title: Single-molecule analysis of RAG-mediated V(D)J DNA cleavage.
abstract: The recombination-activating gene products, RAG1 and RAG2, initiate V(D)J recombination during lymphocyte development by cleaving DNA adjacent to conserved recombination signal sequences (RSSs). The reaction involves DNA binding, synapsis, and cleavage at two RSSs located on the same DNA molecule and results in the assembly of antigen receptor genes. We have developed single-molecule assays to examine RSS binding by RAG1/2 and their cofactor high-mobility group-box protein 1 (HMGB1) as they proceed through the steps of this reaction. These assays allowed us to observe in real time the individual molecular events of RAG-mediated cleavage. As a result, we are able to measure the binding statistics (dwell times) and binding energies of the initial RAG binding events and characterize synapse formation at the single-molecule level, yielding insights into the distribution of dwell times in the paired complex and the propensity for cleavage on forming the synapse. Interestingly, we find that the synaptic complex has a mean lifetime of roughly 400 s and that its formation is readily reversible, with only ∼40% of observed synapses resulting in cleavage at consensus RSS binding sites.
authors.affiliation: Biochemistry and Molecular Biophysics Option, Division of Biology and Biological Engineering, and.
authors.forename: Geoffrey A
authors.initials: GA
authors.lastname: Lovely
authors.affiliation: Division of Biology and Biological Engineering, and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125; and.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Brewster
authors.affiliation: Department of Immunobiology, Yale University School of Medicine and Howard Hughes Medical Institute, New Haven, CT 06520.
authors.forename: David G
authors.initials: DG
authors.lastname: Schatz
authors.affiliation: Division of Biology and Biological Engineering, and baltimo@caltech.edu phillips@pboc.caltech.edu.
authors.forename: David
authors.initials: D
authors.lastname: Baltimore
authors.affiliation: Biochemistry and Molecular Biophysics Option, Division of Biology and Biological Engineering, and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125; and baltimo@caltech.edu phillips@pboc.caltech.edu.
authors.forename: Rob
authors.initials: R
authors.lastname: Phillips
mesh_terms: D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D057809:HEK293 Cells; D024243:HMGB1 Protein / Q000378:metabolism; D018398:Homeodomain Proteins / Q000378:metabolism*; D006801:Humans; D054992:Immunological Synapses / Q000378:metabolism; D009038:Motion; D009154:Mutation; D016011:Normal Distribution; D009687:Nuclear Proteins / Q000378:metabolism*; D011485:Protein Binding; D011946:Receptors, Antigen / Q000235:genetics; D060152:V(D)J Recombination
chemical_list: D004268:DNA-Binding Proteins; D024243:HMGB1 Protein; C585491:HMGB1 protein, human; D018398:Homeodomain Proteins; D009687:Nuclear Proteins; C499311:RAG2 protein, human; D011946:Receptors, Antigen; C064658:RAG-1 protein; D004247:DNA
keywords: V(D)J recombination; recombination-activating gene; single molecule
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