DNA Repair Protocols

Current knowledge of the mechanisms that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly successful Methods in Molecular Biology? series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

Thorough and intuitive, DNA Repair Protocols, Third Edition provides expert guidance for DNA repair, recombination, and replication.

List of contents

DNA repair: Front and Center and Not Going Away!.-Identification of Genes Required for Damage Survival using a Cell Based RNAi Screen against the Drosophila Genome.-Isolating Genes Involved with Genotoxic Drug Response in the Nematode Caenorhabditis elegans using Genome-wide RNAi Screening.-Establishment of the DNA Repair-defective Mutants in DT40 Cells.-Electrophoretic Mobility Shift Assays for Protein-DNA Complexes Involved in DNA Repair.-The Comet Assay A Sensitive Genotoxicity Test for the Detection of DNA Damage and Repair.-Detection of DNA Damage by Comet Fluorescence in situ Hybridization (Comet-FISH).-Quantitative DNA Damage and Repair Measurement with the Yeast Comet Assay.-Analysis of DNA Damage and Repair in Nuclear and Mitochondrial DNA of Animal Cells using Quantitative PCR.-In vitro DNA Mismatch Repair in Human Cells.-Eukaryotic DNA Mismatch Repair in vitro.-Immuno-slot Blot Assay for Detection of UVR-mediated DNA Damage.-Quantification of DNA Photoproductions in Mammalian Cell DNAUsing Radioimmunoassay.-Measuring the Formation and Repair of UV Damage at the DNA Sequence Level by Ligation-mediated PCR.-Construction of Plasmids Containing Site-specific DNA Interstrand Crosslinks for Biochemical and Cell Biological Studies.-Replication-coupled DNA Interstrand Crosslink Repair in Xenopus Egg Extracts.-In Vitro Base Excision Repair using Mammalian Cell Extracts.-Using Arabidopsis Cell Extracts to Monitor Repair of DNA Base Damage in vitro.-In vitro monitoring of Base Excision Repair in Saccharomyces cerevisiae.-Mitochondrial Base Excision Repair Assays.-O-Hydroxylamine-Coupled Alkaline Gel Electrophoresis Assay for the Detection and Measurement of DNA Single-Strand Breaks.-DNA DoubleStand Break Damage and Repair Assessed by Pulse-field Gel Electrophoresis.-Quantitative Amplification of Single Stranded DNA (QAOS).-Simple, Non-radioactive Measurement of Single-stranded DNA at Telomeric, Sub-telomeric and Genomic Loci in Budding Yeast.-Monitoring DNA Recombination Initiated by HO Endonuclease.-Monitoring I-SceI Induced Double Strand Break Repair in DT40 Cells.-I-SceI-based Assays to Examine Distinct Repair Outcomes of Mammalian Chromosomal Double Strand Breaks.-Studying Repair of a Single Protein-bound Nick in vivo using the Flp-nick System.-Measurement of Diversification in the Immunoglobulin Light Chain Gene of DT40 Cells.-Live cell microscopy of DNA damage response in Saccharomyces cerevisiae.-Use of Gene Targeting to Study Recombination in Mammalian Cell DNA
Repair Mutants.-In vitro Rejoining of Double Strand Breaks in Genomic DNA.-An In Vitro DNA Double-Strand Break Repair Assay Based on End Joining of Defined Duplex Oligonucleotides.-Assays of Bypass Replication of Genotoxic Lesions in Cell-Free Extracts
Nana Nikolaishvili-Feinberg and Marila Cordeiro-Stone.-Quantitative Measurement of Translesion DNA Synthesis in Mammalian Cells.-Detection of PCNA Modifications in Saccharomyces cerevisiae.-In vitro PCNA Modification Assays.-Analysis of Inhibition of DNA Replication in Irradiated Cells using the SV40 Based in vitro assay of DNA Replication.-CHK1 Kinase Activity Assay.-Histone H2AX Phosphorylation: A Marker for DNA Damage.

Repair Mutants.-In vitro Rejoining of Double Strand Breaks in Genomic DNA.-An In Vitro DNA Double-Strand Break Repair Assay Based on End Joining of Defined Duplex Oligonucleotides.-Assays of Bypass Replication of Genotoxic Lesions in Cell-Free Extracts
Nana Nikolaishvili-Feinberg andMarila Cordeiro-Stone.-Quantitative Measurement of Translesion DNA Synthesis in Mammalian Cells.-Detection of PCNA Modifications in Saccharomyces cerevisiae.-In vitro PCNA Modification Assays.-Analysis of Inhibition of DNA Replication in Irradiated Cells using the SV40 Based in vitro assay of DNA Replication.-CHK1 Kinase Activity Assay.-Histone H2AX Phosphorylation: A Marker for DNA Damage.

Repair Mutants.-In vitro Rejoining of Double Strand Breaks in Genomic DNA.-An In Vitro DNA Double-Strand Break Repair Assay Based on End Joining of Defined Duplex Oligonucleotides.-Assays of Bypass Replication of Genotoxic Lesions in Cell-Free Extracts
Nana Nikolaishvili-Feinberg and Marila Cordeiro-Stone.-Quantitative Measurement of Translesion DNA Synthesis in Mammalian Cells.-Detection of PCNA Modifications in Saccharomyces cerevisiae.-In vitro PCNA Modification Assays.-Analysis of Inhibition of DNA Replication in Irradiated Cells using the SV40 Based in vitro assay of DNA Replication.-CHK1 Kinase Activity Assay.-Histone H2AX Phosphorylation: A Marker for DNA Damage.

Summary

Current knowledge of the mechanisms that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens.

Additional text

From the book reviews:
“This book covers important aspects of the eukaryotic response to genomic insults and the most recent and advanced protocols on DNA repair, recombination, and replication. … The intended audience is researchers in the field of DNA repair. In my judgment, graduate students, postdoctorals, and researchers in the field of molecular biology, especially those with a focus on DNA repair, will find this book extremely useful.” (Omer Iqbal, Doody’s Book Reviews, February, 2013)

Report

From the book reviews:
"This book covers important aspects of the eukaryotic response to genomic insults and the most recent and advanced protocols on DNA repair, recombination, and replication. ... The intended audience is researchers in the field of DNA repair. In my judgment, graduate students, postdoctorals, and researchers in the field of molecular biology, especially those with a focus on DNA repair, will find this book extremely useful." (Omer Iqbal, Doody's Book Reviews, February, 2013)

Product details

• Assisted by: Lotte Bjergb K. (Editor), Lott Bjergbæk (Editor), Lotte Bjergbæk (Editor)
• Publisher: Springer, Berlin
• Languages: English
• Product format: Paperback / Softback
• Released: 01.01.2016
• EAN: 9781493959549
• ISBN: 978-1-4939-5954-9
• No. of pages: 631
• Dimensions: 179 mm x 254 mm x 37 mm
• Weight: 1222 g
• Illustrations: XVII, 631 p.
• Series: Methods in Molecular Biology; Methods in Molecular Biology
• Subjects: Natural sciences, medicine, IT, technology > Medicine > Clinical medicine; B, Human Genetics, Biomedical and Life Sciences, Medical Genetics, Gene Function, Plasmid DNA, yeast cells, microgel eletrophoresis techinque, repair genes, electrophoretic mobility shift, chromosomal DNA