Advanced Fluorescence Reporters in Chemistry and Biology II (eBook)

Advanced Fluorescence Reporters in Chemistry and Biology II 3
Molecular Constructions, Polymers and Nanoparticles 3
Series Editor 5
Aims and Scope 5
Preface 7
Contents 9
Part I: General Aspects 
11 
Nanocrystals and Nanoparticles Versus Molecular Fluorescent Labels as Reporters for Bioanalysis and the Life Sciences: A Critical Comparison 12
1 Introduction 13
2 Properties of Molecular and Nanoparticular Labels and Reporters 15
2.1 Spectroscopic Properties 15
2.1.1 Luminescent Nanocrystals and Nanoparticles 16
2.1.2 Organic Dyes 21
2.1.3 Metal Ligand Complexes 22
2.1.4 Comparison of Chromophores 23
2.2 Solubility and Aggregation 26
2.3 Thermal and Photochemical Stability 27
2.4 Cyto- and Nanotoxicity 28
3 Application of Molecular and Nanoparticulate Fluorophores 30
3.1 Coupling Chromophores to Biomolecules 30
3.2 Extra- and Intracellular Targeting of Biomolecules 32
3.3 Interactions Between Chromophores and their Microenvironment 33
3.4 Exploitation of Förster Resonance Energy Transfer 35
3.5 Multiplexing Detection Schemes 36
3.5.1 Spectral Multiplexing 36
3.5.2 Lifetime Multiplexing 37
3.6 Strategies for Signal Amplification 38
3.7 Reproducibility, Quality Assurance and Limitations 38
4 Applications of Nanoparticles: State-of-the-Art and Future Trends 40
5 Conclusions 42
References 42
Optimization of the Coupling of Target Recognition and Signal Generation 50
1 Introduction 51
2 Channels of Communication between Binding Site and Fluorophore 53
2.1 pi-Conjugated Binding Site and Fluorophore 55
2.2 Spacer-Separated Binding Site and Fluorophore 59
2.2.1 Single Binding Site-Single Fluorophore Architectures 59
2.2.2 Single Binding Site-Double or Multi Fluorophore Architectures 63
3 Strategies of Signal Optimization in Fluorescent Probes 65
3.1 Combinatorial Synthesis of Functional Fluorophores 66
3.2 Design of Communication Channels for ``Light-Up´´ Probes 66
3.2.1 For Metal Cations 67
3.2.2 For Anions 70
4 Strategies of Signal Amplification 74
4.1 Chemical Reactions 74
4.1.1 Transformation of a Leuko Dye into a Fluorophore (Chemodosimeter) 75
4.1.2 Catalytic Production of Fluorophores 78
4.1.3 Systems Based on Chemi- and Bioluminescence 80
4.2 Displacement of Fluorophores from Binding Sites 83
4.3 Increasing the Number of Fluorophores per Binding Site 86
4.4 Involving Fluorophore Communication 90
4.4.1 In Conjugated Polymers 91
4.4.2 In Nano- and Microparticles 92
4.4.3 In Dendrimers 93
4.5 Resonance Energy Transfer 95
4.5.1 Förster/Fluorescence Resonance Energy Transfer 97
4.5.2 Bioluminescence Resonance Energy Transfer 101
5 Conclusion 101
6 Further Reading 104
References 105
Collective Effects Influencing Fluorescence Emission 116
1 Introduction 117
2 Spectroscopy of Intermolecular Interactions 118
2.1 Universal Intermolecular Interactions 118
2.2 Hydrogen Bonding in the Ground and Excited States 120
2.3 Excimers and Exciplexes 121
3 Resonance Interactions between Fluorophores 122
3.1 Electron Exchange Interactions 122
3.2 Förster Resonance Energy Transfer 122
4 Site-Selective Red-Edge Effects 123
5 Collective Effects Observed with Organic Dyes 125
5.1 Superquenching, Concentrational Quenching, and Directed Homo-FRET 126
5.2 Wavelength Converting 127
5.3 Light-Harvesting (Antenna) Effects 129
5.4 Red-Edge Effects in Energy Transfer 130
6 Collective Effects in Nanocomposites 131
6.1 FRET Modulation of Reporter Lifetime 131
6.2 Plasmonic Enhancement 132
7 Realization of Collective Effects in Sensing and Imaging Technologies 133
7.1 Collective Effects in Sensing 133
7.2 Collective Effects in Imaging 134
8 Concluding Remarks 135
References 136
Part II: Encapsulated Dyes and 
142 
Fluorescent J-Aggregates and Their Biological Applications 143
1 Introduction 144
2 Molecular Aggregates and Their Spectroscopic Properties 144
3 Aggregation in Water Solutions 147
4 Biomembrane-Induced Dye Aggregation 151
5 J-Aggregates Formed on DNA 154
6 Proteins as the Templates for Aggregate Formation 159
7 Membrane Potential-Sensitive Aggregates of the Dyes JC-1 and JC-9 for Mitochondria Imaging 162
8 Possibilities of Application of J-Aggregates in Fluorescent Detection and Testing of the Objects of Biological Origin 163
References 163
Conjugates, Complexes, and Interlocked Systems Based on Squaraines and Cyanines 166
1 Introduction 167
2 Dye-Cyclodextrins 168
3 Dye-Cucurbiturils 174
4 Squaraine Rotaxanes 176
5 Dye-Macromolecule Complexes 187
6 Microporous Solid-Phase Encapsulated Dyes 189
7 Fluorophore - Metallic Nanoparticle Compositions 190
8 Concluding Remarks 192
References 193
Part III: Dye-Doped Nanoparticles and 
198 
Dye-Doped Polymeric Particles for Sensing and Imaging 199
1 Introduction 200
2 Materials Used for Preparation of the Dye-Doped Beads 200
2.1 Monomers and Polymers 200
2.2 Dyes 201
2.3 Functional Additives 206
3 Fabrication Techniques 207
3.1 Preparation of Stained Beads During Polymerization 207
3.2 Staining of the Beads via Surface Modification 208
3.3 Staining by Swelling 209
3.4 Preparation of Stained Beads via Precipitation 209
3.5 Techniques for Preparation of Dye-Doped Microbeads 210
3.6 Purification of the Beads 211
4 Optical Read-Out Schemes 211
5 Selected Examples of Dye-Doped Polymeric Bead Materials 212
5.1 Water-Dispersible Nanosensors 212
5.1.1 Beads for Sensing and Imaging of Oxygen 213
5.1.2 Beads for Sensing and Imaging of pH 215
5.1.3 Beads for Sensing and Imaging of Ionic Species 216
5.1.4 Beads for Sensing and Imaging of Metabolites 217
5.1.5 Beads for Detection of Reactive Oxygen Species 218
5.2 Dye-Doped Beads as Labels 218
5.3 Dye-Doped Beads in Composite Materials 220
5.4 Sensor Arrays Based on Dye-Doped Beads 221
5.4.1 Suspension Arrays 221
5.4.2 Randomly-Ordered Bead Arrays 223
5.5 Magnetic Dye-Doped Polymeric Beads 224
5.5.1 Applications of Fluorescently Labeled Magnetic Beads 225
5.5.2 Magnetic Optical Sensor Particles 226
5.6 Dye-Doped Beads for Other Applications 227
6 Concluding Remarks 227
References 228
Silica-Based Nanoparticles: Design and Properties 235
1 Introduction 236
2 Design of Dye-Doped Silica Nanoparticles 237
2.1 Synthesis of Silica Nanoparticles 238
2.1.1 Stöber Method 238
2.1.2 Reverse Microemulsion Method 239
2.1.3 Manipulation of the Size of Silica Nanoparticles 239
2.2 Methods of Doping Dye Molecules into Silica Nanoparticles 240
2.2.1 Covalent Binding 240
2.2.2 Electrostatic Interaction 241
2.2.3 Water Solubility 242
2.3 Configurations of DDSNs 242
2.3.1 Doping Multiple Dye Molecules 242
2.3.2 Core-Shell Configurations 243
3 Properties of DDSNs 244
3.1 Fluorescence Intensity 245
3.2 Quantum Yield and Lifetime 246
3.3 Photostability of DDSNs 247
3.4 Fluorescence Enhancement 247
3.5 Solubility 250
3.6 Reaction Kinetics of Doped Molecules 251
3.7 Toxicity of DDSNs 252
4 Conclusions 254
References 254
Luminescent Dendrimers as Ligands and Sensors of Metal Ions 258
1 Introduction 258
2 Luminescent Dendrimers Hosting Nonluminescent Metal Ions 261
2.1 Luminescent Dendrimers Hosting Innocent Metal Ions 261
2.1.1 Dendrimers with a Cyclam Coordinating Core 261
2.1.2 Dendrimers with Multiple Amide Coordinating Units 267
2.2 Luminescent Dendrimers Hosting Metal Ion Quenchers 268
2.2.1 Dendrimers with Multiple Amine Coordinating Units 268
2.2.2 Dendrimers with a Cyclam Coordinating Core 270
3 Luminescent Dendrimers Hosting Luminescent Metal Ions 274
3.1 Dendrons with a Coordinating Focal Point 275
3.2 Dendrimers with Amide Coordinating Units 277
3.3 Dendrimers with a Cyclam Coordinating Core 280
4 Conclusions 283
References 283
Prospects for Organic Dye Nanoparticles 290
1 Introduction: Organic Dye Nanoparticles Exhibit Unique Physicochemical Properties 291
2 How to Synthesize Organic Dye Nanoparticles: Preparation Strategies 293
2.1 Reprecipitation Method 294
2.2 Ion-Association Method 295
3 Optical Properties of Organic Dye Nanoparticles 296
3.1 Photocatalytic Properties 296
3.2 Size-Dependent Spectroscopic Properties 297
3.3 Why Can Organic Dye Nanoparticles Be Fluorescent? 300
3.3.1 Aggregation-Induced Enhanced Emission 300
3.3.2 Highly Fluorescent Organic Dye Nanoparticles 301
4 Concluding Remarks and Outlook 305
References 307
Part IV: 
310 
Few-Atom Silver Clusters as Fluorescent Reporters 311
1 Introduction 312
2 Metal Clusters: The Missing Link Between Single Atoms and Plasmonic Nanoparticles 313
3 Terminology 314
4 Synthesis of Fluorescent Silver Clusters in Various Scaffolds and Their Application as Bio-Labels 315
4.1 DNA Oligonucleotides 315
4.2 Proteins and Peptides 321
4.3 Polymers and Dendrimers 325
4.4 Transfer of Silver Clusters Between Scaffolds 327
5 Silver Clusters as Fluorescent Probes for Molecular Sensors 329
5.1 Quenching 329
5.2 Analyte-Induced Synthesis of Fluorescent Silver Clusters 330
5.3 Wavelength-Shifting 331
6 Conclusion 332
References 333
Luminescent Quantum Clusters of Gold as Bio-Labels 337
1 Introduction 338
2 History of Clusters in the Condensed Phase 339
3 Synthetic Approaches 339
3.1 Synthesis From Au3+ Ions 340
3.2 Formation of Quantum Clusters Inside the Cavities of Biologically Relevant Molecules as well as Biomolecules 341
3.3 Synthesis of Quantum Clusters by the Core Etching or Core Size Reduction of Metallic Nanoparticles 341
3.4 Synthesis of Cluster From Another Cluster 342
4 Characterization Techniques 343
5 Stability 345
6 Electronic Structure and Optical Properties 345
7 Photoluminescence 347
7.1 Photostability 348
7.2 Luminescence Enhancement During Aqueous to Organic Phase Transfer 349
7.3 Fluorescence Resonance Energy Transfer 350
7.4 Two-Photon Emission 351
7.5 Photon Antibunching 352
7.6 Photoreactivity at Single-Cluster Level 352
7.7 Quantum Clusters as Metal Ion Sensors 354
7.8 Quantum Clusters for In Vitro Imaging 354
8 Conclusion 356
References 356
Part V: Conjugated Polymers 
358 
Structure, Emissive Properties, and Reporting Abilities of Conjugated Polymers 359
1 Introduction 359
2 Polymer Structures 360
3 OptoElectronics of Conjugated Polymers 362
4 Material Forms 364
4.1 Materials for Aqueous Applications 366
5 Signal Transduction 368
5.1 Turn-Off Sensing 368
5.1.1 ``Turn-Off´´ Detection of Small-Molecules 372
5.1.2 ``Turn-Off´´ Detection of Ions 374
5.1.3 ``Turn-Off´´ Detection of Biological Targets 375
5.2 Turn-On Sensing 377
5.2.1 ``Turn-On´´ From Quencher Displacement 378
5.2.2 ``Turn-On´´ From Change in Conjugation Length 380
5.3 Emission Wavelength Shifts and FRET 381
6 Conclusion 384
References 385
Optical Reporting by Conjugated Polymers via Conformational Changes 391
1 Introduction 392
1.1 Conjugation and Conformation-Dependent Optical Properties 392
2 Chromism 394
2.1 Thermochromism and Solvatochromism 394
2.2 pH Induced Chromic Transitions 395
3 Covalent Ligand Sensors 396
3.1 Ion Sensors 398
3.2 Biosensors 399
4 Noncovalent Ligand Sensors 401
4.1 Nucleic Acid Detection 402
4.2 Protein Detection 404
5 Direct Detection: CPs as Probes 406
5.1 Conformational Changes of Synthetic Peptides 406
5.2 Protein Aggregates 408
5.3 Novel Molecular Scaffolds for In Vivo Imaging 414
6 Concluding Remarks 416
References 416
Fluorescence Reporting Based on FRET Between Conjugated Polyelectrolyte and Organic Dye for Biosensor Applications 419
1 Introduction 420
2 DNA Biosensor 423
2.1 Assay Design 423
2.2 Influencing Factors for FRET 430
2.3 Molecular Design for Efficient FRET 432
3 Protein Biosensor 439
3.1 Antibody-Antigen Based Sensor 439
3.2 Aptamer-Based Sensor 442
3.3 CPE Complex Based Sensor 446
4 Summary 449
References 450
Index 456