationConformational spaceMacromolecular structureFuture adaptationGenomicsMajor regionsSubunitsThe 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