2024
Strand-resolved mutagenicity of DNA damage and repair
Anderson C, Talmane L, Luft J, Connelly J, Nicholson M, Verburg J, Pich O, Campbell S, Giaisi M, Wei P, Sundaram V, Connor F, Ginno P, Sasaki T, Gilbert D, López-Bigas N, Semple C, Odom D, Aitken S, Taylor M. Strand-resolved mutagenicity of DNA damage and repair. Nature 2024, 630: 744-751. PMID: 38867042, PMCID: PMC11186772, DOI: 10.1038/s41586-024-07490-1.Peer-Reviewed Original ResearchConceptsDNA damageDNA damage-induced mutationsSingle-base resolutionCancer genome evolutionDamage-induced mutationsRepair of DNA damageNucleotide excision repairGenome evolutionMultiple distinct mutationsDNA accessibilityGenomic conditionsReplicative strandProcess genomesDNA base damageTranslesion polymerasesExcision repairDNAMutation patternsMutationsBase damageRepair efficiencyStrandsAlkyl adductsReplicationIdentity fidelitySingle-mitosis dissection of acute and chronic DNA mutagenesis and repair
Ginno P, Borgers H, Ernst C, Schneider A, Behm M, Aitken S, Taylor M, Odom D. Single-mitosis dissection of acute and chronic DNA mutagenesis and repair. Nature Genetics 2024, 56: 913-924. PMID: 38627597, PMCID: PMC11096113, DOI: 10.1038/s41588-024-01712-y.Peer-Reviewed Original ResearchConceptsMutational processesUV damageGenome evolutionGenome-wideTranscribed regionsGenome replicationCancer genomesUV mutationCC dinucleotidesDNA mutagenesisSister cellsDriving evolutionGenomeMutagenesisPunctuated burstsSingle cellsRounds of genome replicationMutationsStrandsCellsMitosisDinucleotideSisterROSReplication
2020
Structure and bioactivity of colibactin
Wernke KM, Xue M, Tirla A, Kim CS, Crawford JM, Herzon SB. Structure and bioactivity of colibactin. Bioorganic & Medicinal Chemistry Letters 2020, 30: 127280. PMID: 32527463, PMCID: PMC7309967, DOI: 10.1016/j.bmcl.2020.127280.Peer-Reviewed Original ResearchConceptsColibactin-producing bacteriaStrands of DNABiosynthetic pathwaySecondary metabolitesColibactinMolecular-level explanationHuman gutAdenine residuesCell contactElectrophilic CyclopropanesCertain strainsBacteriaGenotoxic effectsHeterodimersDNABacterial cultureResiduesPathwayCleavageCellsStrandsGut
2019
Origins of DNA replication
Ekundayo B, Bleichert F. Origins of DNA replication. PLOS Genetics 2019, 15: e1008320. PMID: 31513569, PMCID: PMC6742236, DOI: 10.1371/journal.pgen.1008320.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsKingdoms of lifeDomains of lifeDaughter cellsDNA replicationReplication originsCell divisionAccurate duplicationDaughter strandsGenomic DNAHereditary informationSemiconservative replicationGenetic materialFull complementDNA synthesisDiscrete sitesDNABidirectional mannerReplicationDivergent strategiesChromosomesOrganismsDuplicationOriginCellsStrands
2012
Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3′-terminal phosphate and 5′-OH
Englert M, Xia S, Okada C, Nakamura A, Tanavde V, Yao M, Eom SH, Konigsberg WH, Söll D, Wang J. Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3′-terminal phosphate and 5′-OH. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 15235-15240. PMID: 22949672, PMCID: PMC3458315, DOI: 10.1073/pnas.1213795109.Peer-Reviewed Original ResearchConceptsRNA substratesRNA strandRNA phosphate backboneRNA endExtensive mutagenesisSecond RNA substrateKey residuesLigation pathwayBiochemical experimentsOverall ligationRNA ligaseGuanylylationRtcBMechanistic insightsGTP/Critical rolePhosphate backboneGMPActive siteCyclic phosphateDependent reactionDetailed insightStrandsLigaseMutagenesis
2007
Solution Structure of an rRNA Substrate Bound to the Pseudouridylation Pocket of a Box H/ACA snoRNA
Jin H, Loria JP, Moore PB. Solution Structure of an rRNA Substrate Bound to the Pseudouridylation Pocket of a Box H/ACA snoRNA. Molecular Cell 2007, 26: 205-215. PMID: 17466623, DOI: 10.1016/j.molcel.2007.03.014.Peer-Reviewed Original ResearchConceptsPseudouridylation pocketBox H/ACA small nucleolar ribonucleoproteinsBox H/ACA snoRNAsSubstrate sequenceSmall nucleolar ribonucleoproteinSolution structureInteraction motifsNucleolar ribonucleoproteinSpecific uridinesRNA componentRRNA substrateRRNA sequencesSnoRNAsSequencePocketComplexesPseudouridylationSnoRNPsRibonucleoproteinHJ1RNAMotifInteractsStrandsUridine
2005
Analysis and Design of Turns in α-Helical Hairpins
Lahr S, Engel D, Stayrook S, Maglio O, North B, Geremia S, Lombardi A, DeGrado W. Analysis and Design of Turns in α-Helical Hairpins. Journal Of Molecular Biology 2005, 346: 1441-1454. PMID: 15713492, DOI: 10.1016/j.jmb.2004.12.016.Peer-Reviewed Original Research
2004
Exchange of DNA Base Pairs that Coincides with Recognition of Homology Promoted by E. coli RecA Protein
Folta-Stogniew E, O'Malley S, Gupta R, Anderson KS, Radding CM. Exchange of DNA Base Pairs that Coincides with Recognition of Homology Promoted by E. coli RecA Protein. Molecular Cell 2004, 15: 965-975. PMID: 15383285, DOI: 10.1016/j.molcel.2004.08.017.Peer-Reviewed Original ResearchConceptsE. coli RecA proteinRecognition of homologyColi RecA proteinRecA proteinBase pairsStrand exchangeSynaptic complexDouble-strand breaksT base pairsStopped-flow fluorescenceGenetic recombinationSingle strandsHomologyUnresolved mechanismDuplex DNADNA base pairsDNARate of exchangeProteinDynamic structureComplexesStrandsBasis exchangeRate of formationMechanism
2002
The Identification of CVP1 Reveals a Role for Sterols in Vascular Patterning
Carland F, Fujioka S, Takatsuto S, Yoshida S, Nelson T. The Identification of CVP1 Reveals a Role for Sterols in Vascular Patterning. The Plant Cell 2002, 14: 2045-2058. PMID: 12215504, PMCID: PMC150754, DOI: 10.1105/tpc.003939.Peer-Reviewed Original ResearchMeSH KeywordsAllelesArabidopsisArabidopsis ProteinsBiological TransportBrassinosteroidsCholestanolsCloning, MolecularCotyledonGene Expression Regulation, DevelopmentalGene Expression Regulation, PlantIn Situ HybridizationMethyltransferasesMutationPhytosterolsPlants, Genetically ModifiedRNA, MessengerSignal TransductionSteroids, HeterocyclicTriazolesConceptsSterol biosynthetic pathwayBrassinosteroid levelsCell polarityOrgan expansionVascular patterningAllelic seriesBiosynthetic pathwayCell polarizationVascular strandsAdditional functionsEnzymatic activityVascular cellsSterolsPathwayCvp1Branch pointsMutantsGenesRoleMutationsEnzymePatterningCellsStrandsElongation
1992
The cardiac conduction system in the rat expresses the alpha 2 and alpha 3 isoforms of the Na+,K(+)-ATPase.
Zahler R, Brines M, Kashgarian M, Benz E, Gilmore-Hebert M. The cardiac conduction system in the rat expresses the alpha 2 and alpha 3 isoforms of the Na+,K(+)-ATPase. Proceedings Of The National Academy Of Sciences Of The United States Of America 1992, 89: 99-103. PMID: 1309618, PMCID: PMC48183, DOI: 10.1073/pnas.89.1.99.Peer-Reviewed Original ResearchConceptsAlpha 3 isoformAlpha 2Gene expression approachAlpha 1 isoformIsoform genesSpecific hybridization signalAlpha subunitSpecific expressionMembrane channelsSpecific membrane channelsHybridization signalsIsoformsWorking myocytesCardiac conduction systemExcitable tissuesSodium pumpGenesSubunitsATPaseTissueExpressionStrands
1990
The two functional domains of gamma delta resolvase act on the same recombination site: implications for the mechanism of strand exchange.
Dröge P, Hatfull G, Grindley N, Cozzarelli N. The two functional domains of gamma delta resolvase act on the same recombination site: implications for the mechanism of strand exchange. Proceedings Of The National Academy Of Sciences Of The United States Of America 1990, 87: 5336-5340. PMID: 2164677, PMCID: PMC54318, DOI: 10.1073/pnas.87.14.5336.Peer-Reviewed Original ResearchConceptsDNA-protein complexesRecombination sitesSite-specific recombinationGamma delta resolvaseDNA exchangeCatalytic domainStrand exchangeFunctional domainsResolvaseResolvase subunitsDNA strandsRes sitesSynaptic complexDNAStrand breakageRecombinationReunion eventDomainSitesComplexesSubunitsStrandsBreakageSynaptosomes
1985
Polyadenylation of a human mitochondrial ribosomal RNA transcript detected by molecular cloning
Baserga S, Linnenbach A, Malcolm S, Ghosh P, Malcolm A, Takeshita K, Forget B, Benz E. Polyadenylation of a human mitochondrial ribosomal RNA transcript detected by molecular cloning. Gene 1985, 35: 305-312. PMID: 4043734, DOI: 10.1016/0378-1119(85)90009-5.Peer-Reviewed Original Research
1983
A novel repair enzyme: UVRABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region
Sancar A, Rupp W. A novel repair enzyme: UVRABC excision nuclease of Escherichia coli cuts a DNA strand on both sides of the damaged region. Cell 1983, 33: 249-260. PMID: 6380755, DOI: 10.1016/0092-8674(83)90354-9.Peer-Reviewed Original ResearchConceptsUvrABC nucleaseFifth phosphodiester bond 3Escherichia coliDNA strandsPhosphodiester bond 3UvrABC excision nucleasePyrimidine dimersUV-induced mutagenesisUvrC proteinUV-irradiated DNAExcision nucleaseRepair enzymesPhosphodiester bondNucleaseEnzymeProteinBond 3DNAColiUvrBStrandsUvrAMutagenesisDimersSame mechanism
1977
5′-Terminal nucleotide sequences of polio virus polyribosomal RNA and virion RNA are identical
PETTERSSON R, FLANEGAN J, ROSE J, BALTIMORE D. 5′-Terminal nucleotide sequences of polio virus polyribosomal RNA and virion RNA are identical. Nature 1977, 268: 270-272. PMID: 196211, DOI: 10.1038/268270a0.Peer-Reviewed Original ResearchConceptsVirion RNAPolyribosomal RNANucleotide sequenceInitiation of RNAPositive-strand virusesNucleotide sequence relationshipsNascent chainsRNA moleculesRNA chainsPositive strandSequence relationshipsRNANegative strandProteinReplicative intermediatesPoliovirion RNAA-GpViral RNAMRNAVirus RNASequenceStrandsTerminusCells3Virus
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