The only comprehensive database of fluorophores and their physical and photochemical properties
Fluorophores are chemical compounds that strongly absorb in the ultraviolet, visible, and/or near-infrared and with bright emission in these ranges. As a result, they are exceptionally valuable as dyes for various analytical processes, capable of labelling and staining particular targets for purposes of fluorescent imaging, sensitive detection, and quantification (exhibiting linear responses over very wide concentration ranges). These compounds are many and varied, and panoramic views of their options, physical properties and their reactions to light excitations can be critical to their successful integration into chemical analysis, pharmaceutical analysis, clinical analysis, microscopies, optical bioimaging, cancer imaging, real-time PCR, flow cytometry, multiplexing in proteomics, life sciences in general, and many other high-tech fields (material sciences, traceability, photovoltaics, quantum computing).
Fluorescent Dye Labels and Stains incorporates a comprehensive database of such substances and their characteristics. It provides an introduction to basic theories and foundational terminology, in addition to both the molecular structures and photophysical properties of an enormous range of fluorophores. Assembled over the course of a distinguished career in biochemistry, this database presents valuable information that has never before been available in a single volume.
Readers will also find: - Molecular and photochemical information of over 700 fluorophores - A database of parameters, including light excitation ranges, molar absorption coefficients, fluorescence quantum yields, molecular brightness, and many more - Information derived from multiple disciplines, including microscopy, nanoscopy, biochemistry, and molecular biology
Fluorescent Dye Labels and Stains is the essential reference for pharmaceutical and biomedical researchers and professionals, academics who study molecular biology or organic chemistry, and any professional whose work includes strong and photostable molecular absorptions and fluorescence.
Table of Contents
Preface x
Acronyms xii
Symbols and Conventionsxiii
1 Introduction 1
2 Basic Definitions and Fundamentals 5
2.1 Introduction 5
2.2 Light Sources 5
2.3 Filtering and Dispersing Light 6
2.3.1 Absorber Filters 6
2.3.2 Interference Filters 8
2.3.3 Polarizers 8
2.3.4 Prisms 9
2.3.5 Grating 9
2.4 Light Detectors 10
2.5 Light Beams 12
2.5.1 Radiant Power and Radiance in Space: Divergent and Collimated Beams 12
2.5.2 Radiant Power and Radiance in Time: Continuous, Modulated, and Pulsed 13
2.5.3 Spectral Radiant Power (Emission Spectra) of Lamps, LEDs, and Lasers 14
2.5.4 Light Wavelength, Transmittance, and Absorbance 14
2.5.5 Spontaneous Decay and Stimulated Emission in Lasers and STED Nanoscopy 16
2.5.6 Energy, Momentum, Polarization, Spin, and Angular Momentum 17
2.6 Light Collection Set-Ups 17
2.6.1 Microscope Objectives 17
2.6.2 Fluorescence Detection Set-Ups 18
2.6.3 Fluorescence Imaging Set-Ups 18
2.7 Fundamentals of Fluorescence 21
2.7.1 Fluorescence: Fields of Application 22
2.7.2 Molar Absorption Coefficient 23
2.7.3 Excitation Spectra 24
2.7.4 Emission Spectra 25
2.7.5 Stokes Shift 25
2.7.6 Fluorescence Quantum Yield 27
2.7.7 Brightness 27
2.7.8 Effective Brightness 27
2.7.9 Fluorescence Mean-Lifetime 28
2.7.10 Factors Affecting Fluorescence 29
2.7.10.1 Effect of Microenvironment 29
2.7.10.2 Influence of Liquid Viscosity on Fluorescence Quantum Yield and Fluorescence Mean-Lifetime 30
2.7.10.3 Influence of Electric Permittivity and Hydrogen Bonding 30
2.7.10.4 Effects of Temperature 31
2.7.10.5 Quenching 31
2.7.10.6 Self-Quenching 32
2.7.10.7 Singlet Oxygen Production by Sensitizer Dyes 32
2.8 Photostability 32
3 Target-Fluorophore Binding 37
3.1 Introduction 37
3.2 Choosing the Right Solvent 37
3.2.1 Water and PBS 37
3.2.2 Water Miscible Organic Solvents 39
3.3 Fluorogenic Reactions 45
3.3.1 Primary Amines 45
3.3.1.1 Fluorogenic Reactions of Primary Amines With Homocyclic o-Phthaldihaldehydes 45
3.3.1.2 Fluorogenic Reactions of Primary Amines With Heterocyclic o-Dicarboxaldehydes 49
3.3.1.3 Fluorogenic Reactions of Primary Amines With Other Reagents 49
3.3.2 Secondary Amines 52
3.3.3 Thiols 53
3.3.4 Cyanide 53
3.3.5 α-Dicarbonylic Compounds 53
3.4 Labeling Reactions 54
3.4.1 Covalent Labeling of Amines 56
3.4.2 Covalent Labeling of Thiols 57
3.4.3 Covalent Labeling of Carboxylic Acids 57
3.4.4 Covalent Labeling of Alcohols 58
3.4.5 Covalent Labeling of Reducing Saccharides 58
3.4.6 Others 60
3.5 Immunofluorescence 61
4 Classes and Molecular Structures 65
4.1 Introduction 65
4.2 Rhodamines 73
4.2.1 Rhodamines With Absorption Maximum Below 500 nm 73
4.2.2 Rhodamines With Absorption Maximum Between 500 and 550 nm 73
4.2.3 Rhodamines With Absorption Maximum Between 550 and 600 nm 73
4.2.4 Rhodamines With Absorption Maximum Above 600 nm 75
4.2.5 Rhodamines With a High Net Charge 78
4.3 HAS-Rhodamines 79
4.3.1 Carbo-Rhodamines 79
4.3.2 Silico-Rhodamines 79
4.3.3 Other HAS-Rhodamines 79
4.4 Pyronines 79
4.5 HAS-Pyronines 82
4.6 Sulforhodamines 84
4.7 HAS-Sulforhodamines 84
4.8 Fluoresceins 84
4.8.1 Non-Halogenated Fluoresceins 88
4.8.2 Halogenated Fluoresceines 89
4.8.3 Mercaptofluoresceins 91
4.8.4 Fluorescein-Analogs 91
4.9 HAS-Fluoresceins 91
4.10 Sulfofluoresceins 91
4.11 Fluorones 92
4.12 HAS-Fluorones 93
4.13 Cyanines 93
4.13.1 Trimethine Cyanines 95
4.13.2 Pentamethine Cyanines 95
4.13.3 Heptamethine Cyanines 97
4.14 Borondipyrromethenes 97
4.14.1 Small Water-Soluble Borondipyrromethenes 100
4.14.2 Medium-Sized, Water-Soluble Borondipyrromethenes 104
4.14.3 Large Water-Soluble Borondipyrromethenes 106
4.14.4 Other Classes Derived From Borondipyrromethene 108
4.15 Rhodols 109
4.15.1 The First Rhodols Synthesized 109
4.15.2 Rhodols Synthesized More Recently 109
4.15.3 Rhodol Analogs 112
4.16 HAS-Rhodols 113
4.17 Rosamines 114
4.18 HAS-Rosamines 114
4.18.1 Silico-Rosamines 114
4.18.2 Phospha-Rosamines 115
4.18.3 Other HAS-Rosamines 115
4.19 Rosols 118
4.20 HAS-Rosols 118
4.21 Pyrodols and Pyrodones 119
4.22 Trianguleniums 120
4.23 Acridines 120
4.23.1 Simple Acridines 121
4.23.2 Acridones 122
4.24 Merocyanines 122
4.25 Phenoxazines 122
4.26 Coumarins 125
4.26.1 7-Hydroxy Coumarins 125
4.26.2 Small 7-Amino Coumarins 125
4.26.3 More Elaborated 7-Amino Coumarins 126
4.27 Sulforhodols 128
4.28 Pyrenes 128
4.29 Quinolines 129
4.30 Benzothiazoles 132
4.31 Chromones 133
4.32 Naphthalimides 133
4.33 Indoles 134
4.34 Naphthalenes 135
4.35 Squaraines 137
4.36 Pteridines 137
4.37 Isoquinolines 139
4.38 Benzene Derivatives 140
4.39 Other Single Structures 140
4.39.1 Small Structures 140
4.39.2 Medium-Sized Structures 142
4.39.3 Large Structures (Na > 80) 142
4.40 Hybrid Structures 145
4.40.1 Hybrid Structures: Fusion of Two Existing Dyes 146
4.40.2 Hybrid Structures: Single Bond Connected Dyes 146
4.40.3 Hybrid Structures: Polymethine Bridged Dyes 147
4.41 Non-Disclosed Structures 148
4.42 Fluorescent Structures Other Than Small-Molecule Organic Dyes 149
5 Scattergrams of the Photophysical Properties 163
5.1 Introduction 163
5.2 Photophysical Properties Along the Spectrum 164
5.2.1 Molecular Sizes vs. λa,max 164
5.2.2 Molar Absorption Coefficients vs. λa,max169
5.2.3 Fluorescence Quantum Yield vs. λa,max 169
5.2.4 Brightness vs. λa,max 172
5.2.5 Stokes Shift vs. λa,max 173
5.2.6 Stokes Shift vs. Brightness 174
5.2.7 Fluorescence Mean-Lifetime vs. λa,max 177
5.2.8 Fluorescence Mean-Lifetime vs. Brightness 178
5.3 Fluorophore Charges 180
6 Band Shapes and Excitation and Emission Ranges 185
6.1 Introduction 185
6.2 Typical Absorption and Emission Spectra of Some Classes 187
6.3 Coarse Prediction of Excitation and Emission Ranges 191
7 Measuring Photostability and Mitigating Photobleaching 195
7.1 Introduction 195
7.2 Measuring Photostability 196
7.3 Mitigating Photobleaching 202
Appendix A A1. Short Name, Name, Class, Molecular Formula, and References 207
Appendix B B1. Ranked by Excitation Maximum 253
Appendix C C1. Ranked by Emission Maximum 297
Appendix D D1. Ranked by Stokes Shifts 335
Appendix E E1. Ranked by Brightness 371
Appendix F F1. Ranked by Fluorescence Mean-Lifetime 419
Appendix G G1. Ranked by Molecular Net Charge 433
Index 479
