DNA Repair, Part B

Edited by

  • Judith Campbell, California Institute of Technology, Pasadena, California, U.S.A.
  • Paul Modrich, Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA

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.
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Biochemists, biophysicists, cell biologists, molecular biologists, geneticists, developmental biologists


Book information

  • Published: May 2006
  • ISBN: 978-0-12-182814-1

Table of Contents

Table of ContentsChapter 1Overproduction and purification of RFC-related clamp loaders and PCNA-related clamps from Saccharomyces cerevisiaeChapter 2Functional Assays for Replication Protein A (RPA)Chapter 3Human DNA Ligases I, III, and IV – purification and new specific assays for these enzymes. Chapter 4Enzymatic Mechanism of the WRN Helicase/NucleaseChapter 5Analysis of the DNA Unwinding Activity of RECQ Family HelicasesChapter 6Characterization of Checkpoints Responses to DNA damage in Saccharomyces cerevisiae: Basic ProtocolsChapter 7Recruitment of ATR-ATRIP, Rad17, and 9-1-1 Complexes to DNA DamageChapter 8Multiple approaches to study S. cerevisiae Rad9, a prototypical checkpoint proteinChapter 9Methods for studying adaptation to the DNA damage checkpoint in yeastChapter 10DNA damage-induced phosphorylation of Rad55 protein as a sentinel for DNA damage checkpoint activation in S. cerevisiaeChapter 11Methods for studying Mutagenesis and Checkpoints in Schizosaccharomyces pombeChapter 12Methods for Determining Spontaneous Mutation RatesChapter 13Genomic Approaches for Identifying DNA Damage Response Pathways in Saccharomyces cerevisiaeChapter 14Techniques for y-H2AX detectionChapter 15Methods for studying the cellular response to DNA damage: influence of the Mre11 complex on chromosome metabolism Chapter 16Detecting repair intermediates in vivo: effects of DNA damage response genes on single stranded DNA accumulation at uncapped telomeres in budding yeastChapter 17Analysis of Non-B DNA Structure at Chromosomal Sites in the Mammalian Genome Chapter 18Detection and Structural Analysis of R-LoopsChapter 19The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeastChapter 20Assays for transcriptional mutagenesis in active genesChapter 21Methods for studying chromatin assembly coupled to DNA repairChapter 22Structure-fucntion analysis of SWI2/SNF2 enzymesChapter 23Genomic Approach for the Understanding of Dynamic Aspect of Chromosome Behavior Chapter 24Measurement of Chromosomal DNA Single-Strand Breaks and Replication Fork Progression RatesChapter 25 Monitoring DNA replication following UV-induced damage in Escherichia coliChapter 26Methods to study replication fork collapse in budding yeastChapter 27Analysis of Gross-Chromosomal Rearrangements in Saccharomyces cerevisiaeChapter 28Formation and processing of stalled replication forks – utility of two-dimensional agarose gelsChapter 29Poly (ADP-ribose) polymerase-1 activation during DNA damage and repair