Functional analysis of DNA and chromatin
Author(s)
Bibliographic Information
Functional analysis of DNA and chromatin
（Methods in molecular biology / John M. Walker, series editor, v. 1094）（Springer protocols）
Humana Press, c2014
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
1. Predictive Binding Geometry of Ligands to DNA Minor Groove:
Isohelicity and Hydrogen-Bonding Pattern
Juan C. Stockert
2. Using Microchip Gel Electrophoresis to Probe DNA-Drug Binding Interactions
Nan Shi and Victor M. Ugaz
3. Identifying Different Types of Chromatin using Giemsa Staining
Juan C. Stockert, Alfonso Blazquez-Castro, and Richard W. Horobin
4. Analysis of DNA Damage and Repair by Comet Fluorescence in situ Hybridization (Comet-FISH)
M. Glei and W. Schloermann
5. Alkaline Nuclear Dispersion Assays for the Determination of DNA Damage at the Single Cell Level
Piero Sestili, and Carmela Fimognari
6. Polarization Microscopy of Extended Chromatin Fibres
Maria Luiza S. Mello and Benedicto de Campos Vidal
7. DNA Labeling in Vivo: Quantification of Epidermal Stem Cell Chromatin Content in Whole Mouse Hair Follicles Using Fiji Image Processing Software
Elisa Carrasco, Maria I. Calvo, and Jesus Espada
8. A Historical Overview of Bromo-Substituted DNA and Sister Chromatid Differentiation
Roberto Mezzanotte and Mariella Nieddu
9. Image Analysis of Chromatin Remodelling
Benedicto de Campos Vidal, PhD, Marina B. Felisbino, MS, Maria Luiza S. Mello
10. FISH Methods in Cytogenetic Studies
Miguel Pita, Juan Orellana, Paloma Martinez-Rodriguez, Angel Martinez-Ramirez, Begona Fernandez-Calvin, and Jose L. Bella
11. Ultrastructural and Immunofluorescent Methods for the Study of the XY Body as a Biomarker
Roberta B. Sciurano and Alberto J. Solari
12. Atomic Force Microscopy for Analyzing Metaphase Chromosomes. Comparison of AFM Images with Fluorescence Labeling Images of Banding Patterns
Osamu Hoshi, and Tatsuo Ushiki
13. Selective Detection of Phagocytic Phase of Apoptosis in Fixed Tissue Sections
Vladimir V. Didenko
14. Selective Transport of Cationized Fluorescent Topoisomerase into Nuclei of Live Cells for DNA Damage Studies
Candace L. Minchew, and Vladimir V. Didenko
15. Visualization and Interpretation of Eukaryotic DNA Replication Intermediates in vivo by Electron Microscopy
Kai J. Neelsen, Arnab Ray Chaudhuri, Cindy Follonier, Raquel Herrador, and Massimo Lopes
16. Combined Bi-dimensional Electrophoresis and Electron Microscopy to Study Specific Plasmid DNA Replication Intermediates in Human Cells
Cindy Follonier and Massimo Lopes
17. Standard DNA Methylation Analysis in Mouse Epidermis: Bisulfite Sequencing, Methylation-Specific PCR, and 5-Methyl-Cytosine (5mC) Immunological Detection
Jesus Espada, Elisa Carrasco, and Maria I. Calvo
18. Methyl-combing-Single Molecule Analysis of DNA Methylation on Stretched DNA Fibers
Attila Nemeth
19. Investigating 5-Hydroxymethylcytosine (5hmC): The State of the Art
Colm E. Nestor, James P. Reddington, Mikael Benson, and Richard R. Meehan
20. Hydroxymethylated DNA Immunoprecipitation (hmeDIP)
Colm E. Nestor and Richard R. Meehan
21. Microscale Thermophoresis for the Assessment of Nuclear Protein Binding Affinities
Wei Zhang, Stefan Duhr, Philipp Baaske, and Ernest Laue22. Analysis of Histone Post-translational Modifications from Nucleolus-associated Chromatin by Mass Spectrometry
23. Salt-Urea, Sulfopropyl-Sepharose, and Covalent Chromatography Methods for Histone Isolation and Fractionation
Pedro Rodriguez-Collazo, Sanford Leuba, and Jordanka Zlatanova
24. Chromatin Immunoprecipitation
Javier Rodriguez-Ubreva, and Esteban Ballestar
25. Analysis of Chromatin Composition of Repetitive Sequences: the ChIP-chop Assay
Raffaella Santoro
26. Purification of Specific Chromatin Domains from Single-Copy Gene Loci in Saccharomyces cerevisiae
Stephan Hamperl, Christopher Brown, Jorge Perez-Fernandez, Katharina Huber, Manuel Wittner, Virginia Babl, Ulrike Stoeckl, Hinrich Boeger, Herbert Tschochner, Philipp Milkereit, and Joachim Griesenbeck
27. Deep Sequencing of Small Chromatin-Associated RNA - Isolation and Library Preparation
Sarah Diermeier, Thomas Schubert, and Gernot Langst
28. Deep Sequencing of Small Chromatin-Associated RNA - Bioinformatic Analysis
Sarah Diermeier and Gernot Langst
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