2022
Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2
Wang J, Shi Y, Reiss K, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2. Biochemistry 2022, 61: 1966-1973. PMID: 36044776, PMCID: PMC9469760, DOI: 10.1021/acs.biochem.2c00341.Peer-Reviewed Original ResearchConceptsReplication-transcription complexStructural basisCryo-EM structureAdenosine monophosphateRemdesivir triphosphateStructural insightsDuplex productsPrimer extensionNucleotide selectivityBase pairsNucleotide incorporationIncoming substrateRibosyl moietyActive complexSARS-CoV-2 inhibitorsNew detailed informationTriphosphateComplexesMolecular dynamics simulationsAdenosine triphosphate
2020
Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase
Guo LT, Adams RL, Wan H, Huston NC, Potapova O, Olson S, Gallardo CM, Graveley BR, Torbett BE, Pyle AM. Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase. Journal Of Molecular Biology 2020, 432: 3338-3352. PMID: 32259542, PMCID: PMC7556701, DOI: 10.1016/j.jmb.2020.03.022.Peer-Reviewed Original ResearchConceptsLong RNA moleculesLong RNAsRNA moleculesRNA base modificationsGroup II intronsMutational profilingTranscriptome compositionRNA metabolismRNA researchBase modificationsPrimer extensionTool enzymeDiverse aspectsMixed populationEnzymeReverse transcriptionRNAStructural complexityReverse transcriptaseProfilingTranscriptase enzymeIntronsTranscription
2011
Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures
Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W. Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures. Journal Of Molecular Biology 2011, 406: 558-570. PMID: 21216248, PMCID: PMC3059800, DOI: 10.1016/j.jmb.2010.12.033.Peer-Reviewed Original ResearchConceptsDouble mutantMutation rateAmino acid residuesRB69 DNA polymeraseSingle mutantsMutable sequencesPocket mutantsMutantsAcid residuesState kinetic parametersPrimer extensionT4 phageFidelity mutantsNucleotide residuesIncoming dNTPsDNA polymeraseReversion assayTernary complexComplementary strandCrystal structureResiduesBase selectivityPocketPolymeraseMisincorporation
2001
Structure of the Replicating Complex of a Pol α Family DNA Polymerase
Franklin M, Wang J, Steitz T. Structure of the Replicating Complex of a Pol α Family DNA Polymerase. Cell 2001, 105: 657-667. PMID: 11389835, DOI: 10.1016/s0092-8674(01)00367-1.Peer-Reviewed Original ResearchConceptsAlpha familyDNA polymeraseResolution crystal structureTernary complex structureApo-protein structurePrimer-template DNAMinor groove interactionsFamily DNA polymerasesFamily polymerasesRB69 DNA polymerasePol IFidelity mechanismsPrimer 3' terminusPrimer extensionPolymeraseGroove interactionsDNA motionTerminusDNA orientationFamilyDNADegrees rotationCrystal structureComplex structureDTTP
2000
A nucleolar protein related to ribosomal protein L7 is required for an early step in large ribosomal subunit biogenesis
Dunbar D, Dragon F, Lee S, Baserga S. A nucleolar protein related to ribosomal protein L7 is required for an early step in large ribosomal subunit biogenesis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 13027-13032. PMID: 11087857, PMCID: PMC27172, DOI: 10.1073/pnas.97.24.13027.Peer-Reviewed Original ResearchConceptsNucleolar proteinsLarge ribosomal subunit biogenesisLarge ribosomal subunit RNARibosomal subunit biogenesisRNA-binding domainRibosomal subunit RNAPulse-chase labeling experimentsProcessing of precursorsRibosomal protein L7Subunit biogenesisExonucleolytic trimmingEssential genesRibosomal proteinsSpecificity factorMature rRNAPrecursor RNASpacer 2L7 proteinSubunit RNAEndonucleolytic cleavageProtein L7Extensive identityRRNAMajor substratePrimer extension
1996
Genomic structure and regulation of Kcn1, a cGMP-gated potassium channel
Yao X, Liu Y, Tung F, Desir GV. Genomic structure and regulation of Kcn1, a cGMP-gated potassium channel. American Journal Of Physiology 1996, 271: f37-f41. PMID: 8760241, DOI: 10.1152/ajprenal.1996.271.1.f37.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsPromoter regionEnhancer elementsNovel potassium channel geneMajor transcription initiation siteTypical TATA boxTranscription initiation sitePhorbol esterPotassium channel genesLuciferase reporter constructsPotassium channelsGenomic structurePorcine kidney cell lineDeletion analysisRabbit geneTATA boxAcid proteinGene transcriptionKidney cell lineReporter constructsChannel genesSequence analysisPrimer extensionInitiation siteNorthern blot
1993
Identification and characterization of a GC-rich promoter of the human parathyroid hormone-related peptide gene.
Vasavada RC, Wysolmerski JJ, Broadus AE, Philbrick WM. Identification and characterization of a GC-rich promoter of the human parathyroid hormone-related peptide gene. Endocrinology 1993, 7: 273-82. PMID: 8469240, DOI: 10.1210/mend.7.2.8469240.Peer-Reviewed Original ResearchConceptsExon 1cPeptide genesGC-rich promoter elementsCis-regulatory sequencesHuman parathyroid hormone-related peptide geneGC-rich promoterHandful of genesPrimer extension analysisHuman renal carcinoma cellsCanonical TATARenal carcinoma cellsFunctional dissectionCAAT sequencesHuman PTHrP genePutative promoterDNA 5Regulatory sequencesExtension analysisPromoter elementsGene promoterCAT geneGenomic DNAExon 1AAcetyltransferase constructsPrimer extension
1992
Three Novel Functional Variants of Human U5 Small Nuclear RNA
Sontheimer E, Steitz J. Three Novel Functional Variants of Human U5 Small Nuclear RNA. Molecular And Cellular Biology 1992, 12: 734-746. DOI: 10.1128/mcb.12.2.734-746.1992.Peer-Reviewed Original ResearchU5 small nuclear RNASmall nuclear RNAHeLa cellsNuclear RNAAffinity-purified spliceosomesSmall nuclear ribonucleoproteinTri-snRNP complexFull-length speciesSaccharomyces cerevisiaeSplicing extractsPrimer extensionUS variantsHeLa extractsAlternative splicingRNA blotsShort speciesNuclear ribonucleoproteinBase changesMinimal domainHigher abundanceNorthern blottingRNAHeLaAbundant formSplicingThree novel functional variants of human U5 small nuclear RNA.
Sontheimer EJ, Steitz JA. Three novel functional variants of human U5 small nuclear RNA. Molecular And Cellular Biology 1992, 12: 734-746. PMID: 1310151, PMCID: PMC364287, DOI: 10.1128/mcb.12.2.734.Peer-Reviewed Original ResearchConceptsU5 small nuclear RNASmall nuclear RNANuclear RNAHeLa cellsSmall nuclear ribonucleoprotein particleTri-snRNP complexOligonucleotide-directed RNase H cleavageNuclear ribonucleoprotein particleNovel functional variantsFull-length speciesAffinity-purified spliceosomesTrimethylguanosine capAlternative splicingShorter speciesRibonucleoprotein particleMinimal domainHeLa extractsPrimer extensionFunctional variantsHigh abundanceBase changesNorthern blottingAbundant formRNASpeciesThree Novel Functional Variants of Human U5 Small Nuclear RNA
Sontheimer E, Steitz J. Three Novel Functional Variants of Human U5 Small Nuclear RNA. Molecular And Cellular Biology 1992, 12: 734-746. DOI: 10.1128/mcb.12.2.734-746.1992.Peer-Reviewed Original ResearchU5 small nuclear RNASmall nuclear RNANuclear RNAHeLa cellsSmall nuclear ribonucleoprotein particleTri-snRNP complexOligonucleotide-directed RNase H cleavageNuclear ribonucleoprotein particleNovel functional variantsFull-length speciesAffinity-purified spliceosomesTrimethylguanosine capAlternative splicingShorter speciesRibonucleoprotein particleMinimal domainHeLa extractsPrimer extensionFunctional variantsHigh abundanceBase changesNorthern blottingAbundant formUS variantsRNA
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