The DNA Replication-Repair Interface

The DNA Replication-Repair Interface

1st Edition - November 12, 2021
This is the Latest Edition
  • Editor: Brandt Eichman
  • eBook ISBN: 9780323907347
  • Hardcover ISBN: 9780323907330

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Description

Replication-Coupled Repair, Volume 661 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics, including  the Repair of replication-born DNA breaks by sister chromatid recombination, High resolution and high throughput DNA cyclization measurements to interrogate DNA bendability, A programmable detection method for genomic signatures: from disease diagnosis to genome editing, Characterization of the telomerase modulating activities of yeast DNA helicases, Eukaryotic DNA replication with purified budding yeast proteins, Single molecule studies of yeast Rad51 paralogs, Light activation and deactivation of Cas9 for DNA repair studies, and more. Other chapters explore MIDAS: Direct sequencing to map mitotic DNA synthesis and common fragile sites at high precision, Studying the DNA damage response in embryonic systems, GLASS-ChIP to map Mre11 cleavage sites in the human genome, New chemical biology approaches to trap reaction intermediates in living cells, Single-molecule imaging approaches for monitoring replication fork conflicts at genomic DNA G4 structures and R-loops in human cells, Monitoring the replication of structured DNA through heritable epigenetic change, Visualizing replication fork encounters with DNA interstrand crosslinks, and much more.

Key Features

  • Provides the authority and expertise of leading contributors from an international board of authors
  • Presents the latest release in Methods in Enzymology series
  • Includes the latest information on replication-coupled repair

Readership

Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists

Table of Contents

  • Preface

    Brandt F. Eichman

    1. Eukaryotic DNA replication with purified budding yeast proteins

    John Diffley

    2. Monitoring the replication of structured DNA through heritable epigenetic change

    Julian Sale and Guillaume Guilbaud

    3. Visualizing replication fork encounters with DNA interstrand crosslinks

    Michael Seidman

    4. Single-molecule imaging of replication fork conflicts at genomic DNA G4 structures in human cells

    Eli Rothenberg, Dipika Gupta and Wei Ting C. Lee

    5. Studying the DNA damage response in embryonic systems

    Domenico Maiorano, Elena Lo Furno, Bénédicte Recolin, Siem van der Laan and Antoine Aze

    6. Analysis of repair of replication-born double-strand breaks by sister chromatid recombination in yeast

    Andrés Aguilera

    7. Determining the kinetics of break-induced replication (BIR) by the assay for monitoring BIR elongation rate (AMBER)

    James E. Haber

    8. Genomic mapping of DNA reaction intermediates in living cells with engineered DNA structure-trap proteins

    Susan Rosenberg, Jingjing Liu and Qian Mei

    9. A mapping platform for mitotic crossover by single-cell multi-omics

    Yi Yin

    10. Characterization of DNA-PK-bound end fragments using GLASS-ChIP

    Tanya Paull

    11. Light activation and deactivation of Cas9 for DNA repair studies

    Taekjip Ha and Roger Zou

    12. A Detection method for the capture of genomic signatures: from disease diagnosis to genome editing

    Pierre Billon, Orléna Benamozig and Lou Baudrier

    13. A method to sequence genomic sites of mitotic DNA synthesis in mammalian cells

    Thanos Halazonetis, Jonathan Mailler and Laura Padayachy

    14. Loop-seq: a high-throughput technique to measure the mesoscale mechanical properties of DNA

    Aakash Basu

    15. Characterization of the telomerase modulating activities of yeast DNA helicases

    Matthew Bochman

    16. Single-molecule studies of yeast Rad51 paralogs

    Eric Greene and Upasana Roy

    17. Synthesis and polymerase bypass studies of DNA-peptide and DNA-protein conjugates

    Natalia Tretyakova and Suresh S. Pujari

    18. Chemistry and structural screen integrated efficiently for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2

    John Tainer, Davide Moiani, Susan Tsutakawa, Youngchang Kim, Todd Link, Chris Brosey, Panagiotis Katsonis, Olivier Lichtarge, Andrzej Joachimiak, Zhijun Ma, In-Kwon Kim, Zamal Ahmed and Darin E. Jones

Product details

  • No. of pages: 452
  • Language: English
  • Copyright: © Academic Press 2021
  • Published: November 12, 2021
  • Imprint: Academic Press
  • eBook ISBN: 9780323907347
  • Hardcover ISBN: 9780323907330
  • About the Serial Volume Editor

    Brandt Eichman

    Brandt Eichman
    Dr. Eichman is a Professor of Biological Sciences and Biochemistry at Vanderbilt University, where his laboratory investigates the structural mechanisms of protein machines involved in maintenance of genome integrity. Professor Eichman was initially trained as a synthetic organic chemist at the University of Mississippi (B.S., Chemistry, 1993). He received his Ph.D. in Biochemistry and Biophysics in 2000 from Oregon State University, where he used X-ray crystallography to study the effects of crosslinking agents on DNA structure and determined the landmark structure of the Holliday junction, the four-stranded DNA intermediate formed during genetic recombination. As an NIH postdoctoral fellow from 2000-2004 with Tom Ellenberger at Harvard Medical School, Eichman studied the structural enzymology of DNA repair and replication proteins. Current projects in the Eichman lab focus on base excision repair of DNA alkylation damage and restart of stalled replication forks during the DNA damage response. Dr. Eichman holds the 2009 Young Investigator Award from the Sigma Xi Scientific Research Society, the Vanderbilt Chancellor’s Award for Research, two Vanderbilt-Ingram Cancer Center Impact Awards, and in 2013 became a member of the Faculty of 1000. Eichman teaches introductory and advanced undergraduate biochemistry and serves as the co-Director of the Vanderbilt Undergraduate Program in Biochemistry and Chemical Biology.

    Affiliations and Expertise

    Department of Biological Sciences, Vanderbilt University, Nashville, USA