DNA repair protocols / edited by Lotte Bjergbak. — 3rd ed. — New York : Humana Press ; Springer, c2012. – (58.17/M592/v.920)

Contents

    Contents
    
    Contributors
    1 DNA Repair: Front and Center and Not Going Away
    PART I IDENTIFICATION OF REPAIR GENES AND GENERATION Of REPAIR MUTANTS
    2 Identification of Genes Required for Damage Survival Using a Cell-Based RNAi Screen Against the Drosophila Genome 9
    3 Isolating Genes Involved with Genotoxic Drug Response in the Nematode Caenorhabditis elegans Using Genome-Wide RNAi Screening 27
    4 Establishment of the DNA Repair-Defective Mutants in DT40 Cells 39
    PART II ASSESSING DNA DAMAGE AND REPAIR
    5 Electrophoretic Mobility Shift Assays for Protein-DNA Complexes Involved in DNA Repair 53
    6 The Comet Assay: A Sensitive Genotoxicity Test for the Detection of DNA Damage and Repair 79
    7 Detection of DNA Damage by Comet Fluorescence In Situ Hybridization 91
    8 Quantitative DNA Damage and Repair Measurement with the Yeast Comet Assay 101
    9 Analysis of DNA Damage and Repair in Nuclear and Mitochondrial DNA of Animal Cells Using Quantitative PCR 111
    PART III REPAIR OF INCORRECT OR DAMAGED DNA BASES
    10 In Vitro DNA Mismatch Repair in Human Cells
    11 Eukaryotic DNA Mismatch Repair In Vitro
    12 Immuno-Slot Blot Assay for Detection of UVR-Mediated DNA Damage
    13 Quantification of DNA Photoproducts in Mammalian Cell DNA Using Radioimmunoassay
    14 Measuring the Formation and Repair of UV Damage at the DNA Sequence Level by Ligation-Mediated PCR
    15 Construction of Plasmids Containing Site-Specific DNA Interstrand Cross-Links for Biochemical and Cell Biological Studies
    16 Replication-Coupled DNA Interstrand Cross-Link Repair in Xenopus Egg Extracts
    17 In Vitro Base Excision Repair Using Mammalian Cell Extracts
    18 Using Arabidopsis Cell Extracts to Monitor Repair of DNA Base Damage In Vitro
    19 In Vitro Monitoring of Base Excision Repair in Saccharomyces cerevisiae
    20 Mitochondrial Base Excision Repair Assays
    PART IV DNA STRAND BREAKAGE AND REPAIR
    21 O-Hydroxylamine-Coupled Alkaline Gel Electrophoresis Assay for the Detection and Measurement of DNA Single-Strand Breaks
    22 DNA Double-Strand Break Damage and Repair Assessed by Pulsed-Field Gel Electrophoresis
    23 Quantitative Amplification of Single-Stranded DNA
    24 Simple， Non-radioactive Measurement of Single-Stranded DNA at Telomeric， Sub-telomeric， and Genomic Loci in Budding Yeast
    25 Monitoring DNA Recombination Initiated by HO Endonuclease 349
    26 Monitoring I-SceI-Induced Double-Strand Break Repair in DT40 Cells 371
    27 I-SceI-Based Assays to Examine Distinct Repair Outcomes of Mammalian Chromosomal Double Strand Breaks 379
    28 Studying Repair of a Single Protein-Bound Nick In Vivo Using the Flp-Nick System 393
    29 Measurement of Diversification in the Immunoglobulin Light Chain Gene of DT40 Cells 417
    30 Live Cell Microscopy of DNA Damage Response in Saccharomyces cerevisiae 433
    31 Use of Gene Targeting to Study Recombination in Mammalian Cell DNA Repair Mutants 445
    32 In Vitro Rejoining of Double Strand Breaks in Genomic DNA 471
    33 An In Vitro DNA Double-Strand Break Repair Assay Based on End-Joining of Defined Duplex Oligonucleotides 485
    PART V DNA DAMAGE TOLERANCE AND CHECKPOINTS
    34 Assays of Bypass Replication of Genotoxic Lesions in Cell-Free Extracts 503
    35 Quantitative Measurement of Translesion DNA Synthesis in Mammalian Cells 529
    36 Detection of PCNA Modifications in Saccharomyces cerevisiae 543
    37 In Vitro PCNA Modification Assays
    38 Analysis of Inhibition of DNA Replication in Irradiated Cells Using the SV40 Based In Vitro Assay of DNA Replication 591
    39 CHK1 Kinase Activity Assay 603
    40 Histone H2AX Phosphorylation: A Marker for DNA Damage 613
    Index