Single Molecule Analysis

ISBN-13: 9781071633762 / Angielski / Twarda / 2023

Opis

This third edition volume expands on the previous editions with new discussions on the latest techniques and developments in the field. The chapters in this book are organized into four parts, and cover topics such as optical tweezers; single-molecule fluorescence tools; atomic force microscopy; magnetic tweezers; applications to virus protein shells, unfolding of proteins, nucleic acids, motor proteins, in vivo and in vitro; and protocols to establish specific surface interactions and perform force calibration. 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.

Cutting-edge and thorough, Single Molecule Analysis: Methods and Protocols, Third Edition is a valuable resource for all researchers who want to learn more about this exciting and still expanding field.

Chapters 2, 7, 8, 9, 12, 18, and 19 are available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. 

Spis treści

Preface…
Table of Contents…
Contributing Authors…

Part I Optical Tweezers

1. Introduction to Optical Tweezers: Background, System Designs, and Applications
Agata M. Malinowska, Joost van Mameren, Erwin J. G. Peterman, Gijs J. L. Wuite, and Iddo Heller

2. Quantifying ATP-Independent Nucleosome Chaperone Activity with Single Molecule Methods
Micah J. McCauley, Joha Joshi, Nicole Becker, Qi Hu, Maria Victoria Botuyan, Ioulia Rouzina, Georges Mer, L. James Maher III, and Mark C. Williams

3. Protein Tethering for Single-Molecule Force Spectroscopy
Mario J. Avellaneda, Eline J. Koers, Vanda Sunderlikova, and Sander J. Tans

4. Insect Cell-Based Expression of Cytoskeletal Motor Proteins for Single-Molecule Studies
Xinglei Liu and Arne Gennerich

5. Probing Mitotic Chromosome Mechanics Using Optical Tweezers
Tinka V.M. Clement, Constantijn van der Smagt, and Gijs J.L. Wuite

Part II Single-Molecule Fluorescence Microscopy

6. A Brief Introduction to Single-Molecule Fluorescence Methods
Siet M.J.L. van den Wildenberg, Bram Prevo, and Erwin J.G. Peterman

7. Single-Molecule Fluorescence Microscopy in Sensory Cilia of Living Caenorhabditis elegans
Elizaveta Loseva, Jaap van Krugten, Aniruddha Mitra, and Erwin J.G. Peterman

8. Lattice Light-Sheet Motor-PAINT: A Method to Map the Orientations of Microtubules in Complex Three-Dimensional Arrays
Malina K. Iwanski, Eugene A. Katrukha, and Lukas C. Kapitein

9. Fluorescence Microscopy of Nanochannel-Confined DNA
Sriram KK, Fredrik Persson, Joachim Fritzsche, Jason P. Beech, Jonas O. Tegenfeldt, and Fredrik Westerlund

10. Single-Molecule FRET X 
Mike Filius, Raman van Wee, and Chirlmin Joo

11. Single-Molecule Fluorescence Imaging of DNA Replication Stalling at Sites of Nucleoprotein Complexes
Kelsey S. Whinn, Nischal Sharma, Antoine M. van Oijen, and Harshad Ghodke

12. Measuring Transcription Dynamics of Individual Genes Inside Living Cells
Ineke Brouwer, Marit A.C. de Kort, and Tineke L. Lenstra

13. Single-Molecule FRET Resolved Protein Dynamics from Plasmid to Data in Six Steps
Benjamin Vermeer, Jannick van Ossenbruggen, and Sonja Schmid

Part III Atomic Force Microscopy

14. Atomic Force Microscopy: An Introduction
Yuzhen Feng and Wouter H. Roos

15. Atomic Force Microscopy of Viruses: Stability, Disassembly, and Genome Release
Miguel Cantero, María Jesús Rodríguez-Espinosa, Klara Strobl, Pablo Ibáñez, Alejandro Díez-Martínez, Natalia Martín-González, Manuel Jiménez-Zaragoza, Alvaro Ortega-Esteban, and Pedro José de Pablo

16. Unfolding and Refolding Proteins using Single-Molecule AFM
Marc Mora, Rafael Tapia-Rojo, and Sergi Garcia-Manyes

17. Visualizing Molecular Dynamics by High-Speed Atomic Force Microscopy
Chris van Ewijk, Sourav Maity, and Wouter H. Roos

Part IV Magnetic Tweezers and Other High-Throughput Methods

18. An Introduction to Magnetic Tweezers
David Dulin

19. Surface Functionalization, Nucleic Acid Tether Characterization, and Force Calibration for a Magnetic Tweezers Assay
Salina Quack and David Dulin

20. Correlated Single-Molecule Magnetic Tweezers and Fluorescence Measurements of DNA-Enzyme Interactions
Julene Madariaga-Marcos, Pierre Aldag, Dominik J. Kauert, and Ralf Seidel

21. Detecting DNA Loops Using Tethered Particle Motion
Jin Qian, Dylan Collette, Laura Finzi, and David Dunlap

22. Single-Cell Measurements using Acoustic Force Spectroscopy (AFS)
Kees-Karel H. Taris, Douwe Kamsma, and Gijs J.L. Wuite

23. DNA Origami-Based Single-Molecule Force Spectroscopy and Applications
Kevin Kramm, Tim Schröder, Andrés Manuel Vera, Lennart Grabenhorst, Philip Tinnefeld, and Dina Grohmann

Subject Index List…