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Functional Analysis of DNA and Chromatin

  • Book
  • © 2014

Overview

Editors:
  1. Juan C. Stockert

    1. Department of Biology, Autonomous University of Madrid Faculty of Sciences, Madrid, Spain

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  2. Jesús Espada

    1. Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain

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    You can also search for this editor in PubMed   Google Scholar

  3. Alfonso Blázquez-Castro

    1. Department of Biology, Autonomous University of Madrid Faculty of Sciences, Madrid, Spain

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  • Presents an overview of standard and more recent methods for the functional analysis of the genetic material
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1094)

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Table of contents (28 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. Predictive Binding Geometry of Ligands to DNA Minor Groove: Isohelicity and Hydrogen-Bonding Pattern

    • Juan C. Stockert
    Pages 1-12

  3. Using Microchip Gel Electrophoresis to Probe DNA–Drug Binding Interactions

    • Nan Shi, Victor M. Ugaz
    Pages 13-24

  4. Identifying Different Types of Chromatin Using Giemsa Staining

    • Juan C. Stockert, Alfonso Blázquez-Castro, Richard W. Horobin
    Pages 25-38

  5. Analysis of DNA Damage and Repair by Comet Fluorescence In Situ Hybridization (Comet-FISH)

    • Michael Glei, Wiebke Schlörmann
    Pages 39-48

  6. Alkaline Nuclear Dispersion Assays for the Determination of DNA Damage at the Single Cell Level

    • Piero Sestili, Carmela Fimognari
    Pages 49-70

  7. Polarization Microscopy of Extended Chromatin Fibers

    • Maria Luiza S. Mello, Benedicto de Campos Vidal
    Pages 71-78

  8. DNA Labeling In Vivo: Quantification of Epidermal Stem Cell Chromatin Content in Whole Mouse Hair Follicles Using Fiji Image Processing Software

    • Elisa Carrasco, María I. Calvo, Jesús Espada
    Pages 79-88

  9. A Historical Overview of Bromo-Substituted DNA and Sister Chromatid Differentiation

    • Roberto Mezzanotte, Mariella Nieddu
    Pages 89-98

  10. Image Analysis of Chromatin Remodelling

    • Benedicto de Campos Vidal, Marina B. Felisbino, Maria Luiza S. Mello
    Pages 99-108

  11. FISH Methods in Cytogenetic Studies

    • Miguel Pita, Juan Orellana, Paloma Martínez-Rodríguez, Ángel Martínez-Ramírez, Begoña Fernández-Calvín, José L. Bella
    Pages 109-135

  12. Ultrastructural and Immunofluorescent Methods for the Study of the XY Body as a Biomarker

    • Roberta B. Sciurano, Alberto J. Solari
    Pages 137-149

  13. Atomic Force Microscopy for Analyzing Metaphase Chromosomes: Comparison of AFM Images with Fluorescence Labeling Images of Banding Patterns

    • Osamu Hoshi, Tatsuo Ushiki
    Pages 151-157

  14. Selective Detection of Phagocytic Phase of Apoptosis in Fixed Tissue Sections

    • Vladimir V. Didenko
    Pages 159-166

  15. Selective Transport of Cationized Fluorescent Topoisomerase into Nuclei of Live Cells for DNA Damage Studies

    • Candace L. Minchew, Vladimir V. Didenko
    Pages 167-175

  16. Visualization and Interpretation of Eukaryotic DNA Replication Intermediates In Vivo by Electron Microscopy

    • Kai J. Neelsen, Arnab Ray Chaudhuri, Cindy Follonier, Raquel Herrador, Massimo Lopes
    Pages 177-208

  17. Combined Bidimensional Electrophoresis and Electron Microscopy to Study Specific Plasmid DNA Replication Intermediates in Human Cells

    • Cindy Follonier, Massimo Lopes
    Pages 209-219

  18. Standard DNA Methylation Analysis in Mouse Epidermis: Bisulfite Sequencing, Methylation-Specific PCR, and 5-Methyl-Cytosine (5mC) Immunological Detection

    • Jesús Espada, Elisa Carrasco, María I. Calvo
    Pages 221-231

  19. Methyl-Combing: Single-Molecule Analysis of DNA Methylation on Stretched DNA Fibers

    • Attila Németh
    Pages 233-241

  20. Investigating 5-Hydroxymethylcytosine (5hmC): The State of the Art

    • Colm E. Nestor, James P. Reddington, Mikael Benson, Richard R. Meehan
    Pages 243-258
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Keywords

About this book

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.

Editors and Affiliations

  • Department of Biology, Autonomous University of Madrid Faculty of Sciences, Madrid, Spain

    Juan C. Stockert, Alfonso Blázquez-Castro

  • Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain

    Jesús Espada

Bibliographic Information

  • Book Title: Functional Analysis of DNA and Chromatin

  • Editors: Juan C. Stockert, Jesús Espada, Alfonso Blázquez-Castro

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-706-8

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, New York 2014

  • Hardcover ISBN: 978-1-62703-705-1Published: 29 October 2013

  • Softcover ISBN: 978-1-4939-6048-4Published: 23 August 2016

  • eBook ISBN: 978-1-62703-706-8Published: 08 July 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 365

  • Number of Illustrations: 30 b/w illustrations, 44 illustrations in colour

  • Topics: Cell Biology, Human Genetics

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