DNA Repair, Part B

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.

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

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

*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