Reviews in Fluorescence 2008 (eBook)

Dr. Chris D. Geddes, Ph.D., Professor, has extensive experience in fluorescence spectroscopy, particularly in fluorescence sensing and metal-fluorophore interactions (Metal-Enhanced Fluorescence), publishing over 190 papers and 18 books. Dr. Geddes is internationally known in fluorescence. He is the editor-in-chief of the Journal of Fluorescence and founding editor of the Who’s Who in Fluorescence and Annual Reviews in Fluorescence volumes. In addition, due to the labs pioneering efforts in the fields of metallic nanoparticle-fluorophore interactions, Dr. Geddes recently launched a new Springer Journal, Plasmonics, as well as a new annual hard bound book series Annual Reviews in Plasmonics. Dr. Geddes is Director of the Institute of Fluorescence, within the Medical Biotechnology Center which focuses on the nano-bio-technological applications of fluorescence. Dr. Geddes is currently the chair of 1 NIH study section, a frequent member of the NIBIB special emphasis sensing panels and a permanent member of the NIH EBT study section. http://theinstituteoffluorescence.com/

Preface 5
Contents 6
Contributors 8
Fluorescence Anisotropy to Study the Preferential Orientation of Fluorophores in Ordered Bi-Dimensional Systems: Rhodamine 6G/Laponite Layered Films 13
1 Introduction 13
2 Fluorescence Anisotropy in Ordered Bi-Dimensional Systems 15
3 Dye/Clay Systems: Film Characterization 22
4 Dye Orientation in Ordered Clay Films. A Fluorescence Anisotropy Study 30
5 Conclusions 41
References 41
Room Temperature Tryptophan Phosphorescence of Proteins in the Composition of Biological Membranes and Solutions 48
1 Introduction 48
2 Room Temperature Tryptophan Phosphorescence of Proteins of Isolated Human Erythrocyte Membranes 52
3 Room Temperature Tryptophan Phosphorescence of Plant Lectins in Solution 60
3.1 Concanavalin A (Con A) 61
3.2 Phytohemagglutinin-L (PHA-L) 65
3.3 Wheat Germ Agglutinin (WGA) 68
3.4 Peanut Agglutinin (PNA) 69
3.5 Pisum sativum Agglutinin (PSA) 70
3.6 Sambucus nigra Agglutinin (SNA-I) 72
3.7 Laburnum anagyroides Lectin (LAL) 72
3.8 Solanum tuberosum Agglutinin (STA) 72
References 74
Rational Design of FRET-Based Sensor Proteins 79
1 Introduction 79
2 Factors That Affect the Ratiometric Change in FRET-Based Sensor Proteins 81
3 Quantitative Understanding of Energy Transfer by Modeling the Conformational Behavior of Flexible Linkers 83
4 Quantitative Understanding of the Effect of Flexible Peptide Linkers on Effective Concentration 86
5 Chelating Fluorescent Protein Chimeras as Efficient Zn(II) Sensor Proteins 89
6 Taking Advantage of Stickiness: FRET Sensor Proteins Based on Conformational Switching 93
7 Conclusion and Outlook 95
References 96
Fluorescence Imaging of Calcium Loading and Mitochondrial Depolarization in Cancer Cells Exposed to Heat Stress 98
1 Introduction 99
2 Fluorescence Imaging of Mitochondrial Calcium Loading 100
2.1 The Role of Ca 2+ Inside Cells 100
2.1.1 Fluorescent Ca 2+ Indicators 103
2.2 Materials and Methods 104
3 Results 107
3.1 Cell Viability 107
3.2 Visual Evaluation of Fluorescent Ca 2+ Indicators 108
3.3 Fluorescence Imaging of Mitochondrial Transmembrane Potential 111
4 Discussion 119
5 Conclusions 121
References 123
Energy Transfer in Silica Nanoparticles: An Essential Toolfor the Amplification of the Fluorescence Signal 128
1 Introduction 128
2 The Principles of Energy Transfer Processes 129
3 The Power of Energy Transfer Processes 131
4 The Synthesis of Luminescent Silica Nanoparticles 133
5 Photophysical Properties of Luminescent Silica Nanoparticles 135
6 Conclusions 144
References 144
Spectroscopic Characterization of Plasma -- Chemically Functionalized and Fluorophore-Labeled Polymer Surfaces 147
1 Introduction 147
2 Surface Modification 149
2.1 Surface Functionalization of Polypropylene 149
2.2 Determination of Surface Functionalities with XPS 149
2.3 Fluorophore Labeling of PP Surfaces 150
3 Characterization of PP Films with Commonly Used Surface-Sensitive Techniques 153
4 Fluorescence-Based Characterization of Labeled PP Surfaces Pitfalls and Troubleshooting 155
4.1 Environment-Dependent Spectroscopic Properties 155
4.2 Spectral Correction 157
4.3 Reproducibility 157
4.4 Nonspecific Adsorption 158
4.5 Correlation of Fluorescence Measurements and XPS Characterization 160
4.6 Chromogenic and Fluorogenic Labels 161
5 Summary 164
References 164
Fluorescent Labeling and Its Effect on Hybridization of Oligodeoxyribonucleotides 169
1 Introduction 169
2 Fluorophores 170
2.1 General Characteristics of a Fluorophore 171
2.2 Synthesis of Fluorophores 171
2.2.1 4-Nitroacenaphthene (I) 172
2.2.2 4-Nitro-1,8-naphthalic Anhydride or 6-Nitro-benzo[de]isochromene-1,3-dione (II) 173
2.2.3 4-Amino-1,8-naphthalic Anhydride or 6-Amino-benzo[de]isochromene-1,3-dione (III) 173
2.2.4 4-Nitro-1,8-naphthalimido- N -caproic Acid or 6-(6-Nitro-1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-yl)-hexanoic Acid (IV) 175
2.2.5 4-Amino-1,8-naphthalimido- N -caproic Acid or 6-(6-Amino-1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-yl)-hexanoic Acid (V) 175
2.2.6 6-(6-Isobutyrylamino-1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-yl)- hexanoic Acid (1) 175
2.2.7 6-(6-Dimethylamino-1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-yl)- hexanoic Acid (2) 177
2.2.8 6-(6-Benzoylamino-1,3-dioxo-1H,3H-benzo[de]isoquinolin-2-yl)- hexanoic Acid (3) 177
2.2.9 6-(6-Amino-1-oxo-1H,3H-benzo[de]isoquinolin-2-yl)-hexanoic Acid (4) 177
2.2.10 6-(6-Amino-1H,3H-benzo[de]isoquinolin-2-yl)-hexanoic Acid (5) 178
2.3 Fluorescence Studies on Fluorophores 1--5 178
3 Synthesis of Fluorescently Labeled Nucleosides and Nucleotides 181
3.1 Generation of Linker Molecule at Nucleosides 181
3.1.1 5-(9-Fluorenylmethoxycarbonyl) Aminopentanol-1 182
3.1.2 5-[5- N -(9-Fluorenylmethoxycarbonyl)-aminopentanoxy] Uracil and 5-[5- N -(9-Fluorenylmethoxycarbonyl)-aminopentanoxy]-2 -deoxyuridine (7) 183
3.1.3 5-[5- N- (9-Fluorenylmethoxycarbonyl)-aminopentanoxy] Uracil (2 0 ,3 0 ,5 0 -tri- O -benzoyl-0- d -ribofuranose) (8) 183
3.1.4 5 0 - O -Dimethoxytrityl-4- N -(tris-4,9,13-triazatridecane-1-yl)-2 0 - deoxycytidine (9) 183
3.2 Attachment of Fluorophore at Linker Arms of Nucleosides 187
3.3 Synthesis of Labeled Phosphoramidites (10, 11, and 12) 188
3.4 Fluorescence Studies on Labelled Nucleosides and Their Phosphoramidites 189
4 Synthesis of Fluorescently Labeled Oligonucleotides 189
4.1 Labeling of Oligodeoxyribonucleotides Using Post-synthetic Modification Approach 190
4.2 Labeling of Oligodeoxyribonucleotides Using Pre-modification Approach 194
4.3 Hybridization and Fluorescence Studies on Labeled Oligodeoxyribonucleotides 195
4.4 Identification and Electrophoretic Mobility of Labeled Oligodeoxyribonucleotides 199
5 Conclusion 200
References 200
New Method for Determining Histamine Rate in Halieutic Products 203
1 Introduction 204
2 Experimental Study 206
2.1 Products Used 206
2.2 Instrumentation 206
2.3 Experimental Process 207
2.3.1 Preparation of Solutions 207
2.3.2 Preparation of Samples 207
2.3.3 Measurement of Fluorescence 207
3 Experimental Process 208
3.1 Optimization of Repetitive Dosage 208
3.1.1 Verification of the Effect of NaOH Concentration on the Formation of OPA--Histamine Complex by Repetitive Measurement 208
3.1.2 The Effect of Temperature, Formation Kinetics of OPA-- NaOH Complex 209
3.1.3 The Effect of NaCl Concentration on Fluorescence of OPA--Histamine Complex in Basic Medium 211
3.1.4 The Effect of pH on Fluorescence of OPA--Histamine Complex in Basic and Acid Medium 212
3.2 Optimization with Phosphate Buffer 219
3.2.1 Preparation of Phosphate Buffer Solution 219
3.2.2 Standard Straight line Calibration and Calculation of Detection Limits and Quantification 222
3.2.3 Determination of the Recovery by Our Experimental Method 223
3.3 Applications: Determination of Histamine Rate in Fish 223
3.3.1 Determination of Histamine Rate in Sample 1 223
3.3.2 Determination of Histamine Rate in Sample 2 224
4 General Conclusion 225
References 226
Spectroscopy of DNAActinomycin Complexes 227
1 Introduction 227
2 Emission of 7AAMD in Oligonucleotides and DNA 229
3 Negligible Energy Transfer from DNA to 7AAMD 231
4 Estimation of Size of the 7AAMD/HP1 Complex 234
5 Prompt Binding of 7AAMD to HP1 234
6 Binding of 7AAMD to DNA 236
7 Distribution of 7AAMD from HP1 to DNA 237
8 Caffeine as a Potential Carrier of AMD to DNA 238
9 Sorption of 7AAMD on Caffeine Clusters 239
10 Redistribution of 7AAMD from Caffeine Clusters to DNA 242
11 Conclusion 243
References 243
Fluorescence Spectroscopy in Optoelectronics, Photomedicine, and Investigation of Biomolecular Systems 245
1 Introduction 245
2 Fluorescence Spectroscopy as a Tool in Organic Photovoltaics 246
2.1 Fluorescence and Photovoltaics 246
2.2 Fluorescence Quenching -- Donor--Acceptor Pair in Mixed Bimolecular Systems 251
2.3 Fluorescence in Supermolecular Porphyrin--Fullerene Systems 254
2.4 Enhanced Fluorescence -- Dyes in Colloids of Metallic Particles 256
3 Dye Fluorescence for Medical Photodynamic Study 259
3.1 Spectral Properties of Dyes and their Interactions in Model Systems 260
3.2 Incorporation of Dyes into Cells 264
3.3 Photobleaching Processes vs. Photochemical Reaction 266
4 Fast Fluorescence for Studying Photosynthetic Organisms, their Fragments and Model Systems 269
4.1 Review the Advanced Techniques of Time-Resolved Fluorescence Quenching 269
4.2 Application of Ultrafast Fluorescence Spectroscopy to the Study of Dynamic Light-Induced Inter- and Intramolecular Deactivation Processes in Molecular Systems 272
5 Summary 279
References 279
Multicolor Imaging with Fluorescent Proteins in Mice 284
1 Introduction 284
1.1 GFP and Other Fluorescent Proteins as Imaging Agents 284
1.2 First Use of Fluorescent Proteins in Animals to Visualize Tumor Cells 285
1.3 First Use of Fluorescent Proteins for Whole-Body Imaging 285
1.3.1 Whole-Body Imaging of Gene Expression 286
1.3.2 Whole-Body Imaging of Angiogenesis 286
1.3.3 Whole-Body Imaging of Bacterial Infection 287
1.3.4 External Imaging Through Skin Flaps 288
1.3.5 Whole-Body Imaging of Graft--Versus-Host Disease 288
1.4 Autofluorescence Is Not a Problem with Fluorescent Protein-Based In Vivo Imaging 288
1.5 Use of Whole-Body Imaging with Fluorescent Proteins to Measure Drug Response in Real Time 289
1.6 Imaging the Relationship of Tumor Cells and Blood Vessels 290
1.7 Visualizing Cellular and Nuclear Deformation and Dynamics in Small Blood Vessels 291
1.8 Imaging Tumor Cell Deformation and Migration in Blood Vessels of Live Mice in Real Time 292
1.9 Color Coding of Cancer Cells Determines Clonality of Metastasis 292
1.10 Imageable Tumor--Host Models 293
1.11 Advantages of GFP Imaging Over Luciferase and Other Optical Imaging Techniques 294
1.12 New Features and Models with Fluorescent Proteins 296
1.13 Advantages of Fluorescent Protein Imaging Over Quantum Dots 297
1.14 Growth of Fluorescent Protein-Expressing Cells in Syngeneic Models: Lack of Apparent Immunological Response 297
2 Conclusions 298
2.1 Example of the Use of Fluorescent Proteins to Discover Properties of Stem Cells 299
2.2 Future Directions 299
2.3 Multiphoton Imaging 300
2.4 Potential Human Use of Fluorescent Proteins 301
References 302
Genetically Encoded Fluorescent and Bioluminescent Probes for Illuminating Cellular Signaling Pathways 309
1 Introduction 309
2 Second Messengers 310
2.1 Nitric Oxide (NO) 310
2.2 Inositol 1,4,5-Trisphosphate (IP3) 310
2.3 Cyclic GMP 310
2.4 Phosphatidylinositol-3,4,5-trisphosphate (PIP3) 313
3 Fluorescent Indicators for Imaging Protein Phosphorylation 316
4 ProteinProtein Interactions 317
4.1 Split-GFP is Spliced upon Protein--Protein Interactions 317
4.2 Locating a Protein--Protein Interaction by Split Renilla luciferase Complementation 319
5 Protein Localization in Organelles 321
5.1 Mitochondria-Targeting Protein 321
5.2 ER-Targeting Protein 322
5.3 Nucleocytoplasmic Trafficking of Functional Proteins 324
References 326
Fluorescent Protein FRET Applications 327
1 Introduction 327
1.1 FRET Theory 327
1.2 Practical Implications of FRET Theory 328
1.3 Common Applications of FRET 328
1.4 The RRC 329
2 Fluorescent Protein FRET Pairs 330
3 Enhancing FRET Through Directed Evolution 331
3.1 Linker Length Optimization 331
3.2 Directed Evolution of the CFP--YFP Pair 332
4 Using FRET to Screen Libraries 335
5 Future Opportunities for FRET-Based Screening 336
5.1 Protease Evolution 336
5.2 Protein Interaction Screening 337
5.3 Small Molecule Indicator Development 338
5.4 Long Wavelength FRET Pair Optimization 338
6 Conclusions 339
References 339
Imaging Protein Interactions in Living Cells Using the Fluorescent Proteins 342
1 Introduction 342
2 Spectral Variants of the Fluorescent Proteins 343
2.1 The Red Fluorescent Proteins 345
2.2 The Next Generation of Colors 345
2.3 The Photoactivatable FPs 346
3 Quantifying the Dynamic Behavior of Proteins 347
3.1 The Biological Model 347
3.2 Fluorescence Recovery After Photobleaching 347
3.3 Photoactivation 348
3.4 Multicolor Imaging of Protein Co-localization 349
4 Defining the Spatial Relationships Between Proteins 351
4.1 Fluorescence Resonance Energy Transfer 352
4.2 Spectral Bleed-Through Correction 352
4.3 Acceptor Photobleaching 353
4.4 Fluorescence Decay Measurements 355
5 Conclusions 357
References 358
Engineering Green Fluorescent Proteins Using an Expanded Genetic Code 363
1 Introduction 364
2 Major av GFP Classes Generated by Classical Methods 365
3 Expanded Amino Acid Repertoire in Protein Synthesis 366
4 Aminotryptophans and Golden Fluorescent Protein 368
4.1 Basic Features and Translational Activity of Aminotryptophans 368
4.2 Engineering Fluorescent Proteins: From Green to Gold 370
4.3 Steady-State and Dynamic Spectroscopic Features of GdFP 371
4.4 Structural Framework of Golden Fluorescence 373
4.5 Monomeric State and Temperature-Dependent Fluorescence in GdFP 375
5 Chromophores with Amino- and Methoxy-Tyrosines 376
6 Thieno- and Seleno-Pyroles in av GFP 377
7 Fluorinated Trp-Residues in av GFP 378
7.1 Global Fluorination of Trp-Residues in Proteins 378
7.2 Fluorinated Trp-Residues in ECFP and EGFP 378
7.3 Fluorinated Trp-Residues as Reporters of Chromophore Dynamics 379
8 av GFPs with Globally Fluorinated Tyr-Residues 380
8.1 Fluorinated Tyr-Residues as Substrates for Protein Synthesis 380
8.2 Chromophore Fluorination in Ortho- and Meta Positions 380
8.3 Fluorination of the Chromophore Environment in EYFP 385
9 Perspectives and Outlook 385
References 387
Fluorescent Proteins in Transgenic Plants 391
1 Introduction 391
2 FPs in Model Organisms 392
3 GFP in Transgenic Plants 393
4 GFP Variants for Plant Expression 393
5 Other Colors, Other Organisms 394
6 FP Toxicity and Allergenicity 395
7 FPs in Plant Research 397
8 Whole Plant FP Applications 397
8.1 Plant Zygosity Determination Using GFP as a Genetic Marker 397
8.2 Monitoring Transgenic Organisms 398
8.3 Environmental Monitoring 399
9 Instrumentation and Methods for FP Detection and Quantification in Plants 400
9.1 Visual Detection 400
9.2 Lab-Based FluoroMax-4 Spectrofluorometer 401
9.3 Portable Hand-Held GFP-Meter 401
9.4 Stand-Off Laser-Induced Fluorescence Detection 402
10 Customized FPs 402
11 Conclusions 404
References 404
Peptide Foldamers: From Spectroscopic Studies to Applications 408
1 Introduction 408
2 Spectroscopic Studies of Foldamer Structure in Solution 410
2.1 Secondary Structure 410
2.2 More than just a Spectroscopic Ruler: FRET as a Structural Technique 413
2.3 Molecular Mechanics Calculations 415
2.4 Validation of the Computed Structures 416
3 Selected Applications 418
3.1 Peptide Foldamers as Models of Protein Folding 418
3.2 Peptide Foldamers as Building Blocks for Molecular Devices 422
4 Conclusions 424
References 424
Circularly Polarized Luminescence (CPL) of Proteins and Protein Complexes 428
1 Introduction: What Is CPL? 429
2 How to Measure CPL? 431
2.1 Instrumentation 431
2.2 Calibration 434
2.3 Artifacts 435
3 Circularly Polarized Intrinsic Fluorescence of Proteins 436
3.1 Peptides 436
3.2 Poly(-amino acid) 436
3.3 Tyrosine and Tryptophan Residues in Proteins 438
3.4 Complexes of Proteins with Functional Non-fluorescent Agents 442
3.5 Protein Conformation Perturbation 443
4 Protein Complexes with Fluorescent Agents 444
4.1 Probes 444
4.2 Cofactors and Bilirubin 446
4.3 Lanthanides 449
4.4 Light-Harvesting Chlorophyll--Protein Complex of Photosynthetic Photosystem II (LHCII) 452
5 Conclusions 456
References 456
New Dual Fluorescent Dyes Based on Modified Excited State with Extended Conjunction Photophysical Model 463
1 Introduction and Background 464
1.1 Internal Calibration of Fluorescence Signal in Microscale Sensor Systems 464
1.2 Summary of Optical Signal Switching Arrangements 465
1.3 OR--OR Switching in a Ground State 467
1.4 OR--OR Switching in a Fast Reversible Excited-State Reaction 469
2 Results 470
3 Refined Matrix Results 474
4 Discussion 476
References 478
Index 480