DNA REPAIR − ON THE PATHWAYS TO FIXING DNA DAMAGE AND ERRORS Edited by Francesca Storici DNA Repair − On the Pathways to Fixing DNA Damage and Errors Edited by Francesca Storici Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 InTech All chapters are Open Access articles distributed under the Creative Commons Non Commercial Share Alike Attribution 3.0 license, which permits to copy, distribute, transmit, and adapt the work in any medium, so long as the original work is properly cited. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published articles. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Alenka Urbancic Technical Editor Teodora Smiljanic Cover Designer Jan Hyrat Image Copyright suravid, 2011. Used under license from Shutterstock.com First published August, 2011 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] DNA Repair − On the Pathways to Fixing DNA Damage and Errors, Edited by Francesca Storici p. cm. ISBN 978-953-307-649-2 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface IX Chapter 1 Lagging Strand Synthesis and Genomic Stability 1 Tuan Anh Nguyen, Chul-Hwan Lee and Yeon-Soo Seo Chapter 2 Synergy Between DNA Replication and Repair Mechanisms 25 Maria Zannis-Hadjopoulos and Emmanouil Rampakakis Chapter 3 New Insight on Entangled DNA Repair Pathways: Stable Silenced Human Cells for Unraveling the DDR Jigsaw 43 Biard Denis S.F. Chapter 4 Base Excision Repair Pathways 65 Christina Emmanouil Chapter 5 Repair of Viral Genomes by Base Excision Pathways: African Swine Fever Virus as a Paradigm 79 Modesto Redrejo-Rodríguez, Javier M. Rodríguez, José Salas and María L. Salas Chapter 6 Nucleotide Excision Repair in S. cerevisiae 97 Danielle Tatum and Shisheng Li Chapter 7 Biochemical Properties of MutL, a DNA Mismatch Repair Endonuclease 123 Kenji Fukui, Atsuhiro Shimada, Hitoshi Iino, Ryoji Masui and Seiki Kuramitsu Chapter 8 The Pathways of Double-Strand Break Repair 143 Emil Mladenov and George Iliakis Chapter 9 Human CtIP and Its Homologs: Team Players in DSB Resection Games 169 Yasuhiro Tsutsui, Akihito Kawasaki and Hiroshi Iwasaki VI Contents Chapter 10 Archaeal DNA Repair Nucleases 185 Roxanne Lestini, Christophe Creze, Didier Flament, Hannu Myllykallio and Ghislaine Henneke Chapter 11 Nucleases of Metallo--Lactamase and Protein Phosphatase Families in DNA Repair 211 Francisco J Fernandez, Miguel Lopez-Estepa and M. Cristina Vega Chapter 12 Mammalian Spermatogenesis, DNA Repair, Poly(ADP-ribose) Turnover: the State of the Art 235 Maria Rosaria Faraone Mennella Chapter 13 The Ubiquitin-Proteasome System and DNA Repair 255 Christine A. Falaschetti, Emily C. Mirkin, Sumita Raha, Tatjana Paunesku and Gayle E. Woloschak Chapter 14 Virtual Screening for DNA Repair Inhibitors 287 Barakat, K. and Tuszynski, J. Chapter 15 Mitochondrial DNA Repair 313 Sarah A. Martin Chapter 16 Mitochondrial DNA Damage, Repair, Degradation and Experimental Approaches to Studying These Phenomena 339 Inna Shokolenko, Susan LeDoux, Glenn Wilson and Mikhail Alexeyev Chapter 17 DNA Repair in Embryonic Stem Cells 357 Volker Middel and Christine Blattner Preface DNA repair is a central component of DNA transactions. Every day living cells battle to offset DNA damage and errors that lead to aging and could cause cancer or other genetic diseases. DNA repair is an important mechanism of defense against the potential dangers for the integrity of genes and genomes, damage to which derives from environmental genotoxic stress, like chemicals, tobacco smoke and radiation or simply from endogenous sources. There could be mistakes in DNA synthesis or the threat from reactive oxygen species that are produced by normal cellular metabolism. The genetic information is thus always at risk to change and mutate, due to the occurrence of continuous errors and distortions. DNA can be damaged in many different ways. Defects could arise because a wrong nucleotide is introduced, or because nucleotides are modified, or because the DNA has been broken or degraded. How are defects in DNA identified, how do cells recognize the different types of damage, how is the wrong information discarded and how does repair occur? I have been in the field of DNA repair since the beginning of my postdoctoral research work and I have had the opportunity to see how much this field has grown in the last decade. Although we certainly have gained important understanding on the numerous mechanisms of DNA repair, still a lot is unknown. The area is vast, there is much more to discover. We can imagine the DNA repair system to be like a particular cosmos. What is its limit, what its potential? How is DNA repair coordinated? Is it perfect or are there flaws, can it be manipulated? When asked to edit a book on DNA repair, I thought this could be an exciting chance to further navigate into the ‘DNA repair cosmos’. This book was not intended to provide the whole picture (besides impossible task) of DNA repair. Rather, this book was conceived to be like a voyager vessel and its goals are: I) To cover aspects of DNA repair processes that target nucleotide, base or sugar modifications in DNA, starting with basic principles of DNA replication, recombination and the cell cycle to the multiplicity of DNA repair mechanisms and their biological importance, emphasizing recent major advances and future directions in this rapidly expanding field. X Preface II) To convey the fact that DNA repair is not merely a system in which a few factors detect and correct damage in DNA, but instead a complex of dynamic, intricate and interconnected mechanisms. III) Furthermore, to stimulate the readers to read more and especially to explore more into the fascinating field of DNA repair. Putting together the chapters of this book has been a great pleasure and exciting experience. The credit belongs to all the authors of the chapters, who took their effort in sharing their knowledge, expertise and ideas for this book. I wish to express my gratitude to Prof. Ana Nikolic, InTech Editorial Team Manager, who first contacted me to initiate this project under the working title DNA Repair. I would like to thank very much Ms. Alenka Urbancic, InTech Publishing Process Manager, for her constant assistance and support during all phases of preparation of this book. I am also indebted to InTech and its staff for the accomplishment of this book project. Francesca Storici School of Biology Georgia Institute of Technology Atlanta, GA USA 1 Lagging Strand Synthesis and Genomic Stability Tuan Anh Nguyen, Chul-Hwan Lee and Yeon-Soo Seo Korea Advanced Institute of Science and Technology, South Korea 1. Introduction In eukaryotic cells, DNA replication starts at many origins in each chromosome during S phase of cell cycle. Each origin is activated at different time points in S phase, which takes place once and only once per cell cycle. In yeast and most likely higher eukaryotes, the origin-recognition complex (ORC) and several other initiation factors play a pivotal role in activation and regulation of replication origins. Briefly, the ORC-bound origins are sequentially activated and deactivated along the progression of cell cycle. The prereplicative complex (pre-RC) is formed by loading the replicative helicase MCM complex onto the ORC-bound origins with the aid of Cdc6 and Cdt1. This complex is activated by S-phase cyclin dependent kinases (Cdks) when cells enter S phase. The elevated levels of Cdk activities lead to removal of some initiation proteins such as Cdc6 by proteolysis, allowing the pre-RC to be further activated for subsequent DNA synthesis. The irreversible removal of initiation factors is a major mechanism to ensure DNA to be replicated once and only once per cell cycle. The assembly of replication initiation complex and its activation are well reviewed in many literatures (Sclafani & Holzen, 2007; Remus & Diffley, 2009; Araki, 2010). Activation of origins leads to the establishment of bidirectional replication forks for the DNA synthesis of leading and lagging strands. 2. Overview of lagging strand synthesis Leading strand synthesis, once initiated, occurs in a highly processive and continuous manner by a proofreading DNA polymerase. Unlike leading strands, lagging strands are synthesized as discrete short DNA fragments, termed ‘Okazaki fragments’ which are later joined to form continuous duplex DNA. Synthesis of an Okazaki fragment begins with a primer RNA-DNA made by polymerase (Pol) -primase. The synthesis of RNA portion (~ 10 to 15 ribonucleotides) and subsequent extension of short (~20 to 30 nucleotides, nt) DNA are coupled. The recognition of a primer RNA-DNA by the Replication-Factor C (RFC) complex leads to dissociation of Pol-primase and loading of proliferating cell nuclear antigen (PCNA), resulting in recruitment of Pol to the primer-template junction, a process called ‘polymerase switching.’ Then the primer RNA-DNA is elongated by Pol . When Pol encounters a downstream Okazaki fragment, it displaces the 5’ end region of the Okazaki fragment, generating a single-stranded (ss) nucleic acid flap. The flaps formed can be efficiently processed by the combined action of Flap endonuclease 1 (Fen1) and Dna2 to 2 DNA Repair − On the Pathways to Fixing DNA Damage and Errors eventually create nicks.