2025
BRCA2 prevents PARPi-mediated PARP1 retention to protect RAD51 filaments
Lahiri S, Hamilton G, Moore G, Goehring L, Huang T, Jensen R, Rothenberg E. BRCA2 prevents PARPi-mediated PARP1 retention to protect RAD51 filaments. Nature 2025, 640: 1103-1111. PMID: 40140565, PMCID: PMC12161360, DOI: 10.1038/s41586-025-08749-x.Peer-Reviewed Original ResearchConceptsRad51 filamentsFormation of Rad51 filamentsTumor suppressor protein BRCA2Resected single-stranded DNAHomology-directed DNA repairBRCA2 mutationsDNA strand exchangeBRCA2-deficient tumorsBRCA2-deficient cellsDouble-stranded DNA breaksSingle-stranded DNAQuantitative single-molecule localization microscopySingle-molecule approachesStrand exchangeDNA substratesBRCA2 deficiencyCellular contextFilament stabilityDNA repairResponse to PARPiRAD51Sensitivity to PARPiDNA breaksBRCA2PARP1 inhibition
2024
Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β
Alnajjar K, Wang K, Alvarado-Cruz I, Chavira C, Negahbani A, Nakhjiri M, Minard C, Garcia-Barboza B, Kashemirov B, McKenna C, Goodman M, Sweasy J. Modifying the Basicity of the dNTP Leaving Group Modulates Precatalytic Conformational Changes of DNA Polymerase β. Biochemistry 2024, 63: 1412-1422. PMID: 38780930, PMCID: PMC11155676, DOI: 10.1021/acs.biochem.4c00065.Peer-Reviewed Original ResearchDNA polymerase BPolymerase BPol-BBase excision DNA repair pathwayLinear free energy relationshipGapped DNA substratesRemoval of damaged DNA basesFree energy relationshipConformational changesChemical transition stateAccumulation of mutationsDNA repair pathwaysDamaged DNA basesGroup basicityCorrect nucleotideDNA substratesIncoming nucleotideTransition stateEnergy relationshipFingers subdomainRepair pathwaysSubstrate selectivityNucleotideTriphosphate moietyCatalytic function
2022
Structures of a mobile intron retroelement poised to attack its structured DNA target
Chung K, Xu L, Chai P, Peng J, Devarkar S, Pyle A. Structures of a mobile intron retroelement poised to attack its structured DNA target. Science 2022, 378: 627-634. PMID: 36356138, PMCID: PMC10190682, DOI: 10.1126/science.abq2844.Peer-Reviewed Original ResearchConceptsGroup II intronsCryo-electron microscopy structureDNA targetsStem-loop motifMicroscopy structureGenetic diversificationDNA substratesForward splicingRetroelementsAncient elementsDNA targetingIntronsTertiary complexRibozymeRetrotransposonsGenomeRetrotranspositionSplicingComplexesRNPDNAMotifTargetDiversificationTargetingStructural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme
Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry 2022, 61: 785-794. PMID: 35420793, PMCID: PMC9069930, DOI: 10.1021/acs.biochem.2c00127.Peer-Reviewed Original ResearchConceptsShort palindromic repeatsSubstrate specificityPalindromic repeatsAla mutantWT enzymeRNA-binding domainAssociated 9 (Cas9) systemForeign DNA sequencesDNA strandsWild-type enzymeDouble-strand breaksEnhanced substrate specificityHNH active siteDynamics of proteinsType II immunityCas9 proteinDNA substratesDNA sequencesStructural basisMutantsAla substitutionDistinct conformationsSingle LysCatalytic siteEnzymeTumor suppressor CEBPA interacts with and inhibits DNMT3A activity
Chen X, Zhou W, Song R, Liu S, Wang S, Chen Y, Gao C, He C, Xiao J, Zhang L, Wang T, Liu P, Duan K, Cheng Z, Zhang C, Zhang J, Sun Y, Jackson F, Lan F, Liu Y, Xu Y, Wong J, Wang P, Yang H, Xiong Y, Chen T, Li Y, Ye D. Tumor suppressor CEBPA interacts with and inhibits DNMT3A activity. Science Advances 2022, 8: eabl5220. PMID: 35080973, PMCID: PMC8791617, DOI: 10.1126/sciadv.abl5220.Peer-Reviewed Original ResearchDNA methyltransferasesDNA methylationDe novo DNA methylationMammalian embryonic developmentNovo DNA methylationPRC2 target genesLonger splice isoformsCCAAT/enhancer binding protein αAberrant DNA methylationEnhancer binding protein αDNMT3A activityDNMT3a isoformsDNA substratesEmbryonic developmentSpecific lociTarget genesSplice isoformsDNA-hypomethylating agentN-terminusShort isoformProtein αMethylationFunctional differencesIsoformsMutations
2020
DNA Strand Exchange to Monitor Human RAD51-Mediated Strand Invasion and Pairing
Lahiri S, Jensen RB. DNA Strand Exchange to Monitor Human RAD51-Mediated Strand Invasion and Pairing. Methods In Molecular Biology 2020, 2153: 101-113. PMID: 32840775, PMCID: PMC10434838, DOI: 10.1007/978-1-0716-0644-5_8.Peer-Reviewed Original ResearchConceptsDNA double-strand breaksDNA strand exchangeStrand invasionSingle-strand DNA gapsStrand exchangeDNA DSBsHuman Rad51 proteinDNA strand exchange reactionDouble-strand breaksHomologous recombination pathwayHigh-fidelity repairStrand exchange reactionGenomic integrityRad51 proteinReplication forksDNA substratesHomology searchDNA gapsGenetic informationMitotic cellsRecombination pathwayDNA moleculesProteinInvasionMeiosisApplying Live Cell Imaging and Cryo-Electron Tomography to Resolve Spatiotemporal Features of the Legionella pneumophila Dot/Icm Secretion System.
Chetrit D, Park D, Hu B, Liu J, Roy CR. Applying Live Cell Imaging and Cryo-Electron Tomography to Resolve Spatiotemporal Features of the Legionella pneumophila Dot/Icm Secretion System. Journal Of Visualized Experiments 2020 PMID: 32225141, DOI: 10.3791/60693.Peer-Reviewed Original ResearchConceptsDot/Icm secretion systemCryo-electron tomographySecretion systemCryo-ETDot/Icm systemDot/Icm apparatusDot/IcmSuperfolder green fluorescent proteinLive-cell imagingGreen fluorescent proteinIntact bacterial cellsPolar positioningSecretion complexPolar localizationQuantitative fluorescence microscopyBacterial poleATPase geneCytoplasmic complexDelivery of proteinsDNA substratesTiming of productionIcm systemFluorescent proteinLiving cellsBacterial cellsAnalysis of Dot/Icm Type IVB Secretion System Subassemblies by Cryoelectron Tomography Reveals Conformational Changes Induced by DotB Binding
Park D, Chetrit D, Hu B, Roy CR, Liu J. Analysis of Dot/Icm Type IVB Secretion System Subassemblies by Cryoelectron Tomography Reveals Conformational Changes Induced by DotB Binding. MBio 2020, 11: 10.1128/mbio.03328-19. PMID: 32071271, PMCID: PMC7029142, DOI: 10.1128/mbio.03328-19.Peer-Reviewed Original ResearchConceptsType IV secretion systemSecretion systemCryoelectron tomographyInner membraneDot/Icm apparatusConformational changesDot/IcmEukaryotic host cellsBacterial inner membraneWild-type cellsHost cell membraneWhole-cell contextMultiprotein nanomachineSubtomogram analysisSophisticated nanomachinesCytoplasmic substratesProtein effectorsCell polesDNA substratesSubtomogram averagingATPase complexDNA transferHost infectionStructural basisHost cells
2019
Transposon molecular domestication and the evolution of the RAG recombinase
Zhang Y, Cheng TC, Huang G, Lu Q, Surleac MD, Mandell JD, Pontarotti P, Petrescu AJ, Xu A, Xiong Y, Schatz DG. Transposon molecular domestication and the evolution of the RAG recombinase. Nature 2019, 569: 79-84. PMID: 30971819, PMCID: PMC6494689, DOI: 10.1038/s41586-019-1093-7.Peer-Reviewed Original ResearchConceptsRAG1-RAG2 recombinaseMolecular domesticationRAG recombinaseCryo-electron microscopy structureTwo-tiered mechanismAmino acid residuesJawed vertebratesMicroscopy structureEvolutionary adaptationDNA substratesTransposition activityAcid residuesDomesticationDNA cleavageAcidic regionDiverse repertoireAdaptive immune systemRecombinaseTransposonCell receptorTransposasePivotal eventRecombinationCleavageVertebrates
2017
Defective Nucleotide Release by DNA Polymerase β Mutator Variant E288K Is the Basis of Its Low Fidelity
Mahmoud MM, Schechter A, Alnajjar KS, Huang J, Towle-Weicksel J, Eckenroth BE, Doublié S, Sweasy JB. Defective Nucleotide Release by DNA Polymerase β Mutator Variant E288K Is the Basis of Its Low Fidelity. Biochemistry 2017, 56: 5550-5559. PMID: 28945359, PMCID: PMC5654646, DOI: 10.1021/acs.biochem.7b00869.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionBiocatalysisColonic NeoplasmsDNADNA Polymerase betaDNA RepairDNA ReplicationEnzyme StabilityFluorescent DyesHumansKineticsModels, MolecularMutagenesis, Site-DirectedMutationNaphthalenesulfonatesNeoplasm Proteinsp-DimethylaminoazobenzeneProtein ConformationProtein Interaction Domains and MotifsProtein RefoldingRecombinant ProteinsSubstrate Specificity
2016
Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity
Chatterjee G, Jimenez-Sainz J, Presti T, Nguyen T, Jensen RB. Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity. Nucleic Acids Research 2016, 44: 5256-5270. PMID: 27084934, PMCID: PMC4914107, DOI: 10.1093/nar/gkw242.Peer-Reviewed Original ResearchConceptsDNA double-strand breaksDomain of BRCA2Homology-directed repairDouble-strand breaksBRC repeatsDNA damageDNA damage sensitivityPatient-derived mutationsRegulation of RAD51Cellular DNA damageComplementation functionRepair complexRAD51 bindingRad51 filamentsDNA substratesHomologous recombinationFaceted proteinProper regulationStrand pairingRAD51Damage sensitivityCellular propertiesRepeatsCellular featuresRepeat unitsCollaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination
Carmona LM, Fugmann SD, Schatz DG. Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination. Genes & Development 2016, 30: 909-917. PMID: 27056670, PMCID: PMC4840297, DOI: 10.1101/gad.278432.116.Peer-Reviewed Original ResearchConceptsRecombination-activating gene 1Transib transposaseAbsence of RAG2RAG1/RAG2Antigen receptor genesJawed vertebratesRAG2 proteinsTransposable elementsRAG1 proteinRegulatory featuresDNA substratesGene 1RAG2Receptor geneRecombination activityProteinRecombinationTransposaseAdaptive immunityVertebratesTransposonGenesEvolutionLow levelsOrigin
2012
Hypoxia sensing by Fe2+/α‐KG dependent dioxygenases regulate hmU synthesis in trypanosome DNA, chromatin structure and Pol II transcription
sabatini R, cliffe L, ekanayake D, Hirsch G. Hypoxia sensing by Fe2+/α‐KG dependent dioxygenases regulate hmU synthesis in trypanosome DNA, chromatin structure and Pol II transcription. The FASEB Journal 2012, 26: 535.16-535.16. DOI: 10.1096/fasebj.26.1_supplement.535.16.Peer-Reviewed Original ResearchThymidine hydroxylaseBase JIncreased parasite virulenceIncreased Pol II occupancyPol II transcription initiationGene expressionRegulation of gene expressionPol II occupancyPol II transcriptionGenome-wide changesSynthetic DNA substratesParasite virulenceGrowth of T. cruziOxygen-dependent mannerIncreased histone acetylationTranscription initiationDioxygenase superfamilyII transcriptionChromatin structureDNA substratesTranscriptional regulationIn vivo analysisPromoter regionHistone acetylationHost environmentChapter One DNA Translocation of ATP-Dependent Chromatin Remodeling Factors Revealed by High-Resolution Optical Tweezers
Zhang Y, Sirinakis G, Gundersen G, Xi Z, Gao Y. Chapter One DNA Translocation of ATP-Dependent Chromatin Remodeling Factors Revealed by High-Resolution Optical Tweezers. Methods In Enzymology 2012, 513: 3-28. PMID: 22929763, DOI: 10.1016/b978-0-12-391938-0.00001-x.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdenosine TriphosphateBase SequenceBinding SitesChromatin Assembly and DisassemblyDNADNA HelicasesElectrophoresis, Polyacrylamide GelEscherichia coliMicroscopy, Atomic ForceMolecular Sequence DataNucleic Acid ConformationNucleosomesOptical TweezersPlasmidsTandem Repeat SequencesConceptsChromatin remodelingChromatin structureDNA translocationATP-dependent chromatin remodeling factorsATP-dependent chromatin remodelingATP-dependent chromatinChromatin remodeling factorsDNA moleculesOptical tweezersHigh-resolution optical tweezersSingle-molecule assaysRemodeler ATPasesDNA translocasesRemodeling factorsSingle DNA moleculesDNA substratesSingle-molecule levelATP hydrolysisBiological functionsBare DNASingle-molecule experimentsMolecular mechanismsDetailed protocolTranslocationMolecular motors
2007
Activation-induced Cytidine Deaminase-mediated Sequence Diversification Is Transiently Targeted to Newly Integrated DNA Substrates*
Yang SY, Fugmann SD, Gramlich HS, Schatz DG. Activation-induced Cytidine Deaminase-mediated Sequence Diversification Is Transiently Targeted to Newly Integrated DNA Substrates*. Journal Of Biological Chemistry 2007, 282: 25308-25313. PMID: 17613522, DOI: 10.1074/jbc.m704231200.Peer-Reviewed Original ResearchConceptsActivation-induced cytidine deaminaseChicken B cell line DT40B cell line DT40Cytidine deaminaseNon-Ig lociNon-Ig genesSequence diversificationDNA substratesTranscription cassetteMutation targetsCassetteMolecular characteristicsMolecular featuresDeaminaseDT40TranscriptionGenesLociDNADiversificationMutabilityTargetingIgTarget
2004
Synapsis of Recombination Signal Sequences Located in cis and DNA Underwinding in V(D)J Recombination
Ciubotaru M, Schatz DG. Synapsis of Recombination Signal Sequences Located in cis and DNA Underwinding in V(D)J Recombination. Molecular And Cellular Biology 2004, 24: 8727-8744. PMID: 15367690, PMCID: PMC516766, DOI: 10.1128/mcb.24.19.8727-8744.2004.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA substratesSignal sequenceDNA distortionHigh mobility group proteinsProtein conformational changesSame DNA moleculeDouble-strand DNA cleavageRAG proteinsRAG2 proteinsDNA underwindingGroup proteinsSite of cleavagePreferred substrateConformational changesDNA moleculesDNA cleavageProteinRelaxed substrateUnderwindingRecombinationCleavageSequenceSuch substratesHMG1
2003
The Architecture of the γδ Resolvase Crossover Site Synaptic Complex Revealed by Using Constrained DNA Substrates
Leschziner A, Grindley N. The Architecture of the γδ Resolvase Crossover Site Synaptic Complex Revealed by Using Constrained DNA Substrates. Molecular Cell 2003, 12: 775-781. PMID: 14527421, DOI: 10.1016/s1097-2765(03)00351-4.Peer-Reviewed Original Research
2002
Threonine 79 Is a Hinge Residue That Governs the Fidelity of DNA Polymerase β by Helping to Position the DNA within the Active Site*
Maitra M, Gudzelak A, Li SX, Matsumoto Y, Eckert KA, Jager J, Sweasy JB. Threonine 79 Is a Hinge Residue That Governs the Fidelity of DNA Polymerase β by Helping to Position the DNA within the Active Site*. Journal Of Biological Chemistry 2002, 277: 35550-35560. PMID: 12121998, DOI: 10.1074/jbc.m204953200.Peer-Reviewed Original ResearchConceptsHelix motifPol betaDNA synthesisThr-79Vivo genetic screenAccurate DNA synthesisDifferent amino acid residuesAmino acid residuesWild-type pol betaN-terminal 8DNA polymerase βGenetic screenDNA polymerase betaAntimutator phenotypeDNA substratesIncoming dNTP substrateActive siteWild typeBent DNAHinge residuesAcid residuesDNA templateBeta enzymePolymerase βPolymerase beta
2001
Contacts between the 5′ Nuclease of DNA Polymerase I and Its DNA Substrate*
Xu Y, Potapova O, Leschziner A, Grindley N, Joyce C. Contacts between the 5′ Nuclease of DNA Polymerase I and Its DNA Substrate*. Journal Of Biological Chemistry 2001, 276: 30167-30177. PMID: 11349126, DOI: 10.1074/jbc.m100985200.Peer-Reviewed Original ResearchMeSH KeywordsArginineBase SequenceBinding SitesCircular DichroismDNADNA Polymerase IDNA RepairEscherichia coliKineticsLysineModels, ChemicalModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedMutationOrganophosphorus CompoundsPhosphatesProtein BindingProtein Structure, TertiarySubstrate SpecificityTemperatureTime FactorsConceptsDNA substratesDNA polymerase INuclease domainCleavage siteBasic residuesPolymerase IDuplex DNANuclease cleavagePhosphate ethylation interferenceDNA-binding regionActive site regionDNA replicationOne-half turnBacteriophage T5Eukaryotic nucleasesSubstrate bindingAbasic DNAEthylation interferenceDuplex portionHelical archNucleaseSite regionEscherichia coliMethylphosphonate substitutionsPrimer strand
1999
In Vitro Selection of Nucleic Acid Enzymes
Breaker R, Kurz M. In Vitro Selection of Nucleic Acid Enzymes. Current Topics In Microbiology And Immunology 1999, 243: 137-158. PMID: 10453642, DOI: 10.1007/978-3-642-60142-2_8.Peer-Reviewed Original ResearchConceptsDiversity of enzymesYears of evolutionNucleic acid enzymesEvolutionary historyNucleic acidsBiochemical functionsDNA substratesMetabolic machineryVitro SelectionProtein enzymesCatalytic functionBiological catalystsAcid enzymesHydrolysis reactionProteinEnzymeNatural functionRibozymeDistinct classesRNAEssential componentReactionMachineryCatalystDiversity
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply