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In Functional Analysis of DNA and Chromatin, expert researchers in the field provide an overview of standard and more recent methods for the functional analysis of the genetic material. These include methods on DNA-dye binding modes, chromatin staining, nuclear dispersion assays, DNA labeling in vivo, sister chromatid exchanges, FISH, DNA and chromatin imaging by fluorescence, electron and atomic force microscopy, detection of apoptotic DNA, cytosine methylation and hydroxy-methylation, DNA thermophoresis, improved methods for histone analysis, chromatin immunoprecipitation, and analysis of rDNA genes and chromatin-associated RNA. 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 key tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Functional Analysis of DNA and Chromatin seeks to aid scientists in the further study of cellular and molecular biology of the nucleus.
List of contents
Predictive Binding Geometry of Ligands to DNA Minor Groove: Isohelicity and Hydrogen-Bonding Pattern.- Using Microchip Gel Electrophoresis to Probe DNA-Drug Binding Interactions.- Identifying Different Types of Chromatin using Giemsa Staining.- Analysis of DNA Damage and Repair by Comet Fluorescence in situ Hybridization (Comet-FISH).- Alkaline Nuclear Dispersion Assays for the Determination of DNA Damage at the Single Cell Level.- Polarization Microscopy of Extended Chromatin Fibres.- DNA Labeling in Vivo: Quantification of Epidermal Stem Cell Chromatin Content in Whole Mouse Hair Follicles Using Fiji Image Processing Software.- A Historical Overview of Bromo-Substituted DNA and Sister Chromatid Differentiation.- Image Analysis of Chromatin Remodelling.- FISH Methods in Cytogenetic Studies.- Ultrastructural and Immunofluorescent Methods for the Study of the XY Body as a Biomarker.- Atomic Force Microscopy for Analyzing Metaphase Chromosomes. Comparison of AFM Images with Fluorescence Labeling Images of Banding Patterns.- Selective Detection of Phagocytic Phase of Apoptosis in Fixed Tissue Sections.- Transport of Cationized Fluorescent Topoisomerase into Nuclei of Live Cells for DNA Damage Studies.- Visualization and Interpretation of Eukaryotic DNA Replication Intermediates in vivo by Electron Microscopy.- Combined Bi-dimensional Electrophoresis and Electron Microscopy to Study Specific Plasmid DNA Replication Intermediates in Human Cells.- Standard DNA Methylation Analysis in Mouse Epidermis: Bisulfite Sequencing, Methylation-Specific PCR, and 5-Methyl-Cytosine (5mC) Immunological Detection.- Methyl-combing-Single Molecule Analysis of DNA Methylation on Stretched DNA Fibers.- Investigating 5-Hydroxymethylcytosine (5hmC): The State of the Art.- Hydroxymethylated DNA Immunoprecipitation (hmeDIP).- Microscale Thermophoresis for the Assessment of Nuclear Protein Binding Affinities.- Analysis of Histone Post-translational Modificationsfrom Nucleolus-associated Chromatin by Mass Spectrometry.- Salt-Urea, Sulfopropyl-Sepharose, and Covalent Chromatography Methods for Histone Isolation and Fractionation.- Chromatin Immunoprecipitation.- Analysis of Chromatin Composition of Repetitive Sequences: the ChIP-chop Assay.- Purification of Specific Chromatin Domains from Single-Copy Gene Loci in Saccharomyces cerevisiae.- Deep Sequencing of Small Chromatin-Associated RNA - Isolation and Library Preparation.- Deep Sequencing of Small Chromatin-Associated RNA - Bioinformatic Analysis.
Summary
In Functional Analysis of DNA and Chromatin, expert researchers in the field provide an overview of standard and more recent methods for the functional analysis of the genetic material. These include methods on DNA-dye binding modes, chromatin staining, nuclear dispersion assays, DNA labeling in vivo, sister chromatid exchanges, FISH, DNA and chromatin imaging by fluorescence, electron and atomic force microscopy, detection of apoptotic DNA, cytosine methylation and hydroxy-methylation, DNA thermophoresis, improved methods for histone analysis, chromatin immunoprecipitation, and analysis of rDNA genes and chromatin-associated RNA. 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 key tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Functional Analysis of DNA and Chromatin seeks to aid scientists in the further study of cellular and molecular biology of the nucleus.
