Functional analysis of DNA and chromatin / edited by Juan C. Stockert, Jesús Espada, Alfonso Blázquez-Castro.

Contributor(s): Stockert, Juan C [editor] | Espada, Jesús [editor] | Blázquez-Castro, Alfonso [editor]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 1094.Publisher: New York : Humana Press, [2014]Copyright date: ©2014Description: 1 online resource (xv, 365 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781627037068; 1627037063; 1627037055; 9781627037051Subject(s): DNA -- Analysis -- Laboratory manuals | Chromatin -- Analysis -- Laboratory manuals | Chromosome Structures | Nucleic Acids | Nucleoproteins | Publication Formats | Chromosomes | Publication Characteristics | Proteins | Genetic Structures | Nucleic Acids, Nucleotides, and Nucleosides | Amino Acids, Peptides, and Proteins | Genetic Phenomena | Intranuclear Space | Chemicals and Drugs | Phenomena and Processes | Cell Nucleus Structures | Cell Nucleus | Intracellular Space | Cellular Structures | Cells | Anatomy | Chromatin | DNA | Laboratory Manuals | DNA -- AnalysisGenre/Form: Laboratory Manual. | Electronic books. | Laboratory manuals. Additional physical formats: Print version:: Functional analysis of DNA and chromatin.DDC classification: 572.8 LOC classification: QP624 | .F859 2014Online resources: Click here to access online
Contents:
Predictive binding geometry of ligands to DNA minor groove : isohelicity and hydrogen-bonding pattern / Juan C. Stockert -- Using microchip gel electrophoresis to probe DNA-drug binding interactions / Nan Shi and Victor M. Ugaz -- Identifying different types of chromatin using Giemsa staining / Juan C. Stockert, Alfonso Blázquez-Castro, and Richard W. Horobin -- Analysis of DNA damage and repair by comet fluorescence in situ hybridization (comet-FISH) / Michael Glei and Wiebke Schlörmann -- Alkaline nuclear dispersion assays for the determination of DNA damage at the single cell level / Piero Sestili and Carmela Fimognari -- Polarization microscopy of extended chromatin fibers / Maria Luiza S. Mello and Benedicto de Campos Vidal -- 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 -- Historical overview of bromo-substituted DNA and sister chromatid differentiation / Roberto Mezzanotte and Mariella Nieddu -- Image analysis of chromatin remodelling / Benedicto de Campos Vidal, Marina B. Felisbino, and Maria Luiza S. Mello -- FISH methods in cytogenetic studies / Miguel Pita, Juan Orellana, Paloma Martínez-Rodríguez, Ángel Martínez-Ramírez, Begoña Fernández-Calvín, and José L. Bella -- Ultrastructural and immunofluorescent methods for the study of the XY body as a biomarker / Roberta B. Sciurano and Alberto J. Solari -- Atomic force microscopy for analyzing metaphase chromosomes : comparison of AFM images with fluorescence labeling images of banding patterns / Osamu Hoshi and Tatsuo Ushiki -- Selective detection of phagocytic phase of apoptosis in fixed tissue sections / Vladimir V. Didenko -- Selective transport of cationized fluorescent topoisomerase into nuclei of live cells for DNA damage studies / Candace L. Minchew and Vladimir V. Didenko -- 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 -- Combined bidimensional electrophoresis and electron microscopy to study specific plasmid DNA replication intermediates in human cells / Cindy Follonier and Massimo Lopes -- 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 -- Methyl-combing : single-molecule analysis of DNA methylation on stretched DNA fibers / Attila Németh -- Investigating 5-hydroxymethylcytosine (5hmC) : the state of the art / Colm E. Nestor, James P. Reddington, Mikael Benson, and Richard R. Meehan -- Hydroxymethylated DNA immunoprecipitation (hmeDIP) / Colm E. Nestor and Richard R. Meehan -- Microscale thermophoresis for the assessment of nuclear protein-binding affinities / Wei Zhang, Stefan Duhr, Philipp Baaske, and Ernest Laue -- Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry / Stefan Dillinger, Ana Villar Garea, Rainer Deutzmann, and Attila Németh -- Salt-urea, sulfopropyl-sepharose, and covalent chromatography methods for histone isolation and fractionation / Pedro Rodriguez-Collazo -- Chromatin immunoprecipitation / Javier Rodríguez-Ubreva and Esteban Ballestar -- Analysis of chromatin composition of repetitive sequences : the ChIP-Chop assay / Raffaella Santoro -- Purification of specific chromatin domains from single- copy gene loci in Saccharomyces cerevisiae / Stephan Hamperl, Christopher R. Brown, Jorge Perez-Fernandez, Katharina Huber, Manuel Wittner, Virginia Babl, Ulrike Stöckl, Hinrich Boeger, Herbert Tschochner, Philipp Milkereit, and Joachim Griesenbeck -- Deep sequencing of small chromatin-associated RNA : isolation and library preparation / Sarah Daniela Diermeier, Thomas Schubert, and Gernot Längst -- Deep sequencing of small chromatin-associated RNA : bioinformatic analysis / Sarah Daniela Diermeier and Gernot Längst.
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."--Publisher's description.
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Includes bibliographical references and index.

Predictive binding geometry of ligands to DNA minor groove : isohelicity and hydrogen-bonding pattern / Juan C. Stockert -- Using microchip gel electrophoresis to probe DNA-drug binding interactions / Nan Shi and Victor M. Ugaz -- Identifying different types of chromatin using Giemsa staining / Juan C. Stockert, Alfonso Blázquez-Castro, and Richard W. Horobin -- Analysis of DNA damage and repair by comet fluorescence in situ hybridization (comet-FISH) / Michael Glei and Wiebke Schlörmann -- Alkaline nuclear dispersion assays for the determination of DNA damage at the single cell level / Piero Sestili and Carmela Fimognari -- Polarization microscopy of extended chromatin fibers / Maria Luiza S. Mello and Benedicto de Campos Vidal -- 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 -- Historical overview of bromo-substituted DNA and sister chromatid differentiation / Roberto Mezzanotte and Mariella Nieddu -- Image analysis of chromatin remodelling / Benedicto de Campos Vidal, Marina B. Felisbino, and Maria Luiza S. Mello -- FISH methods in cytogenetic studies / Miguel Pita, Juan Orellana, Paloma Martínez-Rodríguez, Ángel Martínez-Ramírez, Begoña Fernández-Calvín, and José L. Bella -- Ultrastructural and immunofluorescent methods for the study of the XY body as a biomarker / Roberta B. Sciurano and Alberto J. Solari -- Atomic force microscopy for analyzing metaphase chromosomes : comparison of AFM images with fluorescence labeling images of banding patterns / Osamu Hoshi and Tatsuo Ushiki -- Selective detection of phagocytic phase of apoptosis in fixed tissue sections / Vladimir V. Didenko -- Selective transport of cationized fluorescent topoisomerase into nuclei of live cells for DNA damage studies / Candace L. Minchew and Vladimir V. Didenko -- 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 -- Combined bidimensional electrophoresis and electron microscopy to study specific plasmid DNA replication intermediates in human cells / Cindy Follonier and Massimo Lopes -- 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 -- Methyl-combing : single-molecule analysis of DNA methylation on stretched DNA fibers / Attila Németh -- Investigating 5-hydroxymethylcytosine (5hmC) : the state of the art / Colm E. Nestor, James P. Reddington, Mikael Benson, and Richard R. Meehan -- Hydroxymethylated DNA immunoprecipitation (hmeDIP) / Colm E. Nestor and Richard R. Meehan -- Microscale thermophoresis for the assessment of nuclear protein-binding affinities / Wei Zhang, Stefan Duhr, Philipp Baaske, and Ernest Laue -- Analysis of histone posttranslational modifications from nucleolus-associated chromatin by mass spectrometry / Stefan Dillinger, Ana Villar Garea, Rainer Deutzmann, and Attila Németh -- Salt-urea, sulfopropyl-sepharose, and covalent chromatography methods for histone isolation and fractionation / Pedro Rodriguez-Collazo -- Chromatin immunoprecipitation / Javier Rodríguez-Ubreva and Esteban Ballestar -- Analysis of chromatin composition of repetitive sequences : the ChIP-Chop assay / Raffaella Santoro -- Purification of specific chromatin domains from single- copy gene loci in Saccharomyces cerevisiae / Stephan Hamperl, Christopher R. Brown, Jorge Perez-Fernandez, Katharina Huber, Manuel Wittner, Virginia Babl, Ulrike Stöckl, Hinrich Boeger, Herbert Tschochner, Philipp Milkereit, and Joachim Griesenbeck -- Deep sequencing of small chromatin-associated RNA : isolation and library preparation / Sarah Daniela Diermeier, Thomas Schubert, and Gernot Längst -- Deep sequencing of small chromatin-associated RNA : bioinformatic analysis / Sarah Daniela Diermeier and Gernot Längst.

"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."--Publisher's description.

Online resource; title from PDF title page (Springer Protocols, viewed January 30, 2014).

English.

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