- Volume
-
pt. A ISBN 9780121828134
Description
DNA Repair, Part A provides detailed coverage of modern methods for molecular analysis of enzymes and enzyme systems that function in the maintenance of genome integrity. Coverage areas include base excision repair, nucleotide excision repair, translesion DNA polymerases, mismatch repair, genetic recombination, and double strand break repair.
Table of Contents
Chapter 1
Assays for determining lesion bypass efficiency and mutagenicity of site-specific DNA lesions in vivo
Chapter 2
Oxidative DNA glycolases: Recipes from Cloning to Characterization
Chapter 3
Purification and Characterization of NEIL1 and NEIL2, Members of a distinct Family of Mammalian DNA Glycosylases for repair of oxidized bases
Chapter 4
Analysis of Base Excision DNA Repair of the Oxidative Lesion 2-Deoxyribonolactone and the Formation of DNA-Protein Cross-links
Chapter 5
Isolation and analyses of MutY and MutY Homologs (MYH)
Chapter 6
Use of yeast for detection of endogenous abasic legions, their source and their repair
Chapter 7
Activities and Mechanism of Pol Beta
Chapter 8
Direct removal of aklylation damage from DNA by AlkB and related DNA dioxygenases
Chapter 9
Purification and Characterization of DNA Photolyases
Chapter 10
Genetic and in vitro assays of DNA deamination
Chapter 11
The XPC complex and UV-DDB: Functional assays for the damage recognition factors involved in global genome repair
Chapter 12
Purification and Characterization of E. coli and Human Nucleotide Excision Repair
Chapter 13
Assays for transcription elongation by RNA polymerase II using oligo (dC)-tailed
template with single DNA damage
Chapter 14
In vivo assays for transcription-coupled repair
Chapter 15
TFIIh enzymatic activities in transcription and nucleotide excision repair
Chapter 16
An assay for studying ubiquitylation of RNA polymerase II and other proteins in crude yeast extracts
Chapter 17
Analysis of the excision step in human DNA mismatch repair
Chapter 18
Characterisation of the "mismatch repairosome" and its role in the processing of modified nucleosides in vitro
Chapter 19
Analysis of DNA Mismatch Repair in Cellular Response to DNA Damage
Chapter 20
Characterization of E. coli Translesion Synthesis Polymerases and Their Accessory Factors
Chapter 21
Measuring the Fidelity of Translesion DNA Synthesis
Chapter 22
DNA Polymerases for Translesion DNA Synthesis: Enzyme Purification and Mouse Models for Studying Their Function
Chapter 23
Purification and Characterization of Escherichia coli DNA Polymerase V
Chapter 24
Yeast and Human Translesion DNA Synthesis Polymerases: Expression, Purification, and Biochemical Characterization
Chapter 25
Localisation of Y-family polymerases and the DNA polymerase switch in mammalian cells
Chapter 26
Repair of DNA Double Strand Breaks - in vivo Biochemistry
Chapter 27
Assays for nonhomologous end-joining in extracts
Chapter 28
Purification and assays of Saccharomyces cerevisiae homologous recombination proteins
Chapter 29
Analysis of DNA recombination and repair proteins in living cells by photobleaching microscopy
Chapter 30
Synthetic Junctions as Tools to Identify and Characterize Holliday Junction Resolvases
Chapter 31
In Vitro Nonhomologous End Joining Assay
Chapter 32
The RAG and HMGB1 proteins: purification and biochemical analysis of recombination signal complexes
Chapter 33
Purification and Biochemical Characterization of ATM and MRN
- Volume
-
pt. B ISBN 9780121828141
Description
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.
Table of Contents
Chapter 1
Overproduction and purification of RFC-related clamp loaders and PCNA-related clamps from Saccharomyces cerevisiae
Chapter 2
Functional Assays for Replication Protein A (RPA)
Chapter 3
Human DNA Ligases I, III, and IV - purification and new specific assays for these enzymes.
Chapter 4
Enzymatic Mechanism of the WRN Helicase/Nuclease
Chapter 5
Analysis of the DNA Unwinding Activity of RECQ Family Helicases
Chapter 6
Characterization of Checkpoints Responses to DNA damage in Saccharomyces cerevisiae: Basic Protocols
Chapter 7
Recruitment of ATR-ATRIP, Rad17, and 9-1-1 Complexes to DNA Damage
Chapter 8
Multiple approaches to study S. cerevisiae Rad9, a prototypical checkpoint protein
Chapter 9
Methods for studying adaptation to the DNA damage checkpoint in yeast
Chapter 10
DNA damage-induced phosphorylation of Rad55 protein as a sentinel for DNA damage checkpoint activation in S. cerevisiae
Chapter 11
Methods for studying Mutagenesis and Checkpoints in Schizosaccharomyces pombe
Chapter 12
Methods for Determining Spontaneous Mutation Rates
Chapter 13
Genomic Approaches for Identifying DNA Damage Response Pathways in Saccharomyces cerevisiae
Chapter 14
Techniques for y-H2AX detection
Chapter 15
Methods for studying the cellular response to DNA damage: influence of the Mre11 complex on chromosome metabolism
Chapter 16
Detecting repair intermediates in vivo: effects of DNA damage response genes on single stranded DNA accumulation at uncapped telomeres in budding yeast
Chapter 17
Analysis of Non-B DNA Structure at Chromosomal Sites in the Mammalian Genome
Chapter 18
Detection and Structural Analysis of R-Loops
Chapter 19
The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast
Chapter 20
Assays for transcriptional mutagenesis in active genes
Chapter 21
Methods for studying chromatin assembly coupled to DNA repair
Chapter 22
Structure-fucntion analysis of SWI2/SNF2 enzymes
Chapter 23
Genomic Approach for the Understanding of Dynamic Aspect of Chromosome Behavior
Chapter 24
Measurement of Chromosomal DNA Single-Strand Breaks and Replication Fork Progression Rates
Chapter 25
Monitoring DNA replication following UV-induced damage in Escherichia coli
Chapter 26
Methods to study replication fork collapse in budding yeast
Chapter 27
Analysis of Gross-Chromosomal Rearrangements in Saccharomyces cerevisiae
Chapter 28
Formation and processing of stalled replication forks - utility of two-dimensional agarose gels
Chapter 29
Poly (ADP-ribose) polymerase-1 activation during DNA damage and repair
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