Fluorescent analogues of biomolecular building blocks : design and applications / edited by Prof. Dr. Marcus Wilhelmsson, Prof. Dr. Yitzhak Tor. -- Hoboken, New Jersey : John Wiley & Sons Inc., c2016. – (54.646/F646)

Contents

List of Contributors

Preface

1  Fluorescence Spectroscopy

1.1  Fundamentals of Fluorescence Spectroscopy, 1

1.2  Common Fluorescence Spectroscopy Techniques, 3

1.3  Summary and Perspective, 10

References, 10

2  Naturally Occurring and Synthetic Fluorescent Biomolecular Building Blocks

2.1  Introduction, 15

2.2  Naturally Occurring Emissive Biomolecular Building Blocks, 16

2.3  Synthetic Fluorescent Analogs of Biomolecular Building Blocks, 18

2.4  Summary and Perspective, 31

References, 32

3  Polarized Spectroscopy with Fluorescent Biomolecular Building Blocks

3.1   Transition Moments, 40

3.2  LinearDichroism, 41

3.3  Magnetic Circular Dichroism, 45

3.4  F~rster Resonance Energy Transfer (FRET), 46

3.5  Fluorescence Anisotropy, 47

3.6  Fluorescent Nucleobases, 47

3.7  Fluorescent Peptide Chromophores, 48

3.8  Site-Specific Linear Dichroism (SSLD), 50

3.9  Single-Molecule Fluorescence Resonance Energy Transfer (smFRET), 50

3.10 Single-Molecule Fluorescence-Detected Linear Dichroism (smFLD), 51

References, 53

4  Fluorescent Proteins: The Show Must go on!

4.1  Introduction, 55

4.2  Historical Survey, 55

4.3  Photophysical Properties, 57

4.4  Photochemical Reactions, 71

4.5  Ion Sensitivity, 75

4.6  Relation Microscopy-Spectroscopy for Fluorescent Proteins, 77

4.7  Prospects and Outlook, 82

Acknowledgments, 82

References, 82

5  Design and Application of Autofluorescent Proteins by Biological Incorporation of Intrinsically Fluorescent Noncanonical Amino Acids                91

5.1  Introduction, 91

5.2  Design and Synthesis of Fluorescent Building Blocks in Proteins, 97

5.3  Application of Fluorescent Building Blocks in Proteins, 111

5.4  Conclusions, 117

5.5  Prospects and Outlook, 118

Acknowledgments, 120

References, 120

6  Fluoromodules: Fluorescent Dye-Protein Complexes for Genetically Encodable Labels                                             124

6.1   Introduction, 124

6.2  Fluoromodule Development and Characterization, 126

6.3  Implementation, 132

6.4  Conclusions, 134

6.5  Prospects and Outlook, 134

Acknowledgments, 134

References, 134

7  Design of Environmentally Sensitive Fluorescent Nucleosides and their Applications                                         137

7.1   Introduction, 137

7.2  Solvatochromic Fluorescent Nucleoside Analogs, 140

7.3  Fluorescently Labeled Nucleosides and Oligonucleotide Probes: Covalent Attachment of Solvatochromic Fluorophores Onto the Natural Bases, 141

7.4  Nucleosides with Dual Fluorescence for Monitoring DNA Hybridization, 153

7.5  Approach for Developing Environmentally Sensitive Fluorescent (ESF) Nucleosides, 154

7.6  Base-Selective Fluorescent ESF Probe, 163

7.7  Molecular Beacon (MB) and ESF Nucleosides, 167

7.8  Summary and Future Outlook, 169

Acknowledgments, 170

References, 170

8  Expanding The Nucleic Acid Chemist's Toolbox: Fluorescent Cytidine Analogs

8.1  Introduction, 174

8.2  Design and Characterization of Fluorescent C Analogs, 176

8.3  Implementation, 190

8.4  Conclusions, 202

8.5  Prospects and Outlook, 202

Acknowledgments, 203

References, 203

9  Synthesis and Fluorescence Properties of Nucleosides with Pyrimidopyrimidine-Type Base Moieties                          208

9.1  Introduction, 209

9.2  Discovery, Design, and Synthesis of Pyrimidopyrimidine Nucleosides, 209

9.3  Implementation, 215

9.4  Conclusions, 220

9.5  Prospects and Outlook, 221

References, 221