Single-Molecule Tools for Bioanalysis

Description

In the last three decades, the fast development of single-molecule techniques has revolutionized the way we observe and understand biological processes. Some of these techniques have been further adapted as tools for bioanalysis. This book summarizes and details the frontiers of the development of these tools as well as their applications. The contributors are young and established researchers in their respective fields. The main content originates from the lecture notes of a chemistry graduate course taught by the book editor at Nanjing University. This book is suitable to be used as a textbook for a high-level undergraduate or an entry-level graduate course. The systematically written content provides a thorough illustration of the mechanisms of each methodology presented. Cover Half Title Title Page Copyright Page Table of Contents Preface Acknowledgements Chapter 1: Single-Molecule Analysis by Biological Nanopores 1.1: Introduction 1.1.1: Single-Molecule Biophysics and Nanopore 1.1.2: Nanopore Methods 1.1.3: Biological Nanopores 1.2: Methodology 1.2.1: Preparation and Engineering of Biological Nanopores 1.2.2: The Instrument and the Device 1.2.3: The Electrochemistry Mechanism 1.2.4: The Nanopore Measurement 1.2.5: Measurement Noise and Bandwidth 1.2.6: Data Analysis 1.3: Applications 1.3.1: DNA Sensing and Sequencing 1.3.2: Efforts toward Protein Sequencing 1.3.3: Sensing of Small Molecules and Single-Molecule Chemistry Intermediates 1.3.4: Single-Molecule Enzymology 1.4: Summary and Prospects Chapter 2: Optical Tweezers for Manipulation of Single Molecules 2.1: Introduction 2.2: Optical Trapping Theory 2.2.1: Rayleigh Optics Approximation 2.2.2: Ray Optics Approximation 2.2.3: Electromagnetic Theory (MDSA Approximation) 2.3: Optical Tweezers Instrumentation 2.3.1: Optical Setup 2.3.2: Trapping Laser 2.3.3: Beam Steering Module 2.3.4: Trapping Objectives 2.3.5: Position Detection 2.4: Force Calibration in Optical Tweezers 2.4.1: Viscous Drag Force Calibration 2.4.2: Brownian Motion Calibration 2.4.3: Direct Measurement 2.5: Combined Optical Trapping and Single-Molecule Fluorescence Spectroscopy 2.6: Nanophotonic Optical Tweezers 2.7: Applications of Optical Tweezers in Single-Molecule Manipulation 2.7.1: Mechanical Properties of DNA 2.7.2: Folding and Structural Dynamics of Proteins and Nucleic Acids 2.7.3: Dynamics of Molecular Motors 2.8: Summary and Perspective Chapter 3: Single-Molecule Biosensing by Fluorescence Resonance Energy Transfer 3.1: Introduction 3.2: Implementation of smFRET 3.2.1: Optical Setup 3.2.2: Fluorophore Labeling 3.2.3: Surface Modification 3.2.4: Photo-Protection Strategy 3.3: Applications of smFRET 3.3.1: Structural Dynamics of Nucleic Acids 3.3.2: Protein Structural Dynamics 3.3.3: Biomolecular Interactions 3.4: New Developments of smFRET 3.4.1: Multicolor smFRET 3.4.2: Strategies to Break Concentrations Barrier 3.4.3: SmFRET under Forces 3.4.4: Surface-Induced Fluorescence Attenuation 3.4.5: Quenchers-in-a-Liposome FRET 3.5: Summary and Perspective Chapter 4: DNA Origami as Single-Molecule Biosensors 4.1: Introduction 4.2: Protein and Nucleic Acid Detection 4.3: Analysis of Biomolecular Interactions and Activity 4.3.1: Protein Activity 4.3.2: Alternative Nucleic Acid Conformations 4.4: Control and Visualization of Chemical Reactions 4.5: Photonic Techniques for Biotechnological Applications 4.6: Summary and Future Perspectives Chapter 5: Single-Molecule Manipulation by Magnetic Tweezers 5.1: Introduction 5.2: Principles and Technical Details of Magnetic Tweezers 5.2.1: Force Generation 5.2.2: Force Calibration 5.2.3: Torque Generation and Measurement 5.2.4: Extension Measurements 5.2.5: Data Analysis 5.3: Applications of Magnetic Tweezers 5.3.1: DNA Elasticity and Conformational Transition 5.3.2: DNA Topoisomerase 5.3.3: DNA and RNA Helicase 5.3.4: DNA–Protein Interactions 5.3.5: Protein Folding and Unfolding 5.3.6: Protein–Protein Interactions 5.3.7: Mechanical Manipulation of Cells 5.4: Emerging Developments 5.4.1: Freely-Orbiting Magnetic Tweezers 5.4.2: Combination of Magnetic Tweezers with Fluorescence 5.4.3: Fast Dynamics Studied by Electromagnets 5.5: Summary and Perspectives Chapter 6: Long-Time Recording of Single-Molecule Dynamics in Solution by Anti-Brownian Trapping 6.1: Introduction 6.2: Principles of Anti-Brownian Trapping 6.2.1: Fundamentals 6.2.2: A Brief History of the Development of the Technique 6.2.3: Essential Components of an ABEL Trap 6.3: Selected Applications of the ABEL Trap 6.3.1: Reaching Ultimate Limit: Trapping Single Organic Fluorophores in Solution 6.3.2: Dissecting Pigment Organization of Single Biliproteins in Solution 6.3.3: Sensing Biomolecular Interactions by Single-Molecule Transport 6.4: Summary and Perspective Index