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Dmitry O. Zharkov - Mechanisms of Genome Protection and Repair

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Dmitry O. Zharkov Mechanisms of Genome Protection and Repair
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Volume 1241 Advances in Experimental Medicine and Biology Series Editors Wim - photo 1
Volume 1241
Advances in Experimental Medicine and Biology
Series Editors
Wim E. Crusio
Institut de Neurosciences Cognitives et Intgratives dAquitaine, CNRS and University of Bordeaux UMR 5287, Pessac Cedex, France
John D. Lambris
University of Pennsylvania, Philadelphia, PA, USA
Heinfried H. Radeke
Institute of Pharmacology & Toxicology, Clinic of the Goethe University Frankfurt Main, Frankfurt am Main, Germany
Nima Rezaei
Research Center for Immunodeficiencies, Childrens Medical Center, Tehran University of Medical Sciences, Tehran, Iran

Advances in Experimental Medicine and Biologyprovides a platform for scientific contributions in the main disciplines of the biomedicine and the life sciences. This series publishes thematic volumes on contemporary research in the areas of microbiology, immunology, neurosciences, biochemistry, biomedical engineering, genetics, physiology, and cancer research. Covering emerging topics and techniques in basic and clinical science, it brings together clinicians and researchers from various fields. provides a platform for scientific contributions in the main disciplines of the biomedicine and the life sciences. This series publishes thematic volumes on contemporary research in the areas of microbiology, immunology, neurosciences, biochemistry, biomedical engineering, genetics, physiology, and cancer research. Covering emerging topics and techniques in basic and clinical science, it brings together clinicians and researchers from various fields.

Advances in Experimental Medicine and Biologyhas been publishing exceptional works in the field for over 40 years, and is indexed in SCOPUS, Medline (PubMed), Journal Citation Reports/Science Edition, Science Citation Index Expanded (SciSearch, Web of Science), EMBASE, BIOSIS, Reaxys, EMBiology, the Chemical Abstracts Service (CAS), and Pathway Studio. has been publishing exceptional works in the field for over 40 years, and is indexed in SCOPUS, Medline (PubMed), Journal Citation Reports/Science Edition, Science Citation Index Expanded (SciSearch, Web of Science), EMBASE, BIOSIS, Reaxys, EMBiology, the Chemical Abstracts Service (CAS), and Pathway Studio.

2018 Impact Factor: 2.126.

More information about this series at http://www.springer.com/series/5584

Editor
Dmitry O. Zharkov
Mechanisms of Genome Protection and Repair
Editor Dmitry O Zharkov Novosibirsk State University Novosibirsk Russia - photo 2
Editor
Dmitry O. Zharkov
Novosibirsk State University, Novosibirsk, Russia
ISSN 0065-2598 e-ISSN 2214-8019
Advances in Experimental Medicine and Biology
ISBN 978-3-030-41282-1 e-ISBN 978-3-030-41283-8
https://doi.org/10.1007/978-3-030-41283-8
Springer Nature Switzerland AG 2020
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use.
The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This Springer imprint is published by the registered company Springer Nature Switzerland AG.

The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface

DNA repair and DNA damage protection is a vibrant field. The past two decades witnessed a transformation of the area from a view mostly concerned with the spontaneous and induced damage and prevention of its consequences to understanding the genomic DNA as a chemically dynamic entity, a subject of targeted and regulated damage, surveillance, and repair toward the cells own ends. It is now hard to find a biochemical process that would not be connected to DNA damage and repair in some way. The early life of DNA repair culminated in the Nobel Prize awarded in 2015 to Tomas Lindahl, Paul Modrich, and Aziz Sancar. The new one is rapidly evolving with many observations, models, and hypotheses yet to be assembled in a consistent network. This volume draws from both sources, covering a wide range of topics, from mechanistic details of DNA repair enzymes to integrated stress responses in animals and plants, in which DNA damage plays a role. As the field has grown tremendously, it is all but impossible to bring all recent significant developments under a single cover. The works collected here were deemed novel, important for translational research, or illuminating connections not often found in the literature.

I am indebted to all contributors and reviewers, whose eagerness and persistence made this book possible. I also thank Springer Nature editorial office for their excellent and timely support. Finally, I express my deepest gratitude to Arthur Grollman, a brilliant scientist and an inspiring mentor, who many years ago introduced me to the wonderful world of DNA repair.

Dmitry O. Zharkov
Novosibirsk, Russia
Abbreviations
AA

aristolochic acid

AA-I

aristolochic acid I; 8-methoxy-6-nitrophenanthro-[3,4-d]-1,3-dioxole-5-carboxylic acid

AA-II

aristolochic acid II; 6-nitrophenanthro-[3,4-d]-1,3-dioxole-5-carboxylic acid

AAN

aristolochic acid nephropathy

ACR

ATP-dependent chromatin remodelling

AEP

archaeo-eukaryotic primase

AL-DNA

aristolactam-DNA adduct

AL-I

aristolactam I

AL-I-NOH

N-hydroxyaristolactam I

AL-I-N-OSO3H

aristolactam-I-N-sulfate orN-sulfonyloxyaristolactam I

AL-II

aristolactam II

AL-II-NOH

N-hydroxyaristolactam II

AP

apurinic/apyrimidinic

aPu

2-aminopurine

BEN

Balkan endemic nephropathy

BER

base excision repair

BHQ1

Black Hole Quencher-1

5-BrU

5-bromouracil

ccRCC

clear cell renal cell carcinoma

CEEC

capillary electrophoresis with electrochemical detection

cfDNA

cell-free DNA

5-ClU

5-chlorouracil

CNT

carbon nanotube

CPD

cyclobutane pyrimidine dimer

Cpy

pyrrolocytosine

CR

control region

CRISPR

clustered regularly interspaced short palindromic repeats

crRNA

CRISPR-associated RNA

dA-AL-I

7-(deoxyadenosine-N6-yl)-aristolactam I

dA-AL-II

7-(deoxyadenosine-N6-yl)-aristolactam II

2D-DIGE

two-dimensional difference gel electrophoresis

DDR

DNA damage response

dG-AL-I

7-(deoxyguanosin-N2-yl)-aristolactam I

dG-AL-II

7-(deoxyguanosin-N2-yl)-aristolactam II

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