Nanoscale Imaging: Methods and Protocols

ISBN-13: 9781493985906 / Angielski / Twarda / 2018 / 600 str.

Yuri L. Lyubchenko

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Imaging and Probing of Biomolecules

1. High Resolution Atomic Force Microscopy Imaging of Nucleic Acids

Pablo Ares, Julio Gomez-Herrero, and Fernando Moreno-Herrero

2. Two Ligand Binding Sites in Serotonin Transporter Revealed by Nanopharmacological Force Sensing

Rong Zhu, Hermann J. Gruber, and Peter Hinterdorfer

3. AFM-Based Single-Molecule Force-Spectroscopy of Proteins

Zackary N. Scholl and Piotr E. Marszalek

4. High Resolution AFM-Based Force Spectroscopy

Krishna P. Sigdel, Anna E. Pittman, Tina R. Matin, and Gavin M. King

5. Polymer Nanoarray Approach for the Characterization of Biomolecular Interactions

Sibaprasad Maity, Ekaterina Viazovkina, Alexander Gall, and Yuri L. Lyubchenko

6. Measuring Single-Molecule Twist and Torque in Multiplexed Magnetic Tweezers

Franziska Kriegel, Willem Vanderlinden, Thomas Nicolaus, Angelika Kardinal, and Jan Lipfert

7. AFM-Based Characterization of Electrical Properties of Materials

John Alexander, Sergey Belikov, and Sergei Magonov

8. Supported Lipid Bilayers for Atomic Force Microscopy Studies

Zhengjian Lv, Siddhartha Banerjee, Karen Zagorski, and Yuri L. Lyubchenko

9. Quantifying Small Molecule Binding Interactions with DNA Nanostructures

Xuye Lang, Yingning Gao, and Ian Wheeldon

Part II High-Speed AFM of Biomolecules

10. Optimum Substrates for Imaging Biological Molecules with High-Speed Atomic Force Microscopy

Takayuki Uchihashi, Hiroki Watanabe, and Noriyuki Kodera

11. High Resolution and High-Speed Atomic Force Microscope Imaging

Francesca Zuttion, Lorena Redondo-Morata, Arin Marchesi, and Ignacio Casuso

12. High-Speed Atomic Force Microscopy of Individual Amyloidogenic Protein Assemblies

Takahiro Watanabe-Nakayama and Kenjiro Ono

13. Direct Observation of Dynamic Movement of DNA Molecules in DNA Origami Imaged using High-Speed AFM

Masayuki Endo and Hiroshi Sugiyama

14. Assembly of Centromere Chromatin for Characterization By High-Speed Time-Lapse Atomic Force Microscopy

Micah P. Stumme-Diers, Siddhartha Banerjee, Zhiqiang Sun, and Yuri L. Lyubchenko

15. High-Speed Force Spectroscopy for Single Protein Unfolding

Fidan Sumbul, Arin Marchesi, Hirohide Takahashi, Simon Scheuring, and Felix Rico

Part III Imaging and Probing of Biomolecular Complexes

16. Probing RNA-Protein Interactions with Single-Molecule Pull-Down Assays

Mohamed Fareh and Chirlmin Joo

17. Preparing Frozen-Hydrated Protein-Nucleic Acid Assemblies for High-Resolution Cryo-EM Imaging

Panchali Goswami, Julia Locke, and Alessandro Costa

18. Probing Chromatin Structure with Magnetic Tweezers

Artur Kaczmarczyk, Thomas B. Brouwer, Chi Pham, Nynke H. Dekker, and John van Noort

19. Single Molecule and Ensemble Methods to Probe Initial Stages of RNP Granule Assembly

Jaya Sarkar and Sua Myong

20. Correlative Atomic Force and Single Molecule Fluorescence Microscopy of Nucleoprotein Complexes

Herlinde De Keersmaecker, Wout Frederickx, Yasuhiko Fujita; Steven De Feyter, Hiroshi Uji-i, Susana Rocha, and Willem Vanderlinden

Part IV Imaging and Probing of Cells and Tissues and Embryos

21. Sensing the Ultrastructure of Bacterial Surfaces and their Molecular Binding Forces using AFM

Yoo Jin Oh and Peter Hinterdorfer

22. Nanoscale Visualization of Bacterial Microcompartments using Atomic Force Microscopy 

Jorge Rodriguez-Ramos, Matthew Faulkner, and Lu-Ning Liu

23. Time-Resolved Imaging of Bacterial Surfaces using Atomic Force Microscopy

Haig Alexander Eskandarian, Adrian Pascal Nievergelt, and Georg Ernest Fantner 

24. Probing Bacterial Adhesion at the Single-Molecule and Single-Cell Levels by AFM-Based Force Spectroscopy

Sofiane El-Kirat-Chatel and Audrey Beaussart

25. Fluorescence Correlation Spectroscopy on Genomic DNA in Living Cells

Cameron Hodges and Jens-Christian Meiners

26. Three-Dimensional Tracking of Quantum Dot-Conjugated Molecules in Living Cells

Lucia Gardini, Martino Calamai, Hiroyasu Hatakeyama, Makoto Kanzaki, Marco Capitanio, and Francesco Saverio Pavone

27. AFM Indentation Analysis of Cells to Study Cell Mechanics and Pericellular Coat

Igor Sokolov and Maxim E. Dokukin

28. Imaging of Soft and Biological Samples using AFM Ringing Mode 

Igor Sokolov and Maxim E. Dokukin

29. Probing Single Virus Binding Sites on Living Mammalian Cells using AFM 

Martin Delguste, Melanie Koehler, and David Alsteens

30. Applications of Atomic Force Microscopy for Adhesion Force Measurements in Mechanotransduction

Andreea Trache, Xie Leike, Huang Huang, Vladislav V. Glinsky, and Gerald A. Meininger

31. Methods for Atomic Force Microscopy of Biological and Living Specimens

Simone Dinarelli, Marco Girasole, and Giovanni Longo

32. Single Molecule Imaging in Live Embryos using Lattice Light-Sheet Microscopy

Mustafa Mir, Armando Reimer, Michael Stadler, Astou Tangara, Anders S. Hansen, Dirk Hockemeyer, Michael B. Eisen, Hernan Garcia, and Xavier Darzacq

33. Silver Filler Pre-Embedding to Enhance Resolution and Contrast in Multidimensional SEM: A Nanoscale Imaging Study on Liver Tissue

Gerald J. Shami, Delfine Cheng, and Filip Braet

Part V Computational Modeling of Biomolecules

34. Nanoscale Dynamics and Energetics of Proteins and Protein-Nucleic Acid Complexes in Classical Molecular Dynamics Simulations

Suresh Gorle and Lela Vuković

Blurb

This volume presents readers with the latest techniques to study nanoimaging and nanoprobing in application to a broad range of biological systems. The chapters in this book are divided into five parts, and cover topics such as imaging and probing of biomacromolecules including high-speed imaging and probing with AFM; probing chromatin structure with magnetic tweezers; and fluorescence correlation spectroscopy on genomic DNA in living cells. 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 through, Nanoscale Imaging: Methods and Protocols is a valuable resource for anyone interested in learning more about this developing and expanding field.