2015
Single-molecule analysis of RAG-mediated V(D)J DNA cleavage
Lovely GA, Brewster RC, Schatz DG, Baltimore D, Phillips R. Single-molecule analysis of RAG-mediated V(D)J DNA cleavage. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e1715-e1723. PMID: 25831509, PMCID: PMC4394307, DOI: 10.1073/pnas.1503477112.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesSingle-molecule assaysSame DNA moleculeAntigen receptor genesConsensus recombination signal sequencesSingle-molecule analysisHigh mobility group box protein 1Individual molecular eventsSignal sequenceSingle-molecule levelGene productsDNA bindingMolecular eventsLymphocyte developmentDNA moleculesDNA cleavageProtein 1Synapse formationSynaptic complexReceptor geneCleavageRAGAssaysRAG1/2Complexes
2009
Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis
Yin FF, Bailey S, Innis CA, Ciubotaru M, Kamtekar S, Steitz TA, Schatz DG. Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nature Structural & Molecular Biology 2009, 16: 499-508. PMID: 19396172, PMCID: PMC2715281, DOI: 10.1038/nsmb.1593.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsBase SequenceChromosome PairingCrystallography, X-RayDNAFluorescence Resonance Energy TransferHomeodomain ProteinsMiceModels, MolecularMolecular Sequence DataNucleic Acid ConformationProtein MultimerizationProtein Structure, QuaternaryProtein Structure, TertiarySolutionsStatic Electricity
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
2002
RAG1-DNA Binding in V(D)J Recombination SPECIFICITY AND DNA-INDUCED CONFORMATIONAL CHANGES REVEALED BY FLUORESCENCE AND CD SPECTROSCOPY*
Ciubotaru M, Ptaszek LM, Baker GA, Baker SN, Bright FV, Schatz DG. RAG1-DNA Binding in V(D)J Recombination SPECIFICITY AND DNA-INDUCED CONFORMATIONAL CHANGES REVEALED BY FLUORESCENCE AND CD SPECTROSCOPY*. Journal Of Biological Chemistry 2002, 278: 5584-5596. PMID: 12488446, DOI: 10.1074/jbc.m209758200.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBinding SitesCircular DichroismCloning, MolecularDNADNA NucleotidyltransferasesDNA-Binding ProteinsEscherichia coliGenes, RAG-1Homeodomain ProteinsKineticsMiceOligodeoxyribonucleotidesProtein ConformationRecombinant ProteinsRecombination, GeneticSubstrate SpecificityTransfectionTransposasesVDJ RecombinasesConceptsRecombination signal sequencesConformational changesSynaptic complex formationAbsence of DNAAssembly of immunoglobulinMajor conformational changesIntrinsic protein fluorophoresProtein intrinsic fluorescenceSolvent-exposed environmentRAG2 proteinsRAG1/2 complexSingle DNA moleculesRAG1 proteinSignal sequenceAcrylamide quenching studiesT-cell receptor genesStrep-tagRecombination specificityDNA moleculesProtein fluorophoresRAG1Receptor geneProteinIntrinsic fluorescenceCircular dichroism
1998
Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system
Agrawal A, Eastman Q, Schatz D. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 1998, 394: 744-751. PMID: 9723614, DOI: 10.1038/29457.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsAntibodiesBinding SitesB-LymphocytesCatalysisCell LineDNADNA Transposable ElementsDNA, CircularDNA-Binding ProteinsDrug Resistance, MicrobialEvolution, MolecularGene Rearrangement, B-LymphocyteGene Rearrangement, T-LymphocyteHigh Mobility Group ProteinsHomeodomain ProteinsImmune SystemMiceMolecular Sequence DataReceptors, Antigen, T-CellRecombination, GeneticRestriction MappingTransposasesVertebratesConceptsT-cell receptor genesRecombination signalsSequence-specific DNA recognitionAncestral receptor geneComponent gene segmentsSite-specific recombination reactionPiece of DNAEvolutionary divergenceJawless vertebratesRecombination-activating geneTransposable elementsDNA recognitionRetroviral integrationGermline insertionDNA moleculesGenesShort duplicationsDNA cleavageRAG1Gene segmentsTransposition reactionRAG2Receptor geneTarget DNA moleculesTarget DNA
1996
T-Cell Receptor α Locus V(D)J Recombination By-Products Are Abundant in Thymocytes and Mature T Cells
Livak F, Schatz D. T-Cell Receptor α Locus V(D)J Recombination By-Products Are Abundant in Thymocytes and Mature T Cells. Molecular And Cellular Biology 1996, 16: 609-618. PMID: 8552089, PMCID: PMC231040, DOI: 10.1128/mcb.16.2.609.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceDNA DamageGene Rearrangement, alpha-Chain T-Cell Antigen ReceptorImmune SystemMiceMice, Inbred C57BLMolecular Probe TechniquesMolecular Sequence DataReceptors, Antigen, T-Cell, alpha-betaReceptors, Antigen, T-Cell, gamma-deltaRecombination, GeneticT-LymphocytesThymus GlandConceptsRecombination signal sequencesSignal sequenceDNA moleculesAlpha locusTCR alpha/delta locusAlpha/delta locusBroken DNA moleculesReciprocal productsJ alpha locusTermination of expressionT-cell receptor α locusC delta regionTCR alpha locusSouthern blot analysisT cell developmentGenome integrityDNA existΑ locusQuantitative Southern blot analysisT-cell receptor genesCoding regionsDevelopmental transitionsLymphoid developmentDelta locusRAG-2