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.
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
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.
Includes cutting-edge methods and protocols
