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E-grāmata: Molecular Manipulation with Atomic Force Microscopy [Taylor & Francis e-book]

Edited by (University of Liege, Belgium), Edited by (University of Liege, Belgium)
  • Formāts: 287 pages, 3 Tables, black and white; 118 Illustrations, black and white
  • Izdošanas datums: 07-Dec-2011
  • Izdevniecība: CRC Press Inc
  • ISBN-13: 9780429092251
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Molecular Manipulation with Atomic Force MicroscopyPalielināt
  • Formāts: 287 pages, 3 Tables, black and white; 118 Illustrations, black and white
  • Izdošanas datums: 07-Dec-2011
  • Izdevniecība: CRC Press Inc
  • ISBN-13: 9780429092251
Citas grāmatas par šo tēmu:
Taylor & Francis e-booksMore info about Taylor & Francis e-books
Rokasgrāmatas mājas lapa: https://www.taylorfrancis.com/books/9780429092251
"The manipulation of molecules is an active area of research with applications in chemistry, biology, physics, engineering, and polymer science. This book provides a comprehensive review of single molecule manipulation with atomic force microscopy (AFM).The text demonstrates that AFMs are capable of meeting the three main challenges in molecular manufacturing: manipulating and positioning each atom or molecule in the right place, making the atom or molecule form certain bonds, and achieving high-throughput fabrication. New and experienced researchers will find a wealth of information in this informative volume which demonstrates the potential of AFMs beyond imaging"--

Provided by publisher.
Preface vii
Editors ix
Contributors xi
PART I Pulling on Single Molecules with Force Spectroscopy
Chapter 1 Molecular Recognition Force Spectroscopy
3(44)
Nicolas Willet
Constanze Lamprecht
Christian Rankl
Martina Rangl
Rhiannon Creasey
Andreas Ebner
Nicolas H. Voelcker
Peter Hinterdorfer
1.1 Single-Molecule Force Spectroscopy
4(10)
1.1.1 Basic Principles
4(3)
1.1.2 Dynamic Single-Molecule Force Spectroscopy and Molecular Recognition
7(2)
1.1.3 Surface Chemistry for Single-Molecule Studies
9(1)
1.1.3.1 Tip Modification
10(3)
1.1.3.2 Substrate Preparation
13(1)
1.2 Molecular Recognition Force Spectroscopy on Synthetic Host-Guest Systems
14(3)
1.3 Molecular Recognition Force Spectroscopy on Biological Systems
17(7)
1.3.1 Model Systems
17(1)
1.3.2 Advanced Systems
18(1)
1.3.2.1 Nuclear Pore Complexes
18(1)
1.3.2.2 DNA
19(3)
1.3.2.3 Human Rhinovirus and Cells
22(2)
1.4 Molecular Recognition Mapping Using Force Spectroscopy
24(3)
1.5 Simultaneous Dynamic Imaging of Topography and Recognition
27(9)
1.5.1 Principle
27(3)
1.5.2 Applications
30(1)
1.5.2.1 Bacterial Surface Layers
30(2)
1.5.2.2 Human Red Blood Cell Membranes
32(1)
1.5.2.3 Cells
33(3)
Acknowledgments
36(1)
References
36(11)
Chapter 2 Mechanics of Proteins and Tailored Mechanics of Engineered Proteins
47(36)
Ashlee Jollymore
Yi Cao
Hongbin Li
2.1 A Brief Introduction: The Utility of Investigating Protein Mechanics on the Single-Molecule Scale
48(2)
2.2 Use of Force Spectroscopy to Explicate Nanomechanical Properties of Protein
50(10)
2.2.1 First Single-Molecule AFM Protein Studies
50(1)
2.2.2 Representing Protein Mechanical Stability Using Single-Molecule AFM
50(2)
2.2.3 Constructing Polyprotein to Pinpoint the Nanomechanics of Protein Domains of Interest
52(1)
2.2.4 How Applied Force Unfolds a Protein
53(1)
2.2.5 Mechanical Stability: A Kinetic, rather than Thermodynamic, Stability
54(1)
2.2.6 Constructing the Free Energy Landscape for Protein Unfolding from Single-Molecule AFM Experiments
55(3)
2.2.7 Structural Features of Proteins Obtained from Force-Extension Spectrum
58(1)
2.2.8 Unfolding Force Depends on Pulling Direction: The Importance of Local Structure to the Mechanical Stability of Proteins
59(1)
2.3 Tuning the Properties of Proteins: Tailoring Protein Mechanics for Use with Single-Molecule AFM
60(14)
2.3.1 Present Modifications and Their Application with Single-Molecule AFM
60(1)
2.3.2 Introducing Point Mutations into the Native Protein Backbone: Nanomechanical Effects of Single-Point Mutations
61(3)
2.3.3 Recombination of Structural Fragments or Structural Grafting
64(3)
2.3.4 Intramolecular Disulfide Bonding and Loop Insertion
67(1)
2.3.5 Ligand Binding Modifies the Unfolding Energy Landscape
68(2)
2.3.6 Investigating the Nanomechanics of a Novel Protein Fold: Top7
70(1)
2.3.7 Environmental/Solvent Tuning of Mechanical Stability
71(2)
2.3.8 Predicting Mechanical Properties Using Modeling Approaches
73(1)
2.4 Future Perspectives: Rationally Controlling and Designing Proteins with Desired Nanomechanical Properties
74(2)
2.4.1 Learning from Nature: How Tunable Functionality Originates within Protein Structure
74(1)
2.4.2 Cracking the Structure/Function Relationship: Further Protein Modifications Investigated Using Single-Molecule AFM
75(1)
2.4.3 The Future: Rationally Designing Proteins with Desired Functionality
75(1)
References
76(7)
Chapter 3 Mechanics of Polysaccharides
83(46)
Whasil Lee
Piotr E. Marszalek
Xiancheng Zeng
Weitao Yang
3.1 Introduction
84(3)
3.2 Overview of Polysaccharide Structure
87(1)
3.3 Overview of Polysaccharide Elasticity
88(2)
3.4 Atomic Force Spectroscopy of Single Polysaccharides
90(26)
3.4.1 Experimental Methods
90(1)
3.4.1.1 Polysaccharides and Their Preparation for AFM Measurements
90(1)
3.4.1.2 AFM Instruments and the Principles of Single-Molecule Atomic Force Spectroscopy
90(2)
3.4.1.3 Interpretation of Force-Extension Relationships: Identifying Single-Molecule Force Spectra
92(1)
3.4.1.4 Normalization of Polysaccharide Extension
93(1)
3.4.1.5 Pulling Geometry Errors
94(1)
3.4.2 Basic Computational Approaches for Modeling Sugar Mechanics
94(1)
3.4.2.1 Quantum Mechanics-Based Methods for Analyzing Strained Sugar Conformations
94(2)
3.4.2.2 Steered Molecular Dynamics Simulations of Polysaccharide Elasticity
96(1)
3.4.3 (1→4) Linked Polysaccharides and Their Force-Induced Conformational Transitions
97(1)
3.4.3.1 Cellulose and Amylose: Force-Induced Chair-Boat Transitions
97(3)
3.4.3.2 Galactan: Identifying Sugar Isomers by AFM Force Spectroscopy
100(3)
3.4.3.3 Pectin: Atomic Levers Control Pyranose Ring Conformations
103(2)
3.4.4 (1→6) Linked Polysaccharides: Atomic Cranks and Levers Control Pyranose Ring Conformations
105(1)
3.4.4.1 Pustulan
105(2)
3.4.4.2 Dextran
107(1)
3.4.5 Molecular Elasticity of Epimerized Polysaccharides
108(1)
3.4.5.1 Alginate
109(4)
3.4.6 Fingerprinting Polysaccharides with AFM
113(2)
3.4.7 Conclusions
115(1)
3.5 Simulations of AFM Experiments for Polysaccharides
116(7)
3.5.1 Obtaining Fully Converged Results from the Samplings under Equilibrium Conditions: Comparisons of SMD, REM-SMD, REM-US
116(3)
3.5.2 Latest Simulation Results and Conformational Transitions, Using REM-US and Glycam06
119(3)
3.5.3 Comparison of the Application of Classical Force Fields and Quantum Mechanics-Based Methods to Modeling of Polysaccharide Mechanics
122(1)
3.5.4 Conclusions
123(1)
Acknowledgments
123(1)
References
123(6)
Chapter 4 Mechanics and Interactions in DNA and RNA
129(20)
Robert Ros
4.1 Introduction
129(1)
4.2 Protein-DNA Interactions
130(8)
4.2.1 Interaction of Transcriptional Regulators with DNA Target Sequences
130(3)
4.2.2 Effector Stimulated Protein-DNA Interactions
133(2)
4.2.3 Improved Model for the Data Analysis
135(3)
4.3 Protein-RNA Interactions
138(3)
4.4 Binding of Small Molecules to dsDNA
141(4)
4.5 Conclusion and Outlook
145(1)
References
146(3)
Chapter 5 Mechanics of Synthetic Polymers
149(16)
Wenke Zhang
Ying Yu
Xi Zhang
5.1 Effect of Chain Composition on the Elasticity of Synthetic Single Polymers
150(6)
5.1.1 Side-Group Effects
150(2)
5.1.2 Linear Charge Density Effects on the Single Chain Elasticity
152(1)
5.1.3 Tacticity Effect on Single-Chain Elasticity
153(1)
5.1.4 Effects of Oxidization/Reduction States on Elasticity
154(2)
5.2 Interaction of Small Molecule with Polymer
156(5)
5.2.1 Effects of Urea on Nanomechanics of Poly(Acrylamide) Derivatives
156(1)
5.2.2 Effect of Water on the Nanomechanics of Poly(Ethylene Glycol)
157(1)
5.2.3 Binding of Water or KI3 Molecules Changes the Elastic Properties of Poly(N-Vinyl-2-Pyrrolidone)
158(1)
5.2.4 Nanomechanics of Single Amylose Chains in Crowding Environment
159(2)
5.3 Aggregating Effect on Nanomechanics of Single Polymer Chain
161(1)
5.3.1 Force-Induced Globule-Coil Transition in Single Polystyrene Chains
161(1)
5.3.2 Forces Required to Disassemble the Block Copolymer Micelles of PAA-PF-PAA
162(1)
References
162(3)
Chapter 6 Interplays between Chemistry and Mechanics in Single Molecules
165(32)
Dhruv Kumar
Bruno Samori
6.1 Introduction
165(1)
6.2 Effect of Force on Thermodynamics and Kinetics of a Reaction
166(5)
6.2.1 Effect of Force on the Free Energy of a Reaction
167(3)
6.2.2 Effect of Force on the Kinetics of a Reaction
170(1)
6.3 Single-Molecule Force Spectroscopy
171(14)
6.3.1 Methodologies for Single-Molecule Force Spectroscopy
172(2)
6.3.2 Mapping the Position of the Barrier according to the Dynamic Force Spectroscopy Approach
174(1)
6.3.3 AFM-Based Single-Molecule Force Spectroscopy of GB1 Protein
175(2)
6.3.4 AFM-Based Single-Molecule Force Spectroscopy of GB1 Protein in the Presence of Chemical Osmolytes
177(2)
6.3.5 Molecular Engineering of Mechanical Properties
179(6)
6.4 Mechanochemistry of a Single Covalent Bond
185(4)
6.4.1 Disulfide Bond Reduction Reactions by Small Nucleophiles
185(4)
6.5 Mechanochemistry for a Targeted Delivery of Single Molecules
189(1)
6.6 Conclusion and Prospective
190(1)
References
190(7)
PART II Manipulation, Repositioning, and Targeted Delivery of Single Molecules on Substrates
Chapter 7 Molecular Construction: Pushing, Moving, Stretching, and Connecting Individual Molecules
197(12)
Fouzia Bano
Anne-Sophie Duwez
7.1 Moving Single Molecules on Surfaces
198(1)
7.2 Stretching Single Molecules on Surfaces
199(4)
7.2.1 Using Contact Mode SFM
199(2)
7.2.2 Using Intermittent Contact Mode SFM
201(2)
7.3 Connecting Individual Molecules on Surfaces
203(2)
7.4 Outlook
205(1)
Acknowledgment
205(1)
References
205(4)
Chapter 8 Extracting Molecules from Surfaces
209(28)
Atsushi Ikai
Rehana Afrin
Takahiro Watanaba-Nakayama
Shin-ichi Machida
8.1 Introduction
209(1)
8.2 Why Extract by Force?
210(1)
8.3 Preparation for Extraction Experiments
211(2)
8.4 Extraction of Lipid Molecules
213(3)
8.5 Pulling Helical Polypeptides from the Lipid Bilayer Membrane
216(1)
8.6 Extraction of Intrinsic Membrane Proteins
217(6)
8.7 Proteins with Lipid Tethers
223(1)
8.8 Retrieval of Genomic DNA from Isolated Chromosomes
224(3)
8.9 Retrieval of Intracellular mRNA
227(1)
8.10 Creating Membrane Holes Using AFM Probes
228(5)
8.11 Conclusions and Future Prospects
233(1)
Acknowledgments
234(1)
References
234(3)
Chapter 9 Single-Molecule Delivery by Mechanochemistry
237(12)
Tiziana Svaldo-Lanero
Anne-Sophie Duwez
Acknowledgment
246(1)
References
246(3)
Chapter 10 Single-Molecule Cut and Paste
249(12)
Stefan W. Stahl
Mathias Strackharn
Hermann E. Gaub
10.1 Molecular Manipulation at the Nanometer Length Scale
249(1)
10.2 DNA as a Programmable Building Block
250(1)
10.3 Load-Driven Unfolding Geometries of DNA
251(1)
10.4 Hierarchical Force System
252(1)
10.5 Accuracy of the Single-Molecule Cut and Paste Process
253(2)
10.6 Applications
255(3)
10.6.1 Controlled Deposition of Nanoscale Objects
255(1)
10.6.1.1 Nanoparticle Self-Assembly on a DNA-Scaffold Written by Single-Molecule Cut and Paste
255(1)
10.6.1.2 Protein-Based SMCP
256(2)
10.6.2 SMCP Patterns as Standard for the Optimization of Super-Resolution Microscopy Techniques
258(1)
10.7 Outlook
258(1)
Acknowledgments
259(1)
References
259(2)
Index 261
Anne-Sophie Duwez received her Ph.D. in Chemistry in 1997 from the University of Namur, Belgium. She then moved to the Catholic University of Louvain as a Post-doctoral Researcher of the Belgian National Fund for Scientific Research. In 2002-2003, she was visiting scientist at the Max-Planck Institute for Polymer Research in Mainz, Germany. She then returned to the Catholic University of Louvain as a senior scientist to develop AFM-based single molecule force spectroscopy. In 2006, she took up the Chair of Chemistry at Surfaces at the University of Ličge. In 2007, she received a Starting Grant from the National Fund for Scientific Research to set up a new lab dedicated to advanced AFM techniques. She is currently professor of surface chemistry, chemistry of organic and bio materials, and nanotechnology. Her research interests focus on the development of AFM-based techniques, probes, and methods to manipulate single molecules. They include the investigation of mechanochemical processes in bio- and synthetic systems and the design of single molecule devices.

Nicolas Willet studied chemistry at the University of Ličge, Belgium. He studied protein folding during his master thesis and received his Ph.D. in 2007 for his work on the synthesis and characterization of triblock copolymer self-assemblies, carried out under the supervision of Professor Robert Jérōme (polymer chemistry). He then moved to the team of Professor Anne-Sophie Duwez where he performed AFM force spectroscopy on bio-inspired polymers. After his postdoctoral work with Professor Peter Hinterdorfer at the Institute of Biophysics of the University of Linz, Austria, he went back to the University of Ličge in 2011, where he is currently working as an FNRS postdoctoral researcher. His research interests concern functional and responsive polymers, single-molecule force spectroscopy, molecular recognition, with a particular focus on the investigation of biological macromolecules' conformation.
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