Functional Analysis of DNA and Chromatin

ISBN-13: 9781627037051 / Angielski / Twarda / 2013 / 365 str.

Juan C. Stockert; Jesus Espada; Alfonso Blazquez-Castro

Opis

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.

Spis treści

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 Blázquez-Castro, and Richard W. Horobin

4. Analysis of DNA Damage and Repair by Comet Fluorescence in situ Hybridization (Comet-FISH)

M. Glei and W. Schlörmann

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, María I. Calvo, and Jesús 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 Martínez-Rodríguez, Ángel Martínez-Ramírez, Begoña Fernández-Calvín, and José 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

Jesús Espada, Elisa Carrasco, and María I. Calvo

18. Methyl-combing—Single Molecule Analysis of DNA Methylation on Stretched DNA Fibers

Attila Németh

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 Laue

22. 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 Rodríguez-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 Stöckl, 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 Längst

28. Deep Sequencing of Small Chromatin-Associated RNA – Bioinformatic Analysis

Sarah Diermeier and Gernot Längst