DNA Damage Responses Methods and Protocols

This volume provides detailed methods and key approaches used to mechanistically study DNA damage, as well as the factors involved in the damage response. Chapters guide readers through proteomics and biophysical approaches, analyzing protein function, quantifying DNA replication dynamics and nucleic acid base damage, as well as biochemical reconstitution of key pathways involved in DNA repair. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 Authoritative and cutting-edge, DNA Damage Responses: Methods and Protocols aims to be a useful practical guide to researches to help further their study in this field.

Robust Computational Approaches to Defining Insights on the Interface of DNA Repair with Replication and Transcription in Cancer.- A Whole Genome CRISPR/Cas9 Screening Approach for Identifying Genes Encoding DNA End-Processing Proteins.- Immunoaffinity Purification of Epitope-Tagged DNA Repair Complexes from Human Cells.- Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.- Assessing DNA damage responses using B lymphocyte cultures.- Studying single stranded DNA gaps a­­t replication intermediates by electron microscopy.- Approaches to monitor termination of DNA replication using Xenopus egg extracts.- Use of high-performance liquid chromatography coupled to mass spectrometry to quantify modified nucleosides.- Targeted Formation of 8-oxoguanine in Telomeres.- Qualitative and Quantitative Analysis of DNA-Cytidine Deaminase Activity.- Characterization of DNA-PK-bound end fragments using GLASS-ChIP.- Monitoring Nuclease Activity by X-ray Scattering Interferometry using Gold Nanoparticle Conjugated DNA.- In Vitro Reconstitution of BRCA1-BARD1/RAD51 Mediated Homologous DNA Pairing.- Purification of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) fromHeLa cells.- Purification and characterization of human DNA ligase III complexes after expression in insect cells.- Generation of monoubiquitin and K63-linked polyubiquitin chains for protein interaction studies.