Introduction to Fluorescence Sensing: Volume 2: Target Recognition and Imaging

Preface
Contents
1 Principles Governing Molecular Recognition
1.1 Multivalency: The Principle of Molecular Recognition
1.1.1 Multivalent Pattern of Molecular Interactions
1.1.2 Energetics and Kinetics in Molecular Recognition
1.1.3 Reversibility in Molecular Interactions and Mass Action Law
1.2 Lock-And-Key, Induced Fit, Conformation Selection and Induced-Assisted Folding Models
1.3 Realization of Principles of Molecular Recognition in Fluorescence Sensing
1.3.1 The Output Parameters Used in Fluorescence Sensors
1.3.2 Different Strategies in Fluorescence Sensing
1.4 Molecular Recognition of Different Strength and Specificity
1.4.1 Sensors Providing Strong Highly Specific Binding
1.4.2 Sensors Based on Competitive Target Binding
1.4.3 Sensors Based on Reversible Specific Binding and Operating in a Large Volume
1.5 Direct Reagent-Independent Sensing
1.6 Simultaneous Analysis of Multiple Analytes
1.6.1 Systems for Detection of Multiple Analytes
1.6.2 Specific Target Recognition Versus Pattern Recognition Sensor Arrays
1.7 Sensing and Thinking. Current Trends that Should Be Highlighted
References
2 Basic Theoretical Description of Sensor-Target Binding
2.1 Parameters that Need to Be Optimized in Every Sensor
2.1.1 The Limit of Detection and Sensitivity
2.1.2 Dynamic Range of Detectable Target Concentrations
2.1.3 The Sensor Selectivity
2.1.4 Multivalent Binding and Cooperativity
2.2 Determination of Binding Constants
2.2.1 Dynamic Association-Dissociation Equilibrium
2.2.2 Determination of Kb by Titration
2.2.3 Determination of Kb by Serial Dilutions
2.3 Modeling the Analyte Binding Isotherms
2.3.1 Receptors Free in Solution or Immobilized to a Surface
2.3.2 Bivalent and Polyvalent Reversible Target Binding
2.3.3 Reversible Binding of Analyte and Competitor
2.3.4 Reversible Interactions in a Small Volume
2.4 Kinetics of Target Binding
2.5 Formats for Fluorescence Detection
2.5.1 Linear Response Format
2.5.2 Intensity-Weighted Format
2.6 Sensing and Thinking. How to Provide the Optimal Quantitative Measure of Target Binding?
References
3 Recognition Units Built of Small Macrocyclic Molecules
3.1 Crown Ethers and Cryptands: Macrocyclic Hosts for Ions
3.2 Cavity-Forming Compounds. Structures and Properties
3.2.1 Cyclodextrins
3.2.2 Calix[n]arenes
3.2.3 Cucurbit[n]urils
3.2.4 Pillar[n]arenes
3.2.5 Comparison of Properties and Prospects of Supramolecular Macrocycles
3.3 Porphyrins and Porphyrinoids. Unique Coupling of Recognition and Reporting
3.4 Sensing and Thinking. The Recognition Properties of Parent Binders and of Their Derivatives
References
4 Sensors Based on Peptides and Proteins as Recognition Units
4.1 Designed and Randomly Synthesized Peptides
4.1.1 The Development of Peptide Sensors
4.1.2 Randomly Synthesized Peptides, Why They Do Not Fold?
4.1.3 Template-Based Approach
4.1.4 The Exploration of ‘Mini-Protein’ Concept
4.1.5 Molecular Display Including Phage Display
4.1.6 Peptide Binders for Protein Targets and the Prospects of Peptide Sensor Arrays
4.1.7 Antimicrobial Peptides and Their Analogs
4.1.8 Advantages of Peptide Technologies and Prospects for Their Development
4.2 Sensors Based on Protein-Based Display Scaffolds
4.2.1 Engineering the Binding Sites by Mutations
4.2.2 Scaffolds Employing Proteins of Lipocalin Family
4.2.3 Other Protein Scaffolds
4.3 Natural Ligand-Binding Proteins and Their Modifications
4.3.1 Bacterial Periplasmic Binding Protein (PBP) Scaffolds
4.3.2 Engineering PBPs Binding Sites and Response of Environment-Sensitive Dyes
4.3.3 Serum Albumins
4.4 Antibodies and Their Recombinant Fragments
4.4.1 Assay Formats Used for Immunosensing
4.4.2 The Types of Antibodies and Their Fragments Used in Sensing
4.4.3 Prospects for Antibody Technologies
4.5 Sensing and Thinking. The Application Range and Benefit from Peptide and Protein Sensors
References
5 Nucleic Acids as Scaffolds and Recognition Units
5.1 DNA and RNA Fragments in Hybridization-Based Sensing
5.1.1 The Types of Nucleic Acid Recognition Units
5.1.2 Fluorescence Reporting in Hybridization Assays
5.2 Nucleic Acid Aptamers
5.2.1 Selection and Production of Aptamers
5.2.2 Integration with Fluorescence-Responding Units
5.2.3 Aptamer Applications and Comparison with Other Binders
5.3 G-quadruplex-Based Analytical Sensing Platforms
5.3.1 Production and Properties of G-quadruplexes
5.3.2 Fluorescence Reporters for G-quadruplex Structures
5.3.3 Applications of G-quadruplex Sensing Technology
5.4 The DNA i-motif in Sensing
5.5 Sensing and Thinking: The Versatile Recognizing Power of Nucleic Acids
References
6 Self-assembled, Porous and Molecularly Imprinted Supramolecular Structures in Sensing
6.1 Molecular Recognition on Supramolecular Scale
6.1.1 Assembly of Organic and Inorganic Functionalities
6.1.2 The Major Building Blocks
6.1.3 Realization of Multiple Recognition Sites in Self-assembled Structures
6.2 Formation and Operation of Supramolecular Fluorescent Sensors
6.3 Fluorescence Sensing with Nanoporous and Mesoporous Materials
6.3.1 Sensing Designed on the Basis of Mesoporous Silica
6.3.2 The Hydrogel Layers in Sensor Technologies
6.3.3 Porous Structures Formed of Organic Polymers
6.3.4 Metal–Organic Frameworks
6.4 Molecularly Imprinting in the Polymer Volume
6.4.1 The Principle of Formation of Imprinted Polymers
6.4.2 The Coupling of Molecular Recognition with Reporting Functionality
6.4.3 Imprinted Polymers in the Form of Nanoparticles and Microspheres
6.4.4 Exploration of Collective Properties of Fluorescent Dye Aggregates and Conjugated Polymers
6.4.5 Nanomaterials with Molecularly Imprinted Sensing
6.4.6 Formation of Nanocomposites with Molecular Imprinting Functionalities
6.5 Sensing and Thinking: Extending the Fluorescence Sensing Possibilities with Designed and Spontaneously Formed Nano-ensembles
References
7 Fluorescence Sensing Operating at Interfaces
7.1 The Structural and Dynamic Properties of Surfaces and Interfaces
7.1.1 Gas–Liquid Interfaces
7.1.2 Liquid–Liquid Interfaces
7.1.3 Solid–Liquid Interfaces
7.1.4 Solid–Solid Interfaces
7.2 The Self-assembled Functional Surfaces
7.2.1 Formation of Functional Surfaces
7.2.2 The Active Surfaces in Active Use
7.2.3 Organic Dyes Forming Active Surfaces
7.2.4 Supported Layers of Conjugated Polymers
7.3 Preferential Location of Solutes in the Systems of Structural Heterogeneity and on Active Surfaces
7.4 Binding Affinity at Interfaces
7.5 Surface-Imprinted Sensors and Biosensors
7.5.1 Surface Imprinting on Support
7.5.2 Nanoparticle-Based Surface Imprinting
7.6 Sensing and Thinking. The Strong Contribution of Surfaces and Interfaces to Sensor Technologies
References
8 Fluorescence Sensing of Physical Parameters and Chemical Composition in Gases and Condensed Media
8.1 Sensing the Physical Parameters of Environment: Temperature and Pressure
8.1.1 Molecular Thermometry
8.1.2 Luminescence for Pressure Measurement
8.2 Fluorescence Studies in a Gas Phase
8.2.1 Optimal Receptors for the Gas State Molecules
8.2.2 Determining the Natural Gas Phase Composition
8.2.3 Detection of Hydrocarbon Gasses
8.2.4 Dangerous Compounds and Explosives
8.3 Characterization of Solvents and Their Intermolecular Interactions
8.3.1 Solvent Polarity Scaling
8.3.2 Physical Modeling of Solvent Polarity Effects
8.3.3 Wavelength-Ratiometric Response to Solvent Polarity
8.3.4 Solvent Polarity and Hydrogen Bonding
8.3.5 Preferential Solvation in Mixed Solvents
8.4 Fluorescence Probing of Molecular Dynamics in Liquid State
8.4.1 Rotating Sphere Approach
8.4.2 Segmental Probe Rotations and Their Application
8.4.3 Molecular Rotors Relaxing to TICT State
8.4.4 Dyes Exhibiting the Excited-State Planarization
8.5 Dynamics of Solvent Relaxations
8.5.1 Solvation Dynamics Studied by Time-Resolved Spectroscopy
8.5.2 Site-Selective Dynamics in Molecular Ensembles
8.6 Detection of Traces of Water in Low-Polar Liquids
8.7 Condensed-Phase Media of Special Interest: Supercritical Liquids, Ionic Liquids and Liquid Crystals
8.7.1 Molecular Structure and Dynamics in Supercritical Fluids
8.7.2 The Properties of Ionic Liquids
8.7.3 Liquid Crystals
8.8 The Structure and Dynamics in Polymers
8.8.1 Monitoring the Polymerization Process
8.8.2 Structures and Structural Transitions in Polymers
8.9 Sensing and Thinking. The Value of Information on Correlation of Macroscopic and Microscopic Variables
References
9 Quantitative Fluorescent Detection of Ions
9.1 Fluorophore-Based Determination of pH
9.2 Determination of Concentration of Cations
9.2.1 Fluorescent Sensors for Alkali and Alkaline Earth Metal Cations
9.2.2 Sensing the Transition Metal Ions
9.2.3 Detection of Heavy Metal Ions
9.2.4 Potential for λ-Ratiometric Sensing Based on Excited-State Intramolecular Proton Transfer
9.3 Sensing the Anions
9.4 Sensing and Thinking. Selecting the Ways to Apply the Principle of Wavelength-Ratiometry to Sensing Ions
References
10 Detection and Imaging of Small Molecules of Biological Significance
10.1 Gaseous Molecules of Physiological Signaling—Gasotransmitters
10.1.1 Carbon Monoxide
10.1.2 Nitric Oxide
10.1.3 Hydrogen Sulfide
10.2 Oxygen and Reactive Oxygen Species
10.2.1 Determination of Oxygen Concentration
10.2.2 Hydrogen Peroxide
10.2.3 Hypochlorous Acid/Hypochlorite
10.3 Detection of Biothiols (Cysteine, Homocysteine and Glutathione)
10.4 Biologically Relevant Phosphate Anions
10.5 Adenosine and Guanosine Triphosphates
10.6 Redox Cofactors NADH/NAD+ and NAD(P)H/ NAD(P)+
10.7 Sensing and Thinking. The Problem of Simultaneous Sensing and Imaging of Many Analytes
References
11 Detection, Structure and Polymorphism of Nucleic Acids
11.1 DNA Detection and Analysis of Its Conformation
11.1.1 Double-Stranded DNA Structures
11.1.2 Analysis of Single-Stranded DNA
11.1.3 Identification of Non-canonical DNA Forms
11.2 Recognition of Specific DNA Sequences by Hybridization
11.2.1 The Microarray ‘DNA Chip’ Hybridization Techniques
11.2.2 Sandwich Assays in DNA Hybridization
11.2.3 Molecular Beacon Technique
11.2.4 Specific DNA Sensing with the Aid of Conjugated Polymer
11.2.5 DNA Structure Recognition with Peptide Nucleic Acids
11.2.6 The Use of Nanomaterials in DNA Hybridization
11.3 Probing on the Level of Single Nucleic Acid Bases
11.3.1 Design of Local Site Responsive Sensors
11.3.2 Operation with Parameters of Fluorescence Emission
11.3.3 Probing the Single-Nucleotide Polymorphism
11.4 RNA Detection, Analysis and Imaging
11.4.1 RNA Detection in Cells
11.4.2 RNA G-quadruplexes
11.5 Sensing and Thinking. Increase of Sensitivity: Amplify the Target or the Detection System?
References
12 Fluorescence Detection of Peptides, Proteins, Glycans
12.1 Targeting Peptides
12.2 Detection of Protein Targets
12.2.1 Determination of Total Protein Content
12.2.2 Labeling the Surface of Native Proteins
12.2.3 The Recognition of Protein Surface by Small Molecules
12.2.4 Protein Sensing with Peptide, Protein and Nucleic Acid Receptors
12.2.5 Molecularly Imprinted Polymers in Protein Sensing
12.2.6 Sensor Arrays and Machine Learning Algorithms
12.3 Analysing Pathological β-Aggregated Forms of Proteins
12.3.1 Organic Dyes as the Sensors for β-Sheets
12.3.2 Following the Kinetics of Amyloid Formation
12.4 Polysaccharides and Glycoproteins
12.5 Sensing and Thinking. Precise Affinity Sensors or Chemical Noses?
References
13 Detection of Harmful Microbes
13.1 Detection and Identification of Vegetative Bacteria
13.1.1 The Whole-Cell Detection
13.1.2 Detection by Characteristic Features of Cell Surface
13.1.3 Detection Based on Bacterial Genome Analysis
13.2 Discovery and Recognition of Bacterial Spores
13.3 Identification and Analysis of Biofilms
13.4 Detection of Toxins
13.5 Sensors for Viruses
13.5.1 Nucleic Acid Based Detection
13.5.2 Recognition of Viruses by Antibodies and Aptamers
13.6 Sensing and Thinking. Future Trends in Pathogen Detection: Single-Particle Sensitivity Versus Signal Amplification
References
14 Clinical Diagnostics Ex-Vivo Based on Fluorescence
14.1 Biological Fluids Available for Sensing
14.2 Detection of Disease Biomarkers
14.2.1 Diagnostics of Cancer
14.2.2 Diagnostics with Cardiac Biomarkers
14.2.3 The Markers of Autoimmune Disorders
14.2.4 Kidney-Related Diseases
14.2.5 Neurodegenerative Diseases
14.3 Glucose Sensing in Diagnosis and Treatment of Diabetes
14.4 Uric Acid
14.5 Cholesterol
14.6 Sensing and Thinking. The Era of Digital Health is Approaching?
References
15 Imaging and Sensing Inside the Living Cells. From Seeing to Believing
15.1 Modern Fluorescence Microscopy
15.1.1 Epi-Fluorescence Microscopy
15.1.2 Total Internal Reflection Fluorescence Microscopy (TIRF)
15.1.3 Confocal Fluorescence Microscopy
15.1.4 Programmable Array Microscope
15.1.5 Two-Photon and Three-Photon Microscopy
15.1.6 Time-Resolved and Time-Gated Imaging
15.1.7 Wavelength-Ratiometric Imaging
15.1.8 Traditional Far-Field Fluorescence Microscopy: Advances and Limitations
15.2 Far-Field Super-Resolution Microscopy
15.2.1 Breaking the Diffraction Limit
15.2.2 Stimulated Emission Depletion (STED) Microscopy
15.2.3 Single Molecule Localization Microcopy
15.2.4 Structured Illumination Microscopy (SIM)
15.2.5 Correlative Light and Electron Microscopy
15.3 Sensing and Imaging on a Single Molecule Level
15.3.1 The Reason to Study Single Molecules
15.3.2 Single-Molecular Studies in Solutions
15.3.3 The Studies of Molecular Motions and Interactions
15.3.4 Single Molecules Inside the Living Cells
15.4 Site-Specific Intracellular Labeling and Genetic Encoding
15.4.1 Attachment of Fluorescent Reporter to Any Cellular Protein
15.4.2 Genetically Engineered Protein Labels
15.4.3 Co-synthetic Incorporation of Fluorescence Dyes
15.5 Advanced Nanosensors Inside the Cells
15.5.1 Fluorescent Dye-Doped Nanoparticles
15.5.2 The Quantum Dots Applications in Imaging
15.5.3 Carbon Nanoparticles in Cell Research
15.6 The Studies of Intracellular Motions
15.6.1 Single-Particle Tracking
15.6.2 Viscosimetry Inside the Living Cell
15.7 Sensing Within the Cell Membrane
15.7.1 Membrane Structure and Dynamics
15.7.2 Lipid Asymmetry and Apoptosis
15.7.3 Sensing the Membrane Potential
15.7.4 Visualizing Membrane Receptors
15.8 Sensing and Thinking. Intellectual and Technical Means to Go Deeper into Cellular Functions
References
16 Fluorescent Imaging In Vivo
16.1 Optical Properties of Biological Tissues
16.1.1 Light Propagation Through Tissues
16.1.2 Optical Windows in Near-Infrared
16.2 Fluorescence Contrast Agents and Reporters
16.2.1 Organic Dyes and Their Nanocomposites
16.2.2 Nanomaterials
16.3 Optimal Imaging Techniques
16.3.1 Imaging and Microscopy in NIR-I Window
16.3.2 Instrumentation for NIR-II Range
16.4 The Studies on the Level of Tissue Imaging
16.4.1 Contrasting the Blood Vessels and Lymph Nodes
16.4.2 Monitoring Inflammatory Diseases and Response to Therapy
16.4.3 Imaging Cancer Tissues
16.5 Fluorescence Image-Guided Surgery
16.6 Cell Tracking Inside the Living Body
16.6.1 The Procedures for Cell Labeling
16.6.2 Tracking Hematopoietic and Cancer Cells
16.6.3 Tracing the Stem Cells
16.7 Combination of Fluorescence with Photoacoustic Tomography
16.8 Sensing and Thinking. Towards the Progress in Functional Bioimaging
References
17 Phototheranostics: Combining Targeting, Imaging, Therapy
17.1 Light in Theranostics Technologies
17.2 Photothermal Therapy
17.2.1 The Choice of Wavelengths
17.2.2 The Choice of Materials
17.3 Photodynamic Therapy
17.3.1 The Factors Needed for Realizing Photodynamic Therapy
17.3.2 The Mechanisms of Tumor Destruction
17.4 Combining All Power of Phototheranostics
17.4.1 Photoactivation of Prodrugs and Controlling the Drug Release
17.4.2 Photoimmunotherapy with Near-Infrared Light
17.4.3 Non-oncological Clinical Applications
17.4.4 Photothermal and Photodynamic Inactivation of Harmful Microbes
17.5 Sensing and Thinking. The Strategy of Controlling the Diagnostics and Treatment by Light
References
18 Fluorescent Light Opening New Horizons
18.1 Genomics, Proteomics and Other ‘Omics’
18.1.1 Genomic and Gene Expression Analysis
18.1.2 The Analysis of Proteome
18.1.3 Addressing Interactome
18.1.4 Outlook. Analysis on a Single-Cellular Level
18.2 Unprecedented Scale of Complexity, How to Deal With It?
18.2.1 Combinatorial Synthetic Approach on a New Level
18.2.2 Advanced Sensors in Discovery of New Products
18.2.3 Electronic (Photonic) Noses and Tongues
18.2.4 Realizing the Pattern Recognition Principle
18.2.5 Navigating Massive Datasets: Transforming Information into Knowledge
18.3 New Level of Clinical Diagnostics
18.3.1 The Progressing Sensor Developments
18.3.2 The Sensing in Whole Blood
18.3.3 Gene-Based Diagnostics
18.3.4 Confronting the Global Virus Pandemic
18.4 Sensors Promising to Change the Society
18.4.1 Industrial Challenges and Safe Workplaces
18.4.2 Biosensor-Based Lifestyle Management
18.4.3 Wearable, Implantable and Digestible Miniature Sensors Are a Reality
18.4.4 Living in a Safe Environment and Eating Safe Products
18.5 Sensing and Thinking. Where Do We Stand and Where Should We Go?
References
Epilogue
Index