DNA repair enzymes : structure, biophysics, and mechanism /

Detalles Bibliográficos
Clasificación:Libro Electrónico
Otros Autores: Eichman, Brandt F. (Editor )
Formato: Electrónico eBook
Idioma:Inglés
Publicado: Cambridge, MA : Academic Press is an imprint of Elsevier, 2017.
Edición:First edition.
Colección:Methods in enzymology ; v. 592.
Temas:
DNA ligases.
Cytology.
Molecular biology.
DNA Ligases > ultrastructure
Molecular Biology
Cell Biology
Cytology
ADN-ligases.
Cytologie.
Biologie mol�eculaire.
molecular biology.
SCIENCE > Life Sciences > Biochemistry.
DNA ligases
Molecular biology
Internet Resources.
Charts.
Acceso en línea:Texto completo
Texto completo
Tabla de Contenidos:
  • 1. MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes / Jill O. Fuss
  • 1. Introduction
  • 2. Entry Cloning Into MacroBac Series 11 or 438 by LIC
  • 3. Building Complexes by Restriction and Ligation: MacroBac Series 11
  • 4. Building Complexes by LIC: MacroBac Series 438
  • 5. Bacmid Preparation and Virus Production
  • 6. Protein Expression and Viral Stock Maintenance
  • 7. Trouble Shooting
  • 8. Future Considerations
  • Acknowledgments
  • References
  • 2. Production and Assay of Recombinant Multisubunit Chromatin Remodeling Complexes / Dale B. Wigley
  • 1. Introduction
  • 2. Cloning
  • 3. Case Studies
  • 4. Nucleosome Sliding and Histone Exchange Kinetic Assays
  • 5. Nucleosome Sliding by Recombinant hINO80 Chromatin Remodeling Complex
  • 6. Histone Exchange by Recombinant y SWR1 Chromatin Remodeling Complex
  • References
  • 3. Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR / Walter J. Chazin
  • 1. Introduction
  • 2. Small-Angle X-Ray Scattering
  • 3. Nuclear Magnetic Resonance
  • 4. Summary and Conclusion
  • Using SAX and NMR to Characterize Architectural Remodeling
  • References
  • 4. Use of Single-Cysteine Variants for Trapping Transient States in DNA Mismatch Repair / Titia K. Sixma
  • 1. Introduction
  • 2. Generation of Defined Cysteine Variants
  • 3. Cross-linking of Defined Cysteine Variants
  • 4. Use of Single-Cysteine Variants to Study Conformational Changes in DNA Mismatch Repair
  • 5. Concluding Remarks
  • Acknowledgments
  • References
  • 5. Expression and Structural Analyses of Human DNA Polymerase [MARC+6B] (POLQ) / Sylvie Doublie
  • 1. Introduction
  • 2. Purification and Structure Determination of Human Pol [MARC+6B]
  • 3. Crystallization and Structure Determination of Human Pol [MARC+6B]
  • 4. Conclusions
  • Acknowledgments
  • References
  • 6. Structural Studies of RNases H2 as an Example of Crystal Structure Determination of Protein-Nucleic Acid Complexes / Marcin Nowotny
  • 1. Introduction
  • 2. Purification of RNases H2
  • 3. Biochemical Assays for RNases H2
  • 4. General Considerations in the Crystallization of Protein-Nucleic Acid Complexes
  • 5. Crystallization and Structure Determination of RNases H2
  • 6. Concluding Remarks
  • Acknowledgment
  • References
  • 7. DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage / Bancinyane L. Sibanda
  • 1. Introduction
  • 2. Defining the Structure of DNA-PKcs
  • 3. Exploiting Multiple Se-Met Substitutions
  • 4. Using Se-Met Sites to Check Sequence Registration
  • 5. DNA-PKcs as a Stage for the Assembly of the Actors in NHEJ
  • Acknowledgments
  • References
  • 8. Single-Particle Electron Microscopy Analysis of DNA Repair Complexes / Xiaodong Zhang
  • 1. Introduction
  • 2. Sample Preparation
  • 3. Grid Preparation
  • 4. Data Collection
  • 5. Data Processing
  • Acknowledgments
  • References
  • 9. Using Atomic Force Microscopy to Characterize the Conformational Properties of Proteins and Protein-DNA Complexes That Carry Out DNA Repair / Dorothy A. Erie
  • 1. Introduction
  • 2. Methods to Study DNA Repair Complexes With AFM
  • 3. Image Analysis
  • 4. DREEM Imaging
  • 5.Complementary Techniques
  • 6. Conclusions
  • Acknowledgments
  • References
  • 10. Single-Molecule Methods for Nucleotide Excision Repair: Building a System to Watch Repair in Real Time / Bennett Van Houten
  • 1. Introduction
  • 2. Preparation of Defined Lesion Substrates for AFM and DNA Tightrope Assay
  • 3. Atomic Force Microscopy
  • 4. Single-Molecule DNA Tightrope Assay
  • 5. Conclusions
  • Acknowledgments
  • References
  • 11. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination / Ilya J. Finkelstein
  • 1. Introduction
  • 2. Methods
  • 3. Applications
  • 4. Notes
  • Acknowledgments
  • References
  • 12. Detection of Reaction Intermediates in Mg2+-Dependent DNA Synthesis and RNA Degradation by Time-Resolved X-Ray Crystallography / Wei Yang
  • 1. Introduction
  • 2. DNA Polymerase [MARC+6A]
  • 3. Ribonuclease H1
  • 4. Endonuclease V
  • 5.X-Ray Data Processing
  • 6. Applications and Future Prospects
  • Acknowledgments
  • References
  • 13. Analyzing the Catalytic Activities and Interactions of Eukaryotic Translesion Synthesis Polymerases / M. Todd Washington
  • 1. Introduction
  • 2. Purification and Structures of Nonclassical Polymerases
  • 3. Catalytic Activities of Nonclassical Polymerases
  • 4. Interactions of Nonclassical Polymerases
  • 5. Conclusions
  • Acknowledgments
  • References
  • 14. Kinetic Methods for Studying DNA Glycosylases Functioning in Base Excision Repair / Alexander C. Drohat
  • 1. Introduction
  • 2. Kinetic Methods to Study Catalysis by DNA Glycosylases
  • 3. Analytical Methods for Monitoring DNA Glycosylase Activity
  • 4. Determining Rate Constants From Kinetics Experiments
  • Acknowledgment
  • References
  • 15. Transient Kinetic Methods for Mechanistic Characterization of DNA Binding and Nucleotide Flipping / Patrick J. O'Brien
  • 1. Introduction
  • 2. General Considerations for Monitoring Binding
  • 3. Association Kinetics
  • 4.Comparison of Binding and Flipping Mechanisms for AAG and AlkA
  • 5. Use of Berkeley Madonna for Evaluating Kinetic Models
  • 6. Useful Equations for Kinetic Analysis
  • Acknowledgments
  • References
  • 16. What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses / John A. Tainer
  • 1. Introduction
  • 2. Metabolic Signaling: NAD and DDR by PARP, PARG, and AIF
  • 3. DNA Double-Strand Break Responses
  • 4. Taking Structural Mechanisms Into Cells by Advanced Imaging
  • 5. What's Ahead
  • Acknowledgments
  • References.

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