Introduction to Fluorescence Sensing: Volume 1: Materials and Devices [3 ed.] 3030601544, 9783030601546

Table of contents :
Preface
Contents
About the Author
1 Principles and Techniques in Chemical and Biological Sensing
1.1 General Definitions and Formulation of Key Problems
1.1.1 Sensors or Assays?
1.1.2 Homogeneous and Heterogeneous Formats
1.2 Elements of a Typical Sensor
1.2.1 The Recognition Element
1.2.2 The Reporter Element
1.2.3 The Transducer
1.3 Diversity of Sensing Techniques and Their Operation Principles
1.3.1 The Label-Free Techniques
1.3.2 The Label-Based Approach
1.4 Distinguishing Features of Fluorescence Technology
1.4.1 Fluorescence as the Technique of Choice
1.4.2 Large-Scale Manipulation with Emission Colors and Lifetimes
1.4.3 Broad Diversity of Molecular and Nanoscale Emitters
1.4.4 Possibilities for Enhancement of Reporting Signal
1.4.5 Catalytic Enhancement in Sensors and Biosensors
1.4.6 Single-Analyte Sensors and Multi-analyte Arrays
1.5 Trends for Future Development
1.6 Sensing and Thinking. High Time for New Endeavor
References
2 Overview of Strategies in Fluorescence Sensing
2.1 Labeling Targets in Fluorescence Assays
2.1.1 Arrays for DNA Hybridization
2.1.2 Labeling in Protein-Protein and Protein-Nucleic Acid Interactions
2.1.3 Advantages and Limitations of the Approach Based on Pool Labeling
2.2 Sandwich Assays
2.2.1 Sensing the Antigens and Antibodies
2.2.2 Labeling with Catalytic Amplification
2.2.3 Ultrasensitive DNA Hybridization Assays
2.2.4 Advantages and Limitations of the Approach
2.3 Competitor Displacement Assays
2.3.1 Unlabeled Sensor and Labeled Competitor in Homogeneous Assay
2.3.2 Labeling of Both Receptor and Competitor
2.3.3 Advantages and Limitations of the Approach
2.4 Direct Reagent-Independent Sensing
2.4.1 The Principle of Direct ‘Mix-and-Read’ Sensing
2.4.2 Contact and Remote Sensors
2.4.3 Advantages and Limitations of the Approach
2.5 Sensing and Thinking. The Cost of Brightness and Amplification in Sensor Response
References
3 Fluorescence Detection in Sensor Technologies
3.1 Fluorescence Fundamentals
3.1.1 The Light Emission Phenomenon
3.1.2 Fluorescence Parameters Used in Sensing
3.1.3 Parameters Characterizing the Properties of Fluorescence Emitters
3.1.4 Fluorophore Emissive Power: The Brightness and Quantum Yield
3.2 Intensity-Based Sensing
3.2.1 Peculiarities of Fluorescence Intensity Measurements
3.2.2 How to Make Use of Quenching Effects?
3.2.3 Quenching: Static and Dynamic
3.2.4 Non-linearity Effects
3.2.5 Internal Calibration in Intensity Sensing
3.2.6 Intensity Change as a Choice for Fluorescence Sensing
3.3 Anisotropy-Based Sensing and Polarization Assays
3.3.1 Background of the Method
3.3.2 Practical Considerations
3.3.3 Applications of Fluorescence Anisotropy in Sensing
3.3.4 Comparisons with Other Methods of Fluorescence Detection
3.4 Lifetime-Based Fluorescence/Luminescence Response
3.4.1 Physical Background of Time-Resolved Detection
3.4.2 Technique Using the Time Resolution
3.4.3 Time-Resolved Anisotropy
3.4.4 Applications of Time-Resolved Fluorescence
3.4.5 Phosphorescence and Long-Lasting Luminescence
3.4.6 Comparison with Other Fluorescence Detection Techniques
3.5 Wavelength-Shifting Sensing
3.5.1 The Physical Background Under the Wavelength Shifts
3.5.2 The Measurements of Wavelength Shifts in Excitation and Emission
3.5.3 Wavelength-Ratiometric Measurements
3.5.4 Application of λ-Ratiometry in Sensing
3.5.5 Comparison with Other Fluorescence Reporting Techniques
3.6 Two-Band λ-Ratiometry with Single Fluorophore
3.6.1 Generation of Two-Band λ-Ratiometric Response by Ground-State Isoforms
3.6.2 Excited-State Reactions Generating Two-Band Response Within Single Dye in Emission
3.6.3 Coupling a Reporting Dye with the Reference
3.6.4 Fluorescent Excimers
3.6.5 The Systems with Excitation Energy Transfer (EET)
3.7 Sensing and Thinking: The Optimal Choice of Fluorescence Detection Technique
References
4 Photophysical Mechanisms of Signal Transduction in Sensing
4.1 Basic Signal Transduction Mechanisms: Electron, Charge and Proton Transfer
4.1.1 Photoinduced Electron Transfer (PET)
4.1.2 Intramolecular Charge Transfer (ICT)
4.1.3 Twisted Intramolecular Charge Transfer (TICT)
4.1.4 Intramolecular Excited-State Proton Transfer
4.1.5 Excited-State Intramolecular Proton Transfer (ESIPT)
4.1.6 Future Directions
4.2 Excimer and Exciplex Formation
4.2.1 The Dyes Forming Excimers and Exciplexes
4.2.2 Nonemissive Dimers
4.2.3 Application in Sensing Technologies
4.2.4 Comparison with Other Fluorescence Reporter Techniques
4.3 Excitation Energy Transfer (EET)
4.3.1 Physical Background of the Method
4.3.2 Applications of EET Technology
4.3.3 Observing New Developments
4.4 Signal Transduction Via Conformational Changes
4.4.1 Excited-State Isomerism in Small Molecular Reporter Dyes
4.4.2 Conformational Changes in Conjugated Polymers
4.4.3 Conformational Changes in Peptide Sensors and Nucleic Acid Aptamers
4.4.4 Molecular Beacons (Hairpin-Like Structures)
4.4.5 Proteins Exhibiting Conformational Changes
4.4.6 Prospects in Exploration of Conformational Changes
4.5 Smart Sensing with Logic Operations
4.5.1 Why Logic Operations in Fluorescence Sensing?
4.5.2 Logic Operations on Molecular Scale
4.5.3 Exploration of Basic Signal Transduction Mechanisms
4.5.4 Prospective Applications in Sensing and Imaging Technologies
4.6 Sensing and Thinking. How to Optimize Photophysical Transformations for Generating the Output Signal?
References
5 Organic Dyes and Visible Fluorescent Proteins as Fluorescence Reporters
5.1 Fluorescent Organic Molecules and Their Characteristics
5.1.1 General Properties of Organic Dyes
5.1.2 The Photostability of Organic Dyes
5.1.3 Protection of Dyes with Macrocyclic Hosts
5.1.4 New Discoveries and Improvements
5.1.5 Labeling and Sensing—Two Basic Methodologies
5.2 Organic Dyes Optimal as Labels and Tags
5.3 The Dyes Providing Fluorescence Response
5.3.1 Special Requirements for Fluorescence Reporters
5.3.2 Fluorophores in Protic Equilibrium. pH-Reporting Dyes
5.3.3 Hydrogen Bond Responsive Dyes
5.3.4 The Environment-Sensitive (Solvatochromic and Solvatofluorochromic) Dyes
5.3.5 Electric Field Sensing (Electrochromic) Dyes
5.3.6 Supersensitive Multicolor λ-Ratiometric Dyes
5.3.7 Prospects in Improving the Target-Responsive Sensitivity
5.4 Organic Dyes Optimal for Particular Applications
5.4.1 Near-IR Dyes
5.4.2 Two-Photonic Dyes
5.4.3 Dyes Demonstrating Phosphorescence and Delayed Fluorescence
5.4.4 Organic Photochromic Compounds
5.4.5 Dyes for Sensing in Protein and Nucleic Acid Science
5.5 Visible Fluorescent Proteins
5.5.1 Green Fluorescent Protein (GFP) and Its Fluorophore
5.5.2 Proteins of GFP Family
5.5.3 Excited-State Reactions in Fluorescent Proteins
5.5.4 Labeling and Sensing Applications of Fluorescent Proteins
5.5.5 Other Proteins with Visible Fluorescence Emission
5.5.6 Finding Analogs of Fluorescent Protein Fluorophores
5.5.7 Prospects
5.6 Sensing and Thinking. The Search for Novel Dyes and for New Mechanisms of Their Response
References
6 Small Luminescent Associates Based on Inorganic Atoms and Ions
6.1 Fluorescent Few-Atom Clusters of Noble Metals
6.1.1 The Cluster Structures and Their Stability
6.1.2 The Mechanisms of Light Absorption and Emission in Noble Metal Clusters
6.1.3 Spectroscopic Properties
6.1.4 Formation, Stabilization and Protection of Metal Clusters
6.1.5 Applications in Sensing and Imaging
6.2 Metal Complexes that Exhibit Phosphorescence
6.2.1 Metal-to-Ligand Charge Transfer (MLCT) Phosphorescence
6.2.2 Phosphorescent Metal-Chelating Porphyrins
6.2.3 Upconversion by Triplet-Triplet Annihilation
6.3 Lanthanides, Their Complexes and Conjugates
6.3.1 Photophysics of Lanthanide Chelates
6.3.2 Luminescence Spectra of Lanthanides
6.3.3 Lanthanide Chelates as Labels and Reference Emitters
6.3.4 Lanthanide-Based Heterogeneous and Homogeneous Immunoassays
6.3.5 Switchable Lanthanide Chelates in Sensing
6.4 Sensing and Thinking. Three Roads to Most Efficient Use of Smallest Metal-Based Emitters
References
7 Fluorescent Inorganic Particles in Nanoscale World
7.1 Introduction to Light-Emitting Nano-world
7.1.1 Size, Shape and Dimensions of Nanomaterials
7.1.2 Variations in Nanoparticles Composition, Crystallinity and Order
7.1.3 Interactions at Nanoscale Surfaces
7.1.4 Excitation Energy Transfer with and between Nanoparticles
7.1.5 Design of Functional Nanomaterials
7.2 Semiconductor Quantum Dots
7.2.1 The Composition of Quantum Dots
7.2.2 The Origin of Emission of Semiconductor Nanomaterials. The Loosely Bound Excitons
7.2.3 The Spectroscopic Properties of Quantum Dots
7.2.4 Stabilization and Functionalization of Quantum Dots
7.2.5 Applications of Quantum Dots in Sensing
7.2.6 Semiconductor Nanocrystals of Different Shapes and Dimensions
7.2.7 Magic-Sized Quantum Dots
7.2.8 Porous Silicon and Silicon Nanoparticles
7.2.9 Prospects in QDs Development and Applications
7.3 Nanoparticles with Long Persistent Luminescence
7.4 Lead Halide Perovskite Nanocrystals
7.5 Upconverting Nanocrystals
7.5.1 The Photophysical Mechanism of Upconversion
7.5.2 The Spectroscopic Properties of Upconversion Nanomaterials
7.5.3 Modulation of Fluorescent Signal
7.5.4 Present and Prospective Applications
7.6 Sensing and Thinking. Small Things Bright and Beautiful, What is Their Advantage?
References
8 Fluorescent Organic Dyes and Conjugated Polymers in Nanoscale Ensembles
8.1 General Effects Observed on Dye-Dye Association
8.1.1 Excitonic Behavior of Organized Dye Assemblies
8.1.2 Modulation of Photoreactions Valuable for Sensing
8.1.3 Exchange of Excitation Energies
8.1.4 Concentration-Dependent Quenching
8.1.5 The Effect of External Quenchers, “Superquenching”
8.1.6 Variations of Anisotropy in Excitation Energy Transfer
8.2 Highly Ordered Nanoscale Associates of Organic Dyes (H- and J-Aggregates)
8.2.1 Excitonic J-Aggregates
8.2.2 Emissive and Quenched H-Aggregates
8.3 Aggregation-Protected and Aggregation-Induced Emission
8.3.1 Dye Aggregates: Emissive and Quenched
8.3.2 Modifying Intermolecular Interactions on Dye Aggregation
8.3.3 Aggregation-Induced Emission (AIE)
8.4 Nanoscale Assemblies Supported by Organic Polymers and Silica Matrices
8.4.1 Compositions of Organic Dyes Based on Organic Polymers
8.4.2 Organic Dyes Incorporated into Dendrimers
8.4.3 DNA-Based Fluorescent Nanostructures
8.4.4 Organic Dyes in Silica-Based Fluorescent Nanoparticles
8.4.5 Summarizing: Dye-Doped Nanoparticles in Sensing
8.5 Light-Emitting Conjugated Polymers
8.5.1 Structure and Spectroscopic Properties
8.5.2 Conjugated Polymer Nanoparticles (P-Dots)
8.5.3 Conjugated Polymers as Fluorescence Reporters in Designed Sensors
8.6 Sensing and Thinking. The Struggle for Brightness and Signal Amplification in Sensor Design
References
9 Fluorescent Carbon Nanostructures
9.1 Light-Emissive Nanodiamonds
9.2 The sp2 Forming Structures: Graphene Sheets, Nanotubes, Fullerenes
9.3 Fluorescent Graphene and Graphene Oxide Nanoparticles
9.4 Fluorescent Carbon Dots (C-dots)
9.4.1 Carbon Dots in the Family of Light-Emissive Nanomaterials
9.4.2 The Spectroscopic Properties of C-dots
9.5 The Origin of Fluorescence Emission of Carbon Nanostructures
9.5.1 Arising Questions to Be Answered
9.5.2 Carbon Nanoparticles as Collective Emitters
9.5.3 The Exciton Model
9.6 Analytical, Bioanalytical and Imaging Applications of Carbon Nanomaterials
9.6.1 General Strategy
9.6.2 Chemical Sensing with Carbon Nanostructures
9.6.3 Applications in Biotechnologies
9.6.4 Cellular Imaging Applications
9.7 Sensing and Thinking: The Values of New Discoveries in the Science of Carbon
References
10 Smart Luminescent Nanocomposites
10.1 Broad-Scale Manipulation with Fluorescence Parameters in Nanocomposites
10.1.1 Assembling, Screening, Immobilization
10.1.2 Plasmonic Enhancement
10.1.3 Excitonic Effects. Coherent and Incoherent Energy Transfer
10.1.4 Exciton-Exciton and Plasmon-Exciton Interactions
10.2 Realization of Electronic Energy Transfer (EET) in Nanocomposites
10.2.1 Homo-Transfer and Hetero-Transfer
10.2.2 General Rules for Collective Effects in EET
10.2.3 Light-Harvesting (Antenna) Effect
10.2.4 Wavelength Converting. Cascade Energy Transfer
10.2.5 Extending the Emission Lifetimes
10.2.6 Variations of Anisotropy
10.2.7 Modulation of Luminescence by Excitation Light
10.3 Superenhancement and Superquenching
10.4 Optical Choice of EET Donors and Acceptors
10.4.1 Lanthanide Chelates and Other Metal-Chelating Luminophores
10.4.2 Semiconductor Quantum Dots (QDs)
10.4.3 Upconverting Nanomaterials
10.4.4 Conjugated Polymers
10.4.5 Organic Dyes and Visible Fluorescent Proteins
10.4.6 Noble Metal Nanoparticles
10.4.7 Fluorescent Carbon Nanoparticles
10.5 Wavelength Referencing, Multiplexing and Multicolor Coding
10.5.1 Wavelength Referencing and λ-Ratiometry
10.5.2 Multiplex Assays and Suspension Arrays
10.5.3 Materials for Multicolor Coding
10.6 Sensing and Thinking: Multiple Functions of Small Nanoparticles, How to Achieve that?
References
11 Passive Support Materials for Fluorescence Sensors
11.1 Self-assembly on the Surface
11.1.1 Template-Assisted Assembly
11.1.2 Formation of Supporting and Transducing Surfaces
11.1.3 Self-assembled Monolayers
11.1.4 Langmuir-Blodgett Films
11.1.5 Layer-by-Layer Approach
11.1.6 Prospects for Designing Smart Surfaces
11.2 Operating with Building Blocks for Nanoscale Sensors
11.2.1 Inorganic Colloidal Scaffolds
11.2.2 Graphene and Graphene Oxide
11.2.3 Carbon Nanotubes
11.2.4 Fullerenes
11.3 Organic and Biological Structures as Scaffolds
11.3.1 Two-Dimensional Self-assembling of S-Layer Proteins
11.3.2 Peptide Scaffolds
11.3.3 DNA Templates. Origamis
11.4 Functional Lipid and Polymer Bilayers
11.4.1 Liposomes as Integrated Sensors
11.4.2 Stabilized Phospholipid Bilayers
11.4.3 Polymersomes
11.4.4 Formation of Protein Layers Over Lipid Bilayers
11.5 The Principles of Formation of Assembled Structures
11.5.1 Affinity Coupling
11.5.2 Self-assembly
11.6 Conjugation, Labeling and Cross-Linking
11.6.1 Nano-Bio Conjugation
11.6.2 Techniques of Conjugation and Labeling
11.6.3 Co-synthetic Modifications
11.6.4 Chemical and Photochemical Cross-Linking
11.7 Sensing and Thinking. Extending Sensing Possibilities with Smart Decorated Surfaces and Nano-Ensembles
References
12 Fluorescent Composites Combining Multiple Sensing and Imaging Modalities
12.1 Multimodal Approach in Sensing and Imaging
12.2 Design and Functioning of Multimodal Supramolecular Structures and Nanoparticles
12.2.1 The Principle of Formation of Materials with Multimodal Properties
12.2.2 Fluorescence Combined with X-Ray Computed Tomography
12.2.3 Combining Fluorescence with NMR Imaging
12.2.4 Nanocomposites Demonstrating Triple-Modal Imaging
12.3 Magnetic-Fluorescent Nanoparticles with Different Functionalities
12.4 Sensing and Thinking. Composites Assembling Several Modalities in Sensing and Imaging. What for?
References
13 Evanescent Field Effects and Plasmonic Enhancement of Luminescence in Sensing Technologies
13.1 Evanescent-Wave Fluorescence Sensing
13.1.1 Excitation of Dyes by Evanescent Field
13.1.2 Evanescent Wave Sensing Technology
13.2 Plasmonic Effects in Fluorescence
13.2.1 General Character of Plasmonic Effects
13.2.2 Fluorescence Enhancement in Surface Plasmon Resonance Conditions
13.2.3 Modulation of Light Emission by Plasmonic Nanoparticles
13.2.4 Exciton-Plasmon Interactions
13.3 Light Absorption and Scattering by Plasmonic Nanoparticles
13.3.1 Going Deeper into the Properties of Localized Plasmons
13.3.2 The Effects of Particle Shape and Hetero-Composition
13.4 Broad-Scale Applications of Plasmonic Sensors
13.5 Microwave Acceleration of Metal-Enhanced Emission
13.6 Sensing and Thinking. Plasmonics, Is that Sole Search for Brightness?
References
14 Non-conventional Generation and Transformation of Sensor Response
14.1 Chemiluminescence and Electrochemiluminescence
14.1.1 Realization of Chemiluminescence
14.1.2 Catalytic Generation and Enhancement of Chemiluminescence
14.1.3 Nanoparticle-Based Platforms in Chemiluminescence
14.2 Electrogenerated Chemiluminescence
14.2.1 Cathodic Generation of Luminescence
14.2.2 Essentials of Chemical Sensing Techniques and Their Prospects
14.3 Bioluminescence. The Luciferin—Luciferase Reactions
14.3.1 The Origin of Bioluminescence
14.3.2 Genetic Manipulations with Luciferase
14.3.3 Bioluminescence Producing Excitation Energy Transfer
14.3.4 Attractive Features of Bioluminescence
14.4 Radioluminescence and Cherenkov Effect
14.4.1 Self-illumination by Radioactive Decay
14.4.2 Optical Luminescence Excited by X-Rays
14.4.3 Emission Tomography Based on Cherenkov Effect
14.4.4 Light-Addressable Potentiometric Sensors
14.4.5 Sensor Operation Based on Photoelectrochemistry
14.4.6 Photocurrent Generation as Informative Signal
14.4.7 Applications of Photoelectrochemical Sensors
14.4.8 Photovoltaic Cell as Sensor Device
14.5 Photoacoustic Spectroscopy and Imaging
14.5.1 Generation of Photoacoustic Waves by Absorbing Light
14.5.2 Photoacoustic Tomography in Life Sciences
14.5.3 Contrast Agents for Photoacoustic Imaging
14.6 Sensing and Thinking. Coupling the Seemingly Uncoupled in Approaches to Sensing
References
15 Techniques and Devices Used in Fluorescence Sensing
15.1 Instrumentation for Fluorescence Spectroscopy
15.1.1 Standard Spectrofluorimeter
15.1.2 The Light Sources
15.1.3 Passive Optical Elements
15.1.4 The Light Detectors and Imagers
15.1.5 Practical Considerations
15.2 Miniaturized Integrated Instrumentation and Imaging with Smartphone
15.2.1 Miniaturized Integrated Optical Systems
15.2.2 Sensing and Imaging Using Lab-On-Smartphone Platforms
15.3 Optical Waveguides and Optodes
15.3.1 Optical Fiber Sensors with Optode Tips
15.3.2 Evanescent-Field Waveguides
15.4 Multi-analyte Spotted Microarrays
15.4.1 Fabrication of Biochips
15.4.2 Success and Problems with Microarray Performance
15.4.3 Read-Out and Data Analysis
15.4.4 Applications of Spotted Microarrays
15.4.5 Prospects of Spotted Microarray Technology
15.5 Suspension Arrays and Barcoding
15.5.1 Construction of Suspension Arrays
15.5.2 Reading the Information from Encoded Microspheres
15.5.3 Present and Future Applications
15.6 Microfluidic Devices
15.6.1 Fabrication and Operation of a Lab-On-A-Chip
15.6.2 Microfluidic Devices as Microscopic Reactors and Analytical Tools
15.6.3 Fluorescence Detection in Microfluidic Devices
15.6.4 Prospects for Broad-Range Practical Applications
15.7 Sensing and Thinking. Optimizing Convenience, Sensitivity and Precision
References
16 Frontiers for Future Research. Two-Photonic, Highly Excited and Single-Molecular Sensors
16.1 Two-Photon Excitation, Stimulated Emission, Lasers as Sensors
16.1.1 Two-Photon and Multi-photon Excited Fluorescence
16.1.2 Amplified Stimulated Emission
16.1.3 Laser as Prospective Sensor
16.2 Light Emission and Photoreactions from High-Energy Electronic States
16.3 Near-Field Photonics: From Imaging to Nanoplasmonics and Nanolasers
16.4 Far-Field Visualization and Sensing of Single Molecules
16.5 Single Molecular Dynamic Studies in Ultra-small Volumes
16.5.1 Operation with Ultra-small Volumes and Single Molecular Detection
16.5.2 Fluorescence Correlation Spectroscopy and Its Extensions
16.5.3 Kinetic Fingerprinting in Analysis on Single-Molecular Level
16.6 Lighting Up the Behavior of Small Systems
16.7 A Word in Conclusion
References
Index