DNA repair [electronic resource] / edited by Judith Campbell, Paul Modrich.

Includes bibliographical references and indexes.

Cover -- Cover Page -- Table of Contents -- Contributors of Volume 408 -- Volumes in Series -- Chapter 1: Assays for Determining Lesion Bypass Efficiency and Mutagenicity of Site-Specific DNA Lesions In Vivo -- Introduction -- Genome Construction -- Genome Normalization -- Lesion Bypass (CRAB) Assay -- Lesion Mutagenesis (REAP) Assay -- Conclusion -- References -- Chapter 2: Oxidative DNA Glycosylases: Recipes from Cloning to Characterization -- Introduction -- Purification of DNA Glycosylases -- Preparation of Oligonucleotide Substrates -- Activity Assays for Oxidative DNA Glycosylases -- Acknowledgment -- References -- Chapter 3: Purification and Characterization of NEIL1 and NEIL2, Members of a Distinct Family of Mammalian DNA Glycosylases for Repair of Oxidized Bases -- Endogenous and Induced DNA Damage -- Repair of Oxidized Base Lesions in the Genome -- Two Classes of Oxidized Base-Specific Glycosylases -- Human Genome Database Analysis and Discovery of MutM/Nei-Like Proteins -- Enzymatic Activity of NEIL1 and NEIL2 with Duplex or Bubble Oligonucleotide Substrates -- Detection of DNA Glycosylase Activity of Recombinant NEILs by Trapping Analysis -- Acknowledgments -- References -- Chapter 4: Analysis of Base Excision DNA Repair of the Oxidative Lesion 2-Deoxyribonolactone and the Formation of DNA-Protein Cross-Links -- Introduction -- Preparation of dL-DNA Substrates -- Analysis of dL-mediated Spontaneous DNA-Protein Cross-Links -- Analysis of dL-Specific BER -- Acknowledgments -- References -- Chapter 5: Isolation and Analyses of MutY Homologs (MYH) -- Introduction -- Isolation of MutY and MYH Proteins -- Functional Assays of MutY and MYH -- Protein Interaction Assays -- Acknowledgments -- References -- Chapter 6: Use of Yeast for Detection of Endogenous Abasic Lesions, Their Source, and Their Repair -- AP Sites in DNA and Related 3'-Blocked and 5'-Blocked Single Strand Breaks Form an Abundant and Deleterious Class of Endogenous DNA Damage -- Endogenous AP Sites Cause Cell Death in the Absence of Apn1, Apn2, and Rad1-Rad10 -- Use of the apn1 apn2 rad1 Triple Mutant to Study the Origin and Repair of Endogenous AP Sites in DNA -- Use of the apn1 apn2 rad14 Triple Mutant to Study the Origin and Repair of Endogenous AP Sites in DNA -- Conclusions and Model -- Acknowledgments -- References -- Chapter 7: Activities and Mechanism of DNA Polymerase beta -- Introduction -- Kinetic Characteristics of DNA Synthesis -- Measurement of dRP Lyase Activity -- Measurement of In Vitro BER -- Reagents -- Acknowledgment -- References -- Chapter 8: Direct Removal of Alkylation Damage from DNA by AlkB and Related DNA Dioxygenases -- Purification of AlkB, ABH2, and ABH3 -- 14C-Methylated Substrates -- Assays -- In Vivo Assay: Survival of Alkylated Single-Stranded DNA Bacteriophage in E. coli AlkB Mutants -- References -- Chapter 9: Purification and Characterization of DNA Photolyases -- Introduction -- Overexpression and Purification of Photolyases -- Spectroscopic Properties and Characterization of Purified Photolyases.

This volume emphasizes the intracellular consequences of DNA damage, describing procedures for analysis of checkpoint responses, DNA repair in vivo, replication fork encounter of DNA damage, as well as biological methods for analysis of mutation production and chromosome rearrangements. It also describes molecular methods for analysis of a number of genome maintenance activities including DNA ligases, helicases, and single-strand binding proteins. *Part B of a 2-part series *Addresses DNA maintenance enzymes *Discusses damage signaling *Presents In vivo analysis of DNA repair *Covers mutation and chromosome rearrangements.