Graduate of Peter the Great St. Petersburg Polytechnic University, Russia (1996 MS diploma with honors (equivalent of cum laude) in physics/biophysics) and Osaka University, Japan (2000 PhD in biological sciences), Dr. Maria Spies is an Associate Professor of Biochemistry at the University of Iowa Carver College of Medicine. Spies’ research career has been focused on deciphering the intricate choreography of the molecular machines orchestrating the central steps in the homology directed DNA repair. Her doctoral research supported by the Japanese Government (MONBUSHO) Graduate Scholarship provided the first detailed biochemical characterization of archaeal recombinase RadA. In her postdoctoral work with Dr. Steve Kowalczykowski (UC Davis) supported by the American Cancer Society, Spies reconstituted at the single-molecule level the initial steps of bacterial recombination and helped to explain how this process is regulated.Spies’ laboratory at the University of Iowa emphasizes the molecular machinery of homologous recombination, how it is integrated into DNA replication, repair and recombination (the 3Rs of genome stability), and how it is misappropriated in the molecular pathways that process stalled DNA replication events and DNA breaks through highly mutagenic, genome destabilizing mechanisms. Her goal is to understand, reconstitute and manipulate an elaborate network of DNA recombination, replication and repair, and to harness this understanding for anticancer drug discovery. The Spies lab utilizes a broad spectrum of techniques from biochemical reconstitutions of the key biochemical reactions in DNA recombination, repair and replication, to structural and single-molecule analyses of the proteins and enzymes coordinating these reactions, to combined HTS/CADD campaigns targeting human DNA repair proteins. Work in Spies Lab has been funded by the American Cancer Society (ACS), Howard Hughes Medical Institute (HHMI), and is currently supported by the National Institutes of Health (NIH). She received several prestigious awards including HHMI Early Career Scientist Award and Margaret Oakley Dayhoff Award in Biophysics. She serves on the editorial board of the Journal of Biological Chemistry, and as an academic editor of the journal Plos-ONE. She is a permanent member and a chair of the American Cancer Society “DNA mechanisms in cancer” review panel. Graduate of the St. Petersburg State University, Russia (1987 MS diploma with honors (equivalent of cum laude) in Genetics and 1993 Ph.D. in Genetics), Dr. Anna Malkova is an Associate Professor of Biology Department at the University of Iowa College of Liberal Arts and Sciences. Malkova’s research is focused on DNA repair mechanisms. She investigates the repair of double-strand DNA breaks (DSBs), the most lethal type of DNA lesions. Using a dependable and powerful model system in yeast, where a single DSB is initiated by a site-specific HO endonuclease, she successfully demonstrated that imprecise or faulty repair of DSBs leads to structural genomic variations including mutations, copy number variations (CNVs), and chromosomal rearrangements similar to those that cause genetic diseases and cancer in humans. She has a longstanding interest in break-induced replication (BIR), a DSB repair pathway that repairs so-called one-ended DNA breaks, similar to those produced at eroded telomeres and by collapsed replication forks. In her postdoctoral work with Dr. James Haber (Brandeis University), she was among the first who identified this mechanism in eukaryotes. Studies in Malkova’s laboratory provided important insights into the mechanism of BIR, which was found to be fundamentally different from the mechanism of S-phase DNA replication. In particular, it was discovered that BIR is carried out by a migrating bubble rather than by a replication fork, and leads to conservative inheritance of newly synthesized DNA. This unusual molecular mechanism explained bursts of genetic instability that were observed in association with BIR, and that were similar to those associated with cancer and other diseases rooted in genetic instability. Work in Malkova’s lab is supported by the National Institutes of Health (NIH). Anna serves as a member to the Cancer Etiology study section of NIH/NCI.

Praise for the Series: "Should be on the shelves of all libraries in the world as a whole collection." --Chemistry in Industry"The work most often consulted in the lab." --Enzymologia"The Methods in Enzymology series represents the gold-standard." --Neuroscience

• 1. Processing of DNA Double-Strand Breaks in YeastRobert Gnügge, Julyun Oh and Lorraine S. Symington2. Methods to Study DNA End Resection I: Recombinant Protein PurificationRoopesh Anand, Cosimo Pinto and Petr Cejka3. Methods to Study DNA End Resection II: Biochemical Reconstitution AssaysCosimo Pinto, Roopesh Anand and Petr Cejka4. Direct Quantitative Monitoring of Homology-Directed DNA Repair of Damaged TelomeresPriyanka Verma, Robert L. Dilley, Melina T. Gyparaki and Roger A. Greenberg5. Kinetic Analysis of the Exonuclease Activity of the Bacteriophage T4 Mre11–Rad50 ComplexTibebe A. Teklemariam, Osvaldo D. Rivera and Scott W. Nelson6. Observation and Analysis of RAD51 Nucleation Dynamics at Single-Monomer ResolutionShyamal Subramanyam, Colin D. Kinz-Thompson, Ruben L. Gonzalez and Maria Spies7. Determining the RAD51-DNA Nucleoprotein Filament Structure and Function By Cryo-Electron MicroscopyLingyun Zhao, Jingfei Xu, Weixing Zhao, Patrick Sung, and Hong-Wei Wang8. Expression, Purification, and Biochemical Evaluation of Human RAD51 ProteinShyamal Subramanyam and Maria Spies9. TIRF-Based Single-Molecule Detection of the RecA Presynaptic Filament DynamicsSung H. Kim10. The RadA Recombinase and Paralogs of the Hyperthermophilic Archaeon Sulfolobus SolfataricusMichael L. Rolfsmeier and Cynthia A. Haseltine11. Reconstituting the 4-Strand DNA Strand ExchangeOlga M. Mazina and Alexander V. Mazin12. Purification Of Saccharomyces Cerevisiae Homologous Recombination Proteins Dmc1 and Rdh54/Tid1 and a Fluorescent D-Loop AssayYuen-Ling Chan and Douglas K. Bishop13. Probing Dynamic Assembly and Disassembly of Rad51 Tuned by Srs2 Using smFRETYupeng Qiu, Hye R. Koh and Sua Myong14. The Recombination Mediator BRCA2: Architectural Plasticity of Recombination Intermediates Revealed by Single-Molecule Imaging (SFM/TIRF)Arshdeep Sidhu, Dejan Ristic, Humberto Sánchez and Claire Wyman15. Single-Molecule Dynamics and Localization of DNA Repair Proteins in CellsMaarten W. Paul, Alex N. Zelensky, Claire Wyman and Roland Kanaar16. Single-Stranded DNA Curtains for Studying the Srs2 Helicase Using Total Internal Reflection Fluorescence MicroscopyLuisina De Tullio, Kyle Kaniecki and Eric C. Greene17. Single-Molecule Analysis of Replication Protein A–DNA InteractionsFletcher E. Bain, Laura A. Fischer, Ran Chen and Marc S. Wold18. Single-Molecule Studies of ssDNA-Binding Proteins ExchangeOlivia Yang and Taekjip Ha19. Dissecting the Recombination Mediator Activity of BRCA2 Using Biochemical MethodsCatharina von Nicolai, Åsa Ehlén, Juan S. Martinez and Aura Carreira20. Approaches to Understanding the Mediator Function of Brh2 in Ustilago maydisQingwen Zhou, William K. Holloman and Milorad Kojic21. GEN1 Endonuclease: Purification and Nuclease AssaysYing Wai Chan and Stephen C. West22. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving EnzymesYijin Liu, Alasdair Freeman, Anne-Cécile Déclais, Anton Gartner and David M. J. Lilley23. Preparation and Resolution of Holliday Junction DNA Recombination IntermediatesRajvee Shah Punatar and Stephen C. West

Graduate of Peter the Great St. Petersburg Polytechnic University, Russia (1996 MS diploma with honors (equivalent of cum laude) in physics/biophysics) and Osaka University, Japan (2000 PhD in biological sciences), Dr. Maria Spies is an Associate Professor of Biochemistry at the University of Iowa Carver College of Medicine. Spies’ research career has been focused on deciphering the intricate choreography of the molecular machines orchestrating the central steps in the homology directed DNA repair. Her doctoral research supported by the Japanese Government (MONBUSHO) Graduate Scholarship provided the first detailed biochemical characterization of archaeal recombinase RadA. In her postdoctoral work with Dr. Steve Kowalczykowski (UC Davis) supported by the American Cancer Society, Spies reconstituted at the single-molecule level the initial steps of bacterial recombination and helped to explain how this process is regulated.Spies’ laboratory at the University of Iowa emphasizes the molecular machinery of homologous recombination, how it is integrated into DNA replication, repair and recombination (the 3Rs of genome stability), and how it is misappropriated in the molecular pathways that process stalled DNA replication events and DNA breaks through highly mutagenic, genome destabilizing mechanisms. Her goal is to understand, reconstitute and manipulate an elaborate network of DNA recombination, replication and repair, and to harness this understanding for anticancer drug discovery. The Spies lab utilizes a broad spectrum of techniques from biochemical reconstitutions of the key biochemical reactions in DNA recombination, repair and replication, to structural and single-molecule analyses of the proteins and enzymes coordinating these reactions, to combined HTS/CADD campaigns targeting human DNA repair proteins. Work in Spies Lab has been funded by the American Cancer Society (ACS), Howard Hughes Medical Institute (HHMI), and is currently supported by the National Institutes of Health (NIH). She received several prestigious awards including HHMI Early Career Scientist Award and Margaret Oakley Dayhoff Award in Biophysics. She serves on the editorial board of the Journal of Biological Chemistry, and as an academic editor of the journal Plos-ONE. She is a permanent member and a chair of the American Cancer Society “DNA mechanisms in cancer” review panel. Graduate of the St. Petersburg State University, Russia (1987 MS diploma with honors (equivalent of cum laude) in Genetics and 1993 Ph.D. in Genetics), Dr. Anna Malkova is an Associate Professor of Biology Department at the University of Iowa College of Liberal Arts and Sciences. Malkova’s research is focused on DNA repair mechanisms. She investigates the repair of double-strand DNA breaks (DSBs), the most lethal type of DNA lesions. Using a dependable and powerful model system in yeast, where a single DSB is initiated by a site-specific HO endonuclease, she successfully demonstrated that imprecise or faulty repair of DSBs leads to structural genomic variations including mutations, copy number variations (CNVs), and chromosomal rearrangements similar to those that cause genetic diseases and cancer in humans. She has a longstanding interest in break-induced replication (BIR), a DSB repair pathway that repairs so-called one-ended DNA breaks, similar to those produced at eroded telomeres and by collapsed replication forks. In her postdoctoral work with Dr. James Haber (Brandeis University), she was among the first who identified this mechanism in eukaryotes. Studies in Malkova’s laboratory provided important insights into the mechanism of BIR, which was found to be fundamentally different from the mechanism of S-phase DNA replication. In particular, it was discovered that BIR is carried out by a migrating bubble rather than by a replication fork, and leads to conservative inheritance of newly synthesized DNA. This unusual molecular mechanism explained bursts of genetic instability that were observed in association with BIR, and that were similar to those associated with cancer and other diseases rooted in genetic instability. Work in Malkova’s lab is supported by the National Institutes of Health (NIH). Anna serves as a member to the Cancer Etiology study section of NIH/NCI.

Praise for the Series: "Should be on the shelves of all libraries in the world as a whole collection." --Chemistry in Industry"The work most often consulted in the lab." --Enzymologia"The Methods in Enzymology series represents the gold-standard." --Neuroscience

• 1. Processing of DNA Double-Strand Breaks in YeastRobert Gnügge, Julyun Oh and Lorraine S. Symington2. Methods to Study DNA End Resection I: Recombinant Protein PurificationRoopesh Anand, Cosimo Pinto and Petr Cejka3. Methods to Study DNA End Resection II: Biochemical Reconstitution AssaysCosimo Pinto, Roopesh Anand and Petr Cejka4. Direct Quantitative Monitoring of Homology-Directed DNA Repair of Damaged TelomeresPriyanka Verma, Robert L. Dilley, Melina T. Gyparaki and Roger A. Greenberg5. Kinetic Analysis of the Exonuclease Activity of the Bacteriophage T4 Mre11–Rad50 ComplexTibebe A. Teklemariam, Osvaldo D. Rivera and Scott W. Nelson6. Observation and Analysis of RAD51 Nucleation Dynamics at Single-Monomer ResolutionShyamal Subramanyam, Colin D. Kinz-Thompson, Ruben L. Gonzalez and Maria Spies7. Determining the RAD51-DNA Nucleoprotein Filament Structure and Function By Cryo-Electron MicroscopyLingyun Zhao, Jingfei Xu, Weixing Zhao, Patrick Sung, and Hong-Wei Wang8. Expression, Purification, and Biochemical Evaluation of Human RAD51 ProteinShyamal Subramanyam and Maria Spies9. TIRF-Based Single-Molecule Detection of the RecA Presynaptic Filament DynamicsSung H. Kim10. The RadA Recombinase and Paralogs of the Hyperthermophilic Archaeon Sulfolobus SolfataricusMichael L. Rolfsmeier and Cynthia A. Haseltine11. Reconstituting the 4-Strand DNA Strand ExchangeOlga M. Mazina and Alexander V. Mazin12. Purification Of Saccharomyces Cerevisiae Homologous Recombination Proteins Dmc1 and Rdh54/Tid1 and a Fluorescent D-Loop AssayYuen-Ling Chan and Douglas K. Bishop13. Probing Dynamic Assembly and Disassembly of Rad51 Tuned by Srs2 Using smFRETYupeng Qiu, Hye R. Koh and Sua Myong14. The Recombination Mediator BRCA2: Architectural Plasticity of Recombination Intermediates Revealed by Single-Molecule Imaging (SFM/TIRF)Arshdeep Sidhu, Dejan Ristic, Humberto Sánchez and Claire Wyman15. Single-Molecule Dynamics and Localization of DNA Repair Proteins in CellsMaarten W. Paul, Alex N. Zelensky, Claire Wyman and Roland Kanaar16. Single-Stranded DNA Curtains for Studying the Srs2 Helicase Using Total Internal Reflection Fluorescence MicroscopyLuisina De Tullio, Kyle Kaniecki and Eric C. Greene17. Single-Molecule Analysis of Replication Protein A–DNA InteractionsFletcher E. Bain, Laura A. Fischer, Ran Chen and Marc S. Wold18. Single-Molecule Studies of ssDNA-Binding Proteins ExchangeOlivia Yang and Taekjip Ha19. Dissecting the Recombination Mediator Activity of BRCA2 Using Biochemical MethodsCatharina von Nicolai, Åsa Ehlén, Juan S. Martinez and Aura Carreira20. Approaches to Understanding the Mediator Function of Brh2 in Ustilago maydisQingwen Zhou, William K. Holloman and Milorad Kojic21. GEN1 Endonuclease: Purification and Nuclease AssaysYing Wai Chan and Stephen C. West22. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving EnzymesYijin Liu, Alasdair Freeman, Anne-Cécile Déclais, Anton Gartner and David M. J. Lilley23. Preparation and Resolution of Holliday Junction DNA Recombination IntermediatesRajvee Shah Punatar and Stephen C. West

Graduate of Peter the Great St. Petersburg Polytechnic University, Russia (1996 MS diploma with honors (equivalent of cum laude) in physics/biophysics) and Osaka University, Japan (2000 PhD in biological sciences), Dr. Maria Spies is an Associate Professor of Biochemistry at the University of Iowa Carver College of Medicine. Spies’ research career has been focused on deciphering the intricate choreography of the molecular machines orchestrating the central steps in the homology directed DNA repair. Her doctoral research supported by the Japanese Government (MONBUSHO) Graduate Scholarship provided the first detailed biochemical characterization of archaeal recombinase RadA. In her postdoctoral work with Dr. Steve Kowalczykowski (UC Davis) supported by the American Cancer Society, Spies reconstituted at the single-molecule level the initial steps of bacterial recombination and helped to explain how this process is regulated.Spies’ laboratory at the University of Iowa emphasizes the molecular machinery of homologous recombination, how it is integrated into DNA replication, repair and recombination (the 3Rs of genome stability), and how it is misappropriated in the molecular pathways that process stalled DNA replication events and DNA breaks through highly mutagenic, genome destabilizing mechanisms. Her goal is to understand, reconstitute and manipulate an elaborate network of DNA recombination, replication and repair, and to harness this understanding for anticancer drug discovery. The Spies lab utilizes a broad spectrum of techniques from biochemical reconstitutions of the key biochemical reactions in DNA recombination, repair and replication, to structural and single-molecule analyses of the proteins and enzymes coordinating these reactions, to combined HTS/CADD campaigns targeting human DNA repair proteins. Work in Spies Lab has been funded by the American Cancer Society (ACS), Howard Hughes Medical Institute (HHMI), and is currently supported by the National Institutes of Health (NIH). She received several prestigious awards including HHMI Early Career Scientist Award and Margaret Oakley Dayhoff Award in Biophysics. She serves on the editorial board of the Journal of Biological Chemistry, and as an academic editor of the journal Plos-ONE. She is a permanent member and a chair of the American Cancer Society “DNA mechanisms in cancer” review panel. Graduate of the St. Petersburg State University, Russia (1987 MS diploma with honors (equivalent of cum laude) in Genetics and 1993 Ph.D. in Genetics), Dr. Anna Malkova is an Associate Professor of Biology Department at the University of Iowa College of Liberal Arts and Sciences. Malkova’s research is focused on DNA repair mechanisms. She investigates the repair of double-strand DNA breaks (DSBs), the most lethal type of DNA lesions. Using a dependable and powerful model system in yeast, where a single DSB is initiated by a site-specific HO endonuclease, she successfully demonstrated that imprecise or faulty repair of DSBs leads to structural genomic variations including mutations, copy number variations (CNVs), and chromosomal rearrangements similar to those that cause genetic diseases and cancer in humans. She has a longstanding interest in break-induced replication (BIR), a DSB repair pathway that repairs so-called one-ended DNA breaks, similar to those produced at eroded telomeres and by collapsed replication forks. In her postdoctoral work with Dr. James Haber (Brandeis University), she was among the first who identified this mechanism in eukaryotes. Studies in Malkova’s laboratory provided important insights into the mechanism of BIR, which was found to be fundamentally different from the mechanism of S-phase DNA replication. In particular, it was discovered that BIR is carried out by a migrating bubble rather than by a replication fork, and leads to conservative inheritance of newly synthesized DNA. This unusual molecular mechanism explained bursts of genetic instability that were observed in association with BIR, and that were similar to those associated with cancer and other diseases rooted in genetic instability. Work in Malkova’s lab is supported by the National Institutes of Health (NIH). Anna serves as a member to the Cancer Etiology study section of NIH/NCI.

Praise for the Series: "Should be on the shelves of all libraries in the world as a whole collection." --Chemistry in Industry"The work most often consulted in the lab." --Enzymologia"The Methods in Enzymology series represents the gold-standard." --Neuroscience

• 1. Processing of DNA Double-Strand Breaks in YeastRobert Gnügge, Julyun Oh and Lorraine S. Symington2. Methods to Study DNA End Resection I: Recombinant Protein PurificationRoopesh Anand, Cosimo Pinto and Petr Cejka3. Methods to Study DNA End Resection II: Biochemical Reconstitution AssaysCosimo Pinto, Roopesh Anand and Petr Cejka4. Direct Quantitative Monitoring of Homology-Directed DNA Repair of Damaged TelomeresPriyanka Verma, Robert L. Dilley, Melina T. Gyparaki and Roger A. Greenberg5. Kinetic Analysis of the Exonuclease Activity of the Bacteriophage T4 Mre11–Rad50 ComplexTibebe A. Teklemariam, Osvaldo D. Rivera and Scott W. Nelson6. Observation and Analysis of RAD51 Nucleation Dynamics at Single-Monomer ResolutionShyamal Subramanyam, Colin D. Kinz-Thompson, Ruben L. Gonzalez and Maria Spies7. Determining the RAD51-DNA Nucleoprotein Filament Structure and Function By Cryo-Electron MicroscopyLingyun Zhao, Jingfei Xu, Weixing Zhao, Patrick Sung, and Hong-Wei Wang8. Expression, Purification, and Biochemical Evaluation of Human RAD51 ProteinShyamal Subramanyam and Maria Spies9. TIRF-Based Single-Molecule Detection of the RecA Presynaptic Filament DynamicsSung H. Kim10. The RadA Recombinase and Paralogs of the Hyperthermophilic Archaeon Sulfolobus SolfataricusMichael L. Rolfsmeier and Cynthia A. Haseltine11. Reconstituting the 4-Strand DNA Strand ExchangeOlga M. Mazina and Alexander V. Mazin12. Purification Of Saccharomyces Cerevisiae Homologous Recombination Proteins Dmc1 and Rdh54/Tid1 and a Fluorescent D-Loop AssayYuen-Ling Chan and Douglas K. Bishop13. Probing Dynamic Assembly and Disassembly of Rad51 Tuned by Srs2 Using smFRETYupeng Qiu, Hye R. Koh and Sua Myong14. The Recombination Mediator BRCA2: Architectural Plasticity of Recombination Intermediates Revealed by Single-Molecule Imaging (SFM/TIRF)Arshdeep Sidhu, Dejan Ristic, Humberto Sánchez and Claire Wyman15. Single-Molecule Dynamics and Localization of DNA Repair Proteins in CellsMaarten W. Paul, Alex N. Zelensky, Claire Wyman and Roland Kanaar16. Single-Stranded DNA Curtains for Studying the Srs2 Helicase Using Total Internal Reflection Fluorescence MicroscopyLuisina De Tullio, Kyle Kaniecki and Eric C. Greene17. Single-Molecule Analysis of Replication Protein A–DNA InteractionsFletcher E. Bain, Laura A. Fischer, Ran Chen and Marc S. Wold18. Single-Molecule Studies of ssDNA-Binding Proteins ExchangeOlivia Yang and Taekjip Ha19. Dissecting the Recombination Mediator Activity of BRCA2 Using Biochemical MethodsCatharina von Nicolai, Åsa Ehlén, Juan S. Martinez and Aura Carreira20. Approaches to Understanding the Mediator Function of Brh2 in Ustilago maydisQingwen Zhou, William K. Holloman and Milorad Kojic21. GEN1 Endonuclease: Purification and Nuclease AssaysYing Wai Chan and Stephen C. West22. Biochemical and Structural Properties of Fungal Holliday Junction-Resolving EnzymesYijin Liu, Alasdair Freeman, Anne-Cécile Déclais, Anton Gartner and David M. J. Lilley23. Preparation and Resolution of Holliday Junction DNA Recombination IntermediatesRajvee Shah Punatar and Stephen C. West