Contents -- Preface -- 1. History and Discovery of DNA Polymerases -- 1.1 Discovering DNA: A First Step Towards Understanding the Basis of Life -- 1.1.1 Nuclein -- 1.1.2 Nucleic Acid -- 1.1.3 Nucleic Acids Are Composed of Nucleotides -- 1.1.4 DNA Is the Genetic Material -- 1.1.5 Structure of DNA: TheWatson-Crick DNA Double Helix and Mechanism of DNA Replication -- 1.2 Imaging an Enzyme that Assembles the Nucleotides into DNA -- 1.2.1 DNA Polymerase Activity in Extracts of Escherichia coli -- 1.2.2 Escherichia coli DNA Polymerase Can Synthesize DNA with Genetic Activity: Creating Life in theTestTube -- 1.2.3 Bacteria Contain Many DNA Polymerases -- 1.2.4 How Is a New DNA Chain Started? Discontinuous DNA Synthesis and the Need for an RNA Primer -- 1.2.5 RNA Priming as a Mechanism for Initiation: DNA Primase -- 1.3 Late 1960s to Early 1970s: DNA Replication Shows Its Complexity -- 1.3.1 DNA Structure Is Much More Complex, Rich of Conformational Flexibility and thus Full of Functional Potentialities than the One Proposed by Watson and Crick -- 1.3.2 DNA Binding Proteins, DNA Helicases, DNA Topoisomerases -- 1.4 Concluding Remarks, Parts 1.1-1.3 -- 1.5 Multiple DNA Polymerases in Eukaryotic Cells: DNA Polymerases α, β and γ as the First Ones -- 1.5.1 DNA Polymerase α -- 1.5.2 DNA Polymerase β -- 1.5.3 Lack of Relationship Between Highand Low-MolecularWeight DNA Polymerases -- 1.5.4 1975: First Nomenclature System for Eukaryotic DNA Polymerases -- 1.5.5 DNA Polymerase γ -- 1.6 Early Attempts to Ascribe an in vivo Function to DNA Polymerases α, β and γ -- 1.6.1 Positive Correlation of DNA Polymerase α with Cellular DNA Replication and Development -- 1.6.2 DNA Polymerase γ Is the Mitochondrial DNA Polymerase and Replicates Mitochondrial DNA.

1.6.3 Further Evidence for a Major Involvement of DNA Polymerase α in DNA Replication and of DNA Polymerase β in DNA Repair -- 1.7 DNA Polymerases δ and ε -- 1.8 1985: Polymerase Chain Reaction (PCR), a Concept with Tremendous Practical Applications -- 1.9 Yeast DNA Polymerases -- 1.9.1 Revised Nomenclature for Eukaryotic DNA Polymerases -- 1.10 Plant Cell DNA Polymerases -- 1.11 Virus-Induced DNA Polymerases -- 1.11.1 Herpes Virus DNA Polymerase -- 1.11.2 Vaccinia Virus DNA Polymerase -- 1.11.3 DNA Polymerase Activity in Hepatitis B Particle -- 1.11.4 Retroviruses Reverse Transcriptase -- 1.12 1999-2000: Nucleotide Sequence Analysis of Eukaryotic Organisms Allowed the Identification of Many Novel Specialized DNA Polymerases -- 1.12.1 DNA Polymerase ζ, the Lesion Extender -- 1.12.2 DNA Polymerases λ and µ, Two Family X DNA Polymerases -- 1.12.3 The ComplexY Family of DNA Polymerases -- 1.12.4 Present Nomenclature for Eukaryotic DNA Polymerases -- 1.13 Concluding Remarks, Parts 1.5-1.12 -- References -- 2. DNA Polymerases in the Three Kingdoms of Life: Bacteria, Archaea and Eukaryotes -- 2.1 Synthesis and Maintenance of DNA in Nature Need DNA Polymerases -- 2.2 The DNA Polymerase Reaction -- 2.3 The Universal Structure of a DNA Polymerase Resembles a Human Right Hand -- 2.4 The Seven DNA Polymerase Families and Their Functions: An Overview -- 2.5 DNA Polymerase Holoenzymes -- 2.6 DNA Polymerases, Ring-Like Clamps and Clamp Loaders -- 2.7 DNA Polymerases, Alternative Clamps and Clamp Loaders -- 2.8 Replicative DNA Polymerases Interacting with Other Proteins -- 2.9 DNA Polymerases and the Single-Stranded DNA Binding Protein Replication Protein A -- 2.10 Chapter Summary -- References -- 3. Structural and Functional Aspects of the Prokaryotic and Archaea DNA Polymerase Families -- 3.1 Escherichia coli -- 3.1.1 Family A: DNA Polymerase I.

3.1.2 Family B: DNA Polymerase II -- 3.1.3 Family C: DNA Polymerase III Holoenzyme -- 3.1.4 FamilyY: DNA Polymerases IV and V -- 3.2 Bacillus subtilis -- 3.2.1 Family A: DNA Polymerase I -- 3.2.2 Family C: DNA Polymerase C and DnaE -- 3.2.3 Family X: DNA Polymerase X -- 3.2.4 FamilyY: DNA Polymerases Y1 and Y2 -- 3.3 Other Bacteria -- 3.3.1 Mycobacteria -- 3.3.2 Deinococcus radiodurans -- 3.4 Archaea -- 3.4.1 Family B: DNA Polymerase B -- 3.4.2 Family D: DNA Polymerase D -- 3.4.3 FamilyY: DNA Polymerases Dbh and Dpo4 -- 3.5 Chapter Summary -- References -- 4. Structural and Functional Aspects of the Eukaryotic DNA Polymerase Families -- 4.1 The High Number of Specialized Pathways in Eukaryotic Cells Requires a Plethora of Specialized DNA Synthesizing Enzymes -- 4.2 Eukaryotic DNA Polymerase Structure: The "Right Hand" of the Cell -- 4.2.1 Common Features -- 4.2.2 Specific Features of the Different Families -- 4.3 Eukaryotic DNA Polymerases Accessory Subunits -- 4.4 Eukaryotic DNA Polymerase Fidelity: Structural and Functional Aspects -- 4.5 Biochemical and Functional Properties of the Different Eukaryotic DNA Polymerases -- 4.5.1 Family A DNA Polymerases -- 4.5.2 Family B DNA Polymerases -- 4.5.3 Family X DNA Polymerases -- 4.5.4 FamilyY DNA Polymerases -- 4.6 Interaction with Auxiliary Factors -- 4.7 Eukaryotic DNA Polymerases Are Tightly Regulated in the Cell Cycle -- 4.8 Chapter Summary -- References -- 5. Global Functions of DNA Polymerases -- 5.1 Fifteen DNA Polymerases: Share ofWorkload and Redundancies -- 5.2 DNA Replication in Living Organisms Requires Three DNA Polymerase Molecules at the Replication Fork -- 5.2.1 Prokaryotes -- 5.2.1.1 Bacteriophage T7: The simplest but best known replisome -- 5.2.1.2 The Escherichia coli replisome -- 5.2.2 Eukaryotes -- 5.2.3 Proofreader versus Non-proofreader DNA Polymerases.

5.3 Different DNA Repair Pathways Have Their Own DNA Polymerases, But Can also Borrow Them from the Replication Machinery -- 5.4 Translesion DNA Synthesis in Eukaryotes Generally Requires Two DNA Polymerases: An Inserter and an Extender -- 5.5 Expression of DNA Polymerases -- 5.6 DNA Polymerases Switch between Different DNA Transactions -- 5.6.1 Prokaryotes -- 5.6.2 Eukaryotes -- 5.6.2.1 Posttranslational modifications of PCNA -- 5.6.2.2 DNA pol switches due to PCNA ubiquitination -- 5.6.2.3 Other ways to regulate DNA polymerases -- 5.7 Functions of DNA Polymerases in Checkpoint Control -- 5.8 Chapter Summary -- References -- 6. Viral DNA Polymerases -- 6.1 Bacteriophage T4 DNA Polymerase -- 6.2 Bacteriophage T7 DNA Polymerase -- 6.3 HSV-1 DNA Polymerase -- 6.4 Protein Primed DNA Replication: Adenoviruses and Bacteriophage φ29 -- 6.4.1 Adenovirus DNA Polymerase -- 6.4.2 Bacteriophage φ29 DNA Polymerase -- 6.5 African Swine Virus DNA Polymerase -- 6.6 RNA-Dependent DNA Synthesis: Reverse Transcriptases -- 6.6.1 HIV-1 Reverse Transcriptase -- 6.6.1.1 The retro-transcription reaction -- 6.6.1.2 Structural features of HIV-1 reverse transcriptase -- 6.6.1.3 Enzymatic features of HIV-1 reverse transcriptase -- 6.6.1.4 The RNase H activity of HIV-1 reverse transcriptase -- 6.6.2 Other Retroviral Reverse Transcriptases -- 6.6.2.1 HIV-2 reverse transcriptase -- 6.6.2.2 Murine Leukemia Virus (MLV) reverse transcriptase -- 6.6.2.3 Equine Infectious Anemia Virus (EIAV) reverse transcriptase -- 6.6.2.4 Feline Immunodeficiency Virus (FIV) reverse transcriptase -- 6.6.2.5 Mouse Mammary Tumor Virus (MMTV) reverse transcriptase -- 6.6.3 Reverse Transcriptase Activity of Mobile Genetic Elements: The Retrotransposons -- 6.6.3.1 Saccharomyces cerevisiae Ty reverse transcriptase -- 6.6.3.2 Schizosaccharomyces pombe Tf1 reverse transcriptase.

6.6.3.3 Bombyx mori R2 reverse transcriptase -- 6.6.4 Hepadnavirus Reverse Transcriptase -- 6.7 Chapter Summary -- References -- 7. Synthetic Evolution of DNA Polymerases with Novel Properties -- 7.1 Why Design Enzymes with Novel Properties? -- 7.2 DNA Polymerases Have a Tight Active Site to Which the Substrates Fit -- 7.3 Methods to Evolve DNA Polymerases with Novel Properties -- 7.3.1 Detection and Characterization of DNA Polymerases and Mutants Thereof by Functional Complementation in Escherichia coli -- 7.3.2 DNA Polymerase Evolution by Random Point Mutagenesis -- 7.3.3 DNA Polymerase Evolution by Compartmentalized Self-Replication (CSR) -- 7.3.4 DNA Polymerase Evolution by Phage Display -- 7.3.5 DNA Polymerase Evolution by Oligonucleotide Addressed Enzyme Assay (OAEA) -- 7.4 Applications of DNA Polymerases with Novel Properties -- 7.5 DNA Polymerases with Novel Properties -- 7.5.1 Increased Fidelity -- 7.5.2 Decreased Fidelity -- 7.5.3 Amplification of Damaged and Ancient DNA -- 7.5.4 A DNA Polymerase Becomes an RNA Polymerase -- 7.5.5 Evolving the dNTP Substrates and Expansion of the Genetic Code -- 7.6 Chapter Summary -- References -- 8. DNA Polymerases and Diseases -- 8.1 Introduction -- 8.2 DNA Polymerases and Genetic Stability -- 8.3 DNA Polymerases and Resistance to Chemotherapy -- 8.4 DNA Polymerase γ and Human Diseases -- 8.5 Chapter Summary -- References -- 9. DNA Polymerases and Chemotherapy -- 9.1 DNA Polymerases Are Important Chemotherapeutic Targets -- 9.2 Strategies and Problems for the Design of Inhibitors of DNA Polymerases -- 9.2.1 Substrate Analogs -- 9.2.2 Non-substrate Analogs -- 9.2.3 Novel in silico Technologies for Designing Inhibitors of DNA Polymerases -- 9.3 Inhibitors of Herpesvirus DNA Replication -- 9.3.1 Anti-Herpetic Nucleoside Analogs Require Activation by the Viral Thymidine Kinase (TK).

9.3.2 Nucleoside Analogs Modified in the Base Ring.