Single-Molecule Tools for Bioanalysis

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