Single Stranded DNA Binding Proteins

ISBN-13: 9781071612927 / Angielski / Miękka / 2022

Opis

This volume provides a comprehensive set of protocols that can be used by any research lab to investigate diverse functional and structural properties of Single Stranded DNA Binding Proteins (SSBs) from eubacterial, archaeal, eukaryotic, mitochondrial and viral systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Single Stranded DNA Binding Proteins aims to be a useful practical guide to researchers to help further their study in this field. 

Spis treści

1. The Essential, Ubiquitous Single-Stranded DNA-binding Proteins

Marcos T. Oliveira and Grzegorz L. Ciesielski

 

2. Single-stranded DNA Binding Proteins in the Archaea

Najwa Taib, Simonetta Gribaldo, and Stuart A. MacNeill

 

3. Single-molecule Fluorescence Methods to Study Protein Exchange Kinetics in Supramolecular Complexes

Richard R. Spinks, Lisanne M. Spenkelink, and Antoine M. van Oijen

 

4. Comparing SSB-PriA Functional and Physical Interactions in Gram-positive and -Negative Bacteria

Yen-Hua Huang and Cheng-Yang Huang

 

5. In vivo binding of Single-stranded DNA-binding Protein to Stalled Replication Fork Helicases

Cong Yu and Piero R. Bianco

 

6. Magnetic Tweezers-based Single Molecule Assays to Study Interaction of E. coli SSB with DNA and RecQ Helicase

Debjani Bagchi, Weiting Zhang, Samar Hodeib, Bertrand Ducos, Vincent Croquette, and Maria Manosas

 

7. High-throughput Screening to Identify Inhibitors of SSB-Protein Interactions

Andrew F. Voter

 

8. Single-Molecule Tethered Particle Motion Studies on the DNA Recombinase Filament Assembly and Disassembly

Chih-Hao Lu, Wei-Hsuan Lan, and Hung-Wen Li

 

9. Generation of Fluorescent Versions of Saccharomyces cerevisiae RPA to Study the Conformational Dynamics of its ssDNA-binding Domains

Sahiti Kuppa, Nilisha Pokhrel, Elliot Corless, Sofia Origanti, and Edwin Antony

 

10. RPA-1 from Leishmania sp.: Recombinant Protein Expression and Purification, Molecular Modeling and Molecular Dynamics Simulations Protocols

Carlos A. H. Fernandes, Edna G. O. Morea, and Maria Isabel. N. Cano

 

11. Single-stranded DNA Curtains for Single-molecule Visualization of Rad51-ssDNA Filament Dynamics

Upasana Roy and Eric C. Greene

 

12. Following Trypanosoma cruzi RPA-DNA Interaction Using Fluorescent in Situ Hybridization Coupled with Immunofluorescence (FISH/IF)

Raphael S. Pavani and Maria Carolina Elias

 

13. Quantifying the affinity of Trypanosoma cruzi RPA-1 to the Single-stranded DNA Overhang of the Telomere using Surface Plasmon Resonance

Marcela de Oliveira Vitarelli and Maria Carolina Elias

 

14. Expression, Purification, and Solution-State NMR Analysis of the Two Human Single-stranded DNA Binding Proteins hSSB1 (NABP2/OBFC2B) and hSSB2 (NAPB1/OBFC2A)

Serene El-Kamand, Mar-Dean Du Plessis, Teegan Lawson, Liza Cubeddu, and Roland Gamsjaeger

 

15. Atomic Force Microscopy Reveals that the Drosophila Telomere-Capping Protein Verrocchio is a Single-stranded DNA Binding Protein

Alessandro Cicconi, Emanuela Micheli, Grazia Daniela Raffa, and Stefano Cacchione

 

16. Analysis of Mitochondrial SSB-DNA Complexes and their Effects on DNA Polymerase γ Activity by Electron Microscopy and Enzymatic Assays

Oya Bermek and Grzegorz L. Ciesielski

 

17. Optical Tweezers to Investigate the Structure and Energetics of Single-Stranded DNA-binding Protein-DNA Complexes

José A. Morin, Fernando Cerrón, Francisco J. Cao-García, and Borja Ibarra

 

18. Measurements of Real-time Replication Kinetics of DNA Polymerases on ssDNA Templates Coated with Single-stranded DNA-binding Proteins

Fernando Cerrón and Borja Ibarra

 

19. Selective Suppression of Endogenous Gene Expression Using RNAi in Drosophila Schneider S2 cells

Yuichi Matsushima

20. Stimulation of Variant forms of the Mitochondrial DNA Helicase Twinkle by the Mitochondrial Single-stranded DNA-binding Protein

Ana P. C. Rodrigues and Marcos T. Oliveira

 

21. Measuring the Complex Effects of the Single-Stranded DNA-Binding Protein gp2.5 on Primer Synthesis and Extension by the Bacteriophage T7 Replisome

Alfredo J. Hernandez

 

22. Strand Displacement and Unwinding Assays to Study the Concerted Action of the DNA Polymerase and SSB during Phi29 TP-DNA rReplication

Alicia del Prado and Margarita Salas

 

23. Structural Characterization of a Single-stranded DNA-binding Protein: A Case Study of the ORF6 protein from Bacteriophage Enc34

Elina Cernooka, Janis Rumnieks, and Andris Kazaks