Fluorescent Dyes

Jiangli Fan, PhD, is Professor at the State Key Laboratory of Fine Chemicals, Dalian University of Technology, China. Her research focuses on small-molecule fluorescent probes for bioimaging and sensing, photosensitizer-based photodynamic therapy, and targeted nanodrug delivery. She serves on the editorial boards of Dyes and Pigments and Scientific Reports, and is a recipient of China's national outstanding youth fund. Xiaojun Peng, PhD, is Director of the State Key Laboratory of Fine Chemicals at Dalian University of Technology, China, and editor-in-chief of Smart Molecules. Elected a member of the Chinese Academy of Sciences in 2017, his research covers dyes for fluorescent bioimaging, labeling, and digital printing. He has published more than 300 research papers with approximately 16,500 citations.

• Chapter 1: Introduction1.1. Development of fluorescence and phosphorescence1.2. Mechanism of fluorescence and phosphorescenceChapter 2: The Rational Design of High-Performance Near Infrared Fluorescent Dyes2.1. Introduction 2.2. Design rationale of NIR absorbing and emitting dyes2.2.1. The necessity of a D-p-A scaffold2.2.2. Further modulation of the HOMO-LUMO gap of a D-p-A scaffold2.2.3. Rigidification of D-p-A scaffold2.2.4. Steric protection of the D-p-A scaffold2.3. Conclusion and outlookChapter 3: Fluorescent Dyes for Organelle Staining3.1. Overview of organelle-staining dyes3.2. Fluorescent dye for cell membrane staining3.2.1. Biomedical functions of the cell membrane3.2.2. Cell membrane staining fluorescent dyes and their applications3.3. Fluorescent dye for mitochondrial staining3.3.1. Biomedical functions of mitochondria3.3.2. Mitochondrial staining fluorescent dyes and their applications3.4 Fluorescent dye for lysosome staining3.4.1. Biomedical functions of lysosomes3.4.2. Lysosome staining fluorescent dyes and their applications3.5 Fluorescent dye for Golgi apparatus staining3.5.1. Biomedical functions of the Golgi apparatus3.5.2. Golgi staining fluorescent dyes and their applications3.6. Fluorescent dye for endoplasmic reticulum staining3.6.1. Biomedical functions of the endoplasmic reticulum3.6.2. Fluorescent dyes for endoplasmic reticulum staining and their applications3.7. Fluorescent dye for cell nucleus staining3.7.1. Biomedical functions of the nucleus3.7.2. Nuclear staining fluorescent dyes and their applicationsChapter 4: Environment-Sensitive Fluorescent Dyes4.1. Polarity-sensitive fluorescent dyes4.1.1. Naphthalimide-based polarity-sensitive fluorescent dyes4.1.2. Coumarin-based polarity-sensitive fluorescent dyes4.1.3. Nile red-based polarity-sensitive fluorescent dyes4.1.4. Naphthalene-based polarity-sensitive fluorescent dyes4.2. Temperature-sensitive fluorescent dyes4.2.1. Organic small molecule-based temperature-sensitive fluorescent dyes 4.2.2. Polymeric macromolecule-based temperature-sensitive fluorescent dyes4.2.3. Nanomaterial-based temperature-sensitive fluorescent dyes 4.3. Viscosity-sensitive fluorescent dyes4.3.1. BODIPY-based viscosity-sensitive fluorescent dyes4.3.2. DCVJ-based viscosity-sensitive fluorescent dyes4.3.3. Cyanine-based viscosity-sensitive fluorescent dyes4.4. pH-sensitive fluorescent dyes4.4.1. pH-sensitive fluorescent dyes based on reversible protonation of amines4.4.2. pH-sensitive fluorescent dyes based on protonation of N-heterocycles4.4.3. pH-sensitive fluorescent dyes based on phenols 4.4.4. pH-sensitive fluorescent dyes based on ring-opening of rhodamine4.5. Prospects of environment-sensitive fluorescent dyes in biomedical applicationsChapter 5: Fluorescent Dyes for Intracellular Imaging of Ions 5.1. Fluorescent dyes for recognition of alkaline and alkaline earth metal ions 5.1.1. Fluorescent dyes for recognition of calcium ion5.1.2. Fluorescent dyes for recognition of magnesium ion5.1.3. Fluorescent dyes for recognition of sodium ion5.1.4. Fluorescent dyes for recognition of potassium ion5.2. Fluorescent dyes for recognition of main transition metal ions5.2.1. Fluorescent dyes for recognition of zinc ion5.2.2. Fluorescent dyes for recognition of iron and ferrous ions5.2.3. Fluorescent dyes for recognition of copper ion5.3. Fluorescent dyes for recognition of anions5.3.1. Fluorescent dyes for recognition of halide ions5.3.2. Fluorescent dyes for recognition of phosphate and pyrophosphate5.4. Fluorescent dyes for recognition of harmful heavy metal ions5.4.1. Fluorescent dyes for recognition of mercury ion5.4.2. Fluorescent dyes for recognition of cadmium ion5.4.3. Fluorescent dyes for recognition of lead ion5.4.4. Fluorescent dyes for recognition of palladium ionChapter 6: Fluorescent Dyes for Recognition of Bioactive Small Molecules6.1. Fluorescent dyes for recognition of reactive oxygen species 6.1.1. Fluorescent dyes for recognition of singlet oxygen6.1.2. Fluorescent dyes for recognition of hydrogen peroxide6.1.3. Fluorescent dyes for recognition of superoxide anion6.1.4. Fluorescent dyes for recognition of hydroxyl radical6.1.5. Fluorescent dyes for recognition of hypochlorous acid6.1.6. Fluorescent dyes for recognition of peroxynitrite6.2. Fluorescent dyes for recognition of biomercaptan compounds6.2.1. Fluorescent dyes for recognition of cysteine and homocysteine6.2.2. Fluorescent dyes for recognition of glutathione6.3. Fluorescent dyes for recognition of gasotransmitters6.3.1. Fluorescent dyes for recognition of nitric oxide6.3.2. Fluorescent dyes for recognition of hydrogen sulfide6.3.3. Fluorescent dyes for recognition of carbon monoxideChapter 7: Fluorescent Probes to Detect Enzymatic Activity7.1. Introduction7.2. Fluorescent probes for oxidoreductases7.2.1. Fluorescent probes for cyclooxygenase7.2.2. Fluorescent probes for tyrosinase7.2.3. Fluorescent probes for nitroreductase7.2.4. Fluorescent probes for monoamine oxidase7.2.5. Fluorescent probes for peroxidase7.3. Fluorescent probes for transferases7.3.1. Fluorescent probes for glutamyl transferase 7.3.2. Fluorescent probes for sulfate transferase7.3.3. Fluorescent probes for methyl transferase7.4. Fluorescent probes for hydrolases7.4.1. Fluorescent probes for proteinase 7.4.2. Fluorescent probes for carboxylesterase 7.4.3. Fluorescent probes for phosphatase7.5 ConclusionChapter 8: Development of Functional Dyes Sensing Nucleic Acid8.1. The principle of nucleic acid8.2. The categories of sensing mechanism8.2.1. Electrostatic interaction8.2.2. Groove combination8.2.3. Embedded interaction8.3. Fluorescent dyes for sensing DNA8.3.1. Alkaline dyes for DNA8.3.2. Cationic dyes8.3.3. Other dyes 8.4. Fluorescent dyes for sensing RNA8.5. Fluorescent dyes for sensing G-quadruplex8.5.1. Dyes for DNA G-quadruplex8.5.2. Dyes for RNA G-quadruplex8.6. Functional dyes or emissive compounds in living system for advanced imaging 8.6.1. Superresolution probes for nucleus8.6.2. Superresolution probes for nuclear microenvironment8.6.3. Emissive analogs of secondary messengers and cofactorsChapter 9: Development of Fluorescent Probes for Sensing and Labelling Proteins9.1. Techniques for specifically labeling of proteins9.2. Labelling strategies base on small molecule ligand9.2.1. Fluorescent probes for labelling cytoskeleton9.2.2. Fluorescent probes for labelling ATP-sensitive potassium channel protein9.3. Labelling strategies base on peptide9.3.1. a dye-tetracysteine polypeptides and similar labelling dyes9.3.2. Random screening of dye-peptide specific binding from peptide library9.4. Labelling strategies base on protein tags9.4.1. SNAP Tag 9.4.2. Halo Tag 9.5. Labelling strategies base on nucleic acid aptamers9.6. Conclusion and outlookChapter 10: Dyes with Thermally Activated Delayed Fluorescence10.1. Basic information about TADF dyes10.1.1. Concepts and luminescence mechanisms of TADF dyes10.1.2. Physical parameters involved in TADF dyes10.1.3. Molecular structures and designing principles of TADF dyes10.2. TADF dyes used as fluorescence bioimaging probes10.3. TADF dyes used as theranostic photosensitizers10.4. Perspectives in biological and medical field of TADF dyes.Chapter 11: Fluorescent Dyes for Super-Resolution Imaging11.1. Introduction 11.2. Super-resolution imaging techniques11.3. Fluorescent dyes11.3.1. Dyes for STED11.3.2. Dyes for SMLM11.4. Summary and outlookChapter 12: Fluorescent Molecular Prodrug12.1. Introduction12.2. Reductive thiol-activated prodrug systems12.3. Hydrogen peroxide-activated prodrug systems12.4. Enzyme-activated prodrug systems12.5. Acidic pH-activated prodrug systems12.6. External light-activated prodrug systemsChapter 13: Photosensitive Dyes for Photon-Triggered Cancer Therapy 13.1. Introduction13.2. Photosensitive dyes for photodynamic therapy13.2.1. Type II mechanism photosensitizers13.2.2. Type I mechanism photosensitizers13.2.3. Clinical photosensitive drugs13.3. Photosensitive dyes for photothermal therapy13.3.1. Porphyrins13.3.2. Cyanines13.3.3. Phthalocyanines13.3.4. Diketopyrrolopyrrole dyes13.3.5. Croconic acid dyes 13.3.6. Bodipys13.4. Conclusion