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 bindingAMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids
Shine M, Zhang C, Pyle AM. AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids. Bioinformatics 2022, 38: 2937-2939. PMID: 35561202, PMCID: PMC9113296, DOI: 10.1093/bioinformatics/btac207.Peer-Reviewed Original Research
2005
Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II
Kawaoka J, Pyle AM. Choosing between DNA and RNA: the polymer specificity of RNA helicase NPH-II. Nucleic Acids Research 2005, 33: 644-649. PMID: 15681616, PMCID: PMC548353, DOI: 10.1093/nar/gki208.Peer-Reviewed Original Research
2004
Big engine finds small breaks
Pyle AM. Big engine finds small breaks. Nature 2004, 432: 157-158. PMID: 15538349, DOI: 10.1038/432157a.Peer-Reviewed Original Research
2003
The 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
The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding
Pang PS, Jankowsky E, Planet PJ, Pyle AM. The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding. The EMBO Journal 2002, 21: 1168-1176. PMID: 11867545, PMCID: PMC125889, DOI: 10.1093/emboj/21.5.1168.Peer-Reviewed Original ResearchConceptsRNA unwindingHelicase activityDNA helicase activityCytoplasmic RNA virusesProcessive DNA helicaseImportant drug targetsReplicative DNA intermediatesNS3 helicase activityViral NS3 proteinDNA helicaseDuplex unwindingPhylogenetic analysisReplicative roleProcessive helicaseDNA intermediatesHelicaseHost DNARNA virusesRNA activityRNA replicationDrug targetsNS3 proteinUnwindingCentral roleDNA