Fluorescent Dye Labels and Stains: A Database of Photophysical Properties

Fluorescent Dye Labels and Stains
Contents
Preface
Acronyms
Symbols and Conventions
1 Introduction
2 Basic Definitions and Fundamentals
2.1 Introduction
2.2 Light Sources
2.3 Filtering and Dispersing Light
2.3.1 Absorber Filters
2.3.2 Interference Filters
2.3.3 Polarizers
2.3.4 Prisms
2.3.5 Grating
2.4 Light Detectors
2.5 Light Beams
2.5.1 Radiant Power and Radiance in Space: Divergent and Collimated Beams
2.5.2 Radiant Power and Radiance in Time: Continuous, Modulated, and Pulsed
2.5.3 Spectral Radiant Power (Emission Spectra) of Lamps, LEDs, and Lasers
2.5.4 Light Wavelength, Transmittance, and Absorbance
2.5.5 Spontaneous Decay and Stimulated Emission in Lasers and STED Nanoscopy
2.5.6 Energy, Momentum, Polarization, Spin, and Angular Momentum
2.6 Light Collection Set-Ups
2.6.1 Microscope Objectives
2.6.2 Fluorescence Detection Set-Ups
2.6.3 Fluorescence Imaging Set-Ups
2.7 Fundamentals of Fluorescence
2.7.1 Fluorescence: Fields of Application
2.7.2 Molar Absorption Coefficient
2.7.3 Excitation Spectra
2.7.4 Emission Spectra
2.7.5 Stokes Shift
2.7.6 Fluorescence Quantum Yield
2.7.7 Brightness
2.7.8 Effective Brightness
2.7.9 Fluorescence Mean-Lifetime
2.7.10 Factors Affecting Fluorescence
2.7.10.1 Effect of Microenvironment
2.7.10.2 Influence of Liquid Viscosity on Fluorescence Quantum Yield and Fluorescence Mean-Lifetime
2.7.10.3 Influence of Electric Permittivity and Hydrogen Bonding
2.7.10.4 Effects of Temperature
2.7.10.5 Quenching
2.7.10.6 Self-Quenching
2.7.10.7 Singlet Oxygen Production by Sensitizer Dyes
2.8 Photostability
3 Target-Fluorophore Binding
3.1 Introduction
3.2 Choosing the Right Solvent
3.2.1 Water and PBS
3.2.2 Water Miscible Organic Solvents
3.3 Fluorogenic Reactions
3.3.1 Primary Amines
3.3.1.1 Fluorogenic Reactions of Primary Amines With Homocyclic o-Phthaldihaldehydes
3.3.1.2 Fluorogenic Reactions of Primary Amines With Heterocyclic o-Dicarboxaldehydes
3.3.1.3 Fluorogenic Reactions of Primary Amines With Other Reagents
3.3.2 Secondary Amines
3.3.3 Thiols
3.3.4 Cyanide
3.3.5 α-Dicarbonylic Compounds
3.4 Labeling Reactions
3.4.1 Covalent Labeling of Amines
3.4.2 Covalent Labeling of Thiols
3.4.3 Covalent Labeling of Carboxylic Acids
3.4.4 Covalent Labeling of Alcohols
3.4.5 Covalent Labeling of Reducing Saccharides
3.4.6 Others
3.5 Immunofluorescence
4 Classes and Molecular Structures
4.1 Introduction
4.2 Rhodamines
4.2.1 Rhodamines With Absorption Maximum Below 500 nm
4.2.2 Rhodamines With Absorption Maximum Between 500 and 550 nm
4.2.3 Rhodamines With Absorption Maximum Between 550 and 600 nm
4.2.4 Rhodamines With Absorption Maximum Above 600 nm
4.2.5 Rhodamines With a High Net Charge
4.3 HAS-Rhodamines
4.3.1 Carbo-Rhodamines
4.3.2 Silico-Rhodamines
4.3.3 Other HAS-Rhodamines
4.4 Pyronines
4.5 HAS-Pyronines
4.6 Sulforhodamines
4.7 HAS-Sulforhodamines
4.8 Fluoresceins
4.8.1 Non-Halogenated Fluoresceins
4.8.2 Halogenated Fluoresceines
4.8.3 Mercaptofluoresceins
4.8.4 Fluorescein-Analogs
4.9 HAS-Fluoresceins
4.10 Sulfofluoresceins
4.11 Fluorones
4.12 HAS-Fluorones
4.13 Cyanines
4.13.1 Trimethine Cyanines
4.13.2 Pentamethine Cyanines
4.13.3 Heptamethine Cyanines
4.14 Borondipyrromethenes
4.14.1 Small Water-Soluble Borondipyrromethenes
4.14.2 Medium-Sized, Water-Soluble Borondipyrromethenes
4.14.3 Large Water-Soluble Borondipyrromethenes
4.14.4 Other Classes Derived From Borondipyrromethene
4.15 Rhodols
4.15.1 The First Rhodols Synthesized
4.15.2 Rhodols Synthesized More Recently
4.15.3 Rhodol Analogs
4.16 HAS-Rhodols
4.17 Rosamines
4.18 HAS-Rosamines
4.18.1 Silico-Rosamines
4.18.2 Phospha-Rosamines
4.18.3 Other HAS-Rosamines
4.19 Rosols
4.20 HAS-Rosols
4.21 Pyrodols and Pyrodones
4.22 Trianguleniums
4.23 Acridines
4.23.1 Simple Acridines
4.23.2 Acridones
4.24 Merocyanines
4.25 Phenoxazines
4.26 Coumarins
4.26.1 7-Hydroxy Coumarins
4.26.2 Small 7-Amino Coumarins
4.26.3 More Elaborated 7-Amino Coumarins
4.27 Sulforhodols
4.28 Pyrenes
4.29 Quinolines
4.30 Benzothiazoles
4.31 Chromones
4.32 Naphthalimides
4.33 Indoles
4.34 Naphthalenes
4.35 Squaraines
4.36 Pteridines
4.37 Isoquinolines
4.38 Benzene Derivatives
4.39 Other Single Structures
4.39.1 Small Structures
4.39.2 Medium-Sized Structures
4.39.3 Large Structures (Na > 80)
4.40 Hybrid Structures
4.40.1 Hybrid Structures: Fusion of Two Existing Dyes
4.40.2 Hybrid Structures: Single Bond Connected Dyes
4.40.3 Hybrid Structures: Polymethine Bridged Dyes
4.41 Non-Disclosed Structures
4.42 Fluorescent Structures Other Than Small-Molecule Organic Dyes
5 Scattergrams of the Photophysical Properties
5.1 Introduction
5.2 Photophysical Properties Along the Spectrum
5.2.1 Molecular Sizes vs. λa,max
5.2.2 Molar Absorption Coefficients vs. λa,max
5.2.3 Fluorescence Quantum Yield vs. λa,max
5.2.4 Brightness vs. λa,max
5.2.5 Stokes Shift vs. λa,max
5.2.6 Stokes Shift vs. Brightness
5.2.7 Fluorescence Mean-Lifetime vs. λa,max
5.2.8 Fluorescence Mean-Lifetime vs. Brightness
5.3 Fluorophore Charges
6 Band Shapes and Excitation and Emission Ranges
6.1 Introduction
6.2 Typical Absorption and Emission Spectra of Some Classes
6.3 Coarse Prediction of Excitation and Emission Ranges
7 Measuring Photostability and Mitigating Photobleaching
7.1 Introduction
7.2 Measuring Photostability
7.3 Mitigating Photobleaching
Appendix A A1. Short Name, Name, Class, Molecular Formula, and References
Appendix B B1. Ranked by Excitation Maximum
Appendix C C1. Ranked by Emission Maximum
Appendix D D1. Ranked by Stokes Shifts
Appendix E E1. Ranked by Brightness
Appendix F F1. Ranked by Fluorescence Mean-Lifetime
Appendix G G1. Ranked by Molecular Net Charge
Index
EULA