Fluorescent Analogs of Biomolecular Building Blocks

Name: Fluorescent Analogs of Biomolecular Building Blocks | Design and Applications
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Design and Applications

Marcus Wilhelmsson Yitzhak Tor(Herausgeber*in)

Wiley (Verlag)

Erschienen am 16. März 2016

448 Seiten

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Inhalt

Cover
Title Page
Copyright
Contents
List of Contributors
Preface
Chapter 1 Fluorescence Spectroscopy
1.1 Fundamentals of Fluorescence Spectroscopy
1.2 Common Fluorescence Spectroscopy Techniques
1.2.1 Steady-State Fluorescence Spectroscopy
1.2.2 Time-Resolved Fluorescence Spectroscopy
1.2.3 Fluorescence Anisotropy
1.2.4 Resonance Energy Transfer and Quenching
1.2.5 Fluorescence Microscopy and Single Molecule Spectroscopy
1.2.6 Fluorescence-Based in vivo Imaging
1.3 Summary and Perspective
References
Chapter 2 Naturally Occurring and Synthetic Fluorescent Biomolecular Building Blocks
2.1 Introduction
2.2 Naturally Occurring Emissive Biomolecular Building Blocks
2.3 Synthetic Fluorescent Analogs of Biomolecular Building Blocks
2.3.1 Synthetic Emissive Analogs of Membranes Constituents
2.3.2 Synthetic Emissive Analogs of Amino Acids
2.3.3 Synthetic Emissive Analogs of Nucleosides
2.4 Summary and Perspective
References
Chapter 3 Polarized Spectroscopy with Fluorescent Biomolecular Building Blocks
3.1 Transition Moments
3.2 Linear Dichroism
3.3 Magnetic Circular Dichroism
3.4 Forster Resonance Energy Transfer (FRET)
3.5 Fluorescence Anisotropy
3.6 Fluorescent Nucleobases
3.7 Fluorescent Peptide Chromophores
3.8 Site-Specific Linear Dichroism (SSLD)
3.9 Single-Molecule Fluorescence Resonance Energy Transfer (smFRET)
3.10 Single-Molecule Fluorescence-Detected Linear Dichroism (smFLD)
References
Chapter 4 Fluorescent Proteins: The Show Must go on!
4.1 Introduction
4.2 Historical Survey
4.3 Photophysical Properties
4.3.1 Absorption Properties and Color Hue Modification
4.3.2 Chromophore Formation
4.3.3 Fluorescence Color and Dynamics
4.3.4 Directional Properties along with Optical Transitions
4.3.5 Energy Transfer and Energy Migration
4.4 Photochemical Reactions
4.4.1 Excited-state Proton Transfer (ESPT)
4.4.2 Isomerization Reactions: Reversible Photoswitching
4.4.3 Photoconversion: Irreversible Bond Rupture
4.4.4 Other Photochemical Reactions
4.5 Ion Sensitivity
4.5.1 Ground-State Equilibria of Protonation States
4.5.2 Quenching by Small Ions
4.6 Relation Microscopy-Spectroscopy for Fluorescent Proteins
4.6.1 Brightness Alteration from Cuvette to Microscopic Experiments
4.6.2 Lessons from Microspectrometry
4.6.3 Tools for Advanced Microscopic Techniques
4.7 Prospects and Outlook
Acknowledgments
References
Chapter 5 Design and Application of Autofluorescent Proteins by Biological Incorporation of Intrinsically Fluorescent Noncanonical Amino Acids
5.1 Introduction
5.2 Design and Synthesis of Fluorescent Building Blocks in Proteins
5.2.1 Extrinsic Fluorescent Labels
5.2.2 Intrinsic Fluorescent Labels
5.2.3 Extrinsic Labels Chemically Ligated using Cycloaddition Chemistry
5.2.4 Modification of the Genetic Code to Incorporate ncAAs
5.3 Application of Fluorescent Building Blocks in Proteins
5.3.1 Azatryptophans
5.3.2 FlAsH-EDT$_2$ Extrinsic Labeling System
5.3.3 Huisgen Dipolar Cycloaddition System
5.4 Conclusions
5.5 Prospects and Outlook
5.5.1 Heteroatom-Containing Trp Analogs
5.5.2 Expanded Genetic Code-Orthogonal Pairs
Acknowledgments
References
Chapter 6 Fluoromodules: Fluorescent Dye-Protein Complexes for Genetically Encodable Labels
6.1 Introduction
6.2 Fluoromodule Development and Characterization
6.2.1 Fluorogenic Dyes
6.2.2 Fluorogen-Activating Protein (FAP) Optimization
6.2.3 Fluoromodule Recycling
6.3 Implementation
6.3.1 Fusion Constructs for Protein Tagging
6.3.2 Protein Tagging and pH Sensing
6.3.3 Super-Resolution Imaging
6.3.4 Protease Biosensors
6.4 Conclusions
6.5 Prospects and Outlook
Acknowledgments
References
Chapter 7 Design of Environmentally Sensitive Fluorescent Nucleosides and their Applications
7.1 Introduction
7.1.1 Solvatochromic Fluorophores
7.1.2 Origin of Solvatochromism
7.2 Solvatochromic Fluorescent Nucleoside Analogs
7.2.1 Designing Criteria for Solvatochromic Fluorescent Nucleosides
7.3 Fluorescently Labeled Nucleosides and Oligonucleotide Probes: Covalent Attachment of Solvatochromic Fluorophores Onto the Natural Bases
7.3.1 Base-Discriminating Fluorescent Nucleosides (BDF)
7.4 Nucleosides with Dual Fluorescence for Monitoring DNA Hybridization
7.5 Approach for Developing Environmentally Sensitive Fluorescent (ESF) Nucleosides
7.5.1 Concept for Designing ESF Nucleosides
7.5.2 Examples and Photophysical Properties of ESF Nucleosides
7.6 Base-Selective Fluorescent ESF Probe
7.6.1 Cytosine Selective ESF Probe
7.6.2 Thymine Selective Fluorescent ESF Probe
7.6.3 Specific Detection of Adenine by Exciplex Formation with Donor-Substituted ESF Guanosine
7.7 Molecular Beacon (MB) and ESF Nucleosides
7.7.1 Ends-Free and Self-Quenched MB
7.7.2 Single-Stranded Molecular Beacon Using ESF Nucleoside in a Bulge Structure
7.8 Summary and Future Outlook
Acknowledgments
References
Chapter 8 Expanding The Nucleic Acid Chemist's Toolbox: Fluorescent Cytidine Analogs
8.1 Introduction
8.2 Design and Characterization of Fluorescent C Analogs
8.2.1 1,3-Diaza-2-Oxophenothiazine (tC)
8.2.2 1,3-Diaza-2-Oxophenoxazine (tCO)
8.2.3 7-Nitro-1,3-Diaza-2-Oxophenothiazine (tCnitro)
8.2.4 G-Clamp and 8-oxoG-Clamp
8.2.5 C and Cf
8.2.6 Benzopyridopyrimidine (BPP)
8.2.7 Napthopyridopyrimidine (NPP)
8.2.8 dChpp
8.2.9 dChpd, dCmpp, dCtpp, dCppp
8.2.10 dCPPI
8.2.11 dxC
8.2.12 rxC
8.2.13 Methylpyrrolo-dC (MepdC)
8.2.14 5-(Fur-2-yl)-2'-Deoxycytidine (CFU)
8.2.15 Thiophen-2-yl pC
8.2.16 Thiophene Fused pC
8.2.17 Thieno[3,4-d]-Cytidine (thC)
8.2.18 Triazole Appended
8.3 Implementation
8.3.1 PNA
8.3.2 DNA
8.3.3 RNA
8.4 Conclusions
8.5 Prospects and Outlook
Acknowledgments
References
Chapter 9 Synthesis and Fluorescence Properties of Nucleosides with Pyrimidopyrimidine-Type Base Moieties
9.1 Introduction
9.2 Discovery, Design, and Synthesis of Pyrimidopyrimidine Nucleosides
9.2.1 Synthesis and Fluorescence Properties of dChpp
9.2.2 Design, Synthesis, and Fluorescence Properties of dCPPP, dCPPI, and dCPPI Derivatives
9.2.3 Fluorescence Properties of the Oligonucleotides Containing dCPPI
9.3 Implementation
9.3.1 Application to a DNA Triplex System
9.3.2 Double Labeling of an Oligonucleotide with dCPPI and 2-Aminopurine
9.4 Conclusions
9.5 Prospects and Outlook
References
Chapter 10 Forster Resonance Energy Transfer (FRET) Between Nucleobase Analogues-a Tool for Detailed Structure and Dynamics Investigations
10.1 Introduction
10.2 The Tricyclic Cytosine Family
10.2.1 Structural Aspects, Dynamics, and Ability to Serve as Cytosine Analogs
10.2.2 Photophysical Properties
10.3 Development of the First Nucleic Acid Base Analog FRET Pair
10.3.1 The Donor-Acceptor Pair tCO-tCnitro
10.3.2 Applications of Tricyclic Cytosines in FRET Measurements
10.4 Conclusions
10.5 Prospects and Outlook
Acknowledgments
References
Chapter 11 Fluorescent Purine Analogs that Shed Light on DNA Structure and Function
11.1 Introduction
11.2 Design, Photophysical Properties, and Applications of Purine Mimics
11.2.1 Early Examples of Fluorescent Purine Mimics
11.2.2 Chromophore-Conjugated Purine Analogs
11.2.3 Pteridines
11.2.4 Isomorphic Purine Analogs
11.2.5 Fused-Ring Purine Analogs
11.2.6 Substituted Purine Derivatives
11.3 Implementation
11.3.1 Probing G-Quadruplex Structures with 2PyG
11.3.2 Energy Transfer Quantification
11.3.3 Metal-Ion Localization to N7
11.4 Conclusions
11.5 Prospects and Outlook
Appendix
References
Chapter 12 Design and Photophysics of Environmentally Sensitive Isomorphic Fluorescent Nucleosides
12.1 Introduction
12.2 Designing Environmentally Sensitive Emissive Nucleosides
12.2.1 Structural and Electronic Elements that Impart Environmental Sensitivity
12.2.2 Sensitivity to Polarity
12.2.3 Sensitivity to Viscosity
12.2.4 Sensitivity to pH
12.3 Two Isomorphic Environmentally Sensitive Designs
12.4 Probing Environmental Sensitivity
12.4.1 Probing Sensitivity to Polarity
12.4.2 Probing Sensitivity to Viscosity
12.4.3 Probing Sensitivity to pH
12.5 Recent Advancements in Isomorphic Fluorescent Nucleoside Analogs
12.6 Summary
12.7 Prospects and Outlook
Acknowledgments
References
Chapter 13 Site-Specific Fluorescent Labeling of Nucleic Acids by Genetic Alphabet Expansion Using Unnatural Base Pair Systems
13.1 Introduction
13.2 Development of Unnatural Base Pair Systems and Their Applications
13.2.1 Site-Specific Fluorescent Labeling of DNA by Unnatural Base Pair Replication Systems
13.2.2 Site-Specific Fluorescent Labeling of RNA by Unnatural Base Pair Transcription Systems
13.3 Implementation
13.3.1 Fluorescence Sensor System Using an RNA Aptamer by Fluorophore-Linked y Labeling
13.3.2 Local Structure Analyses of Functional RNA Molecules by s Labeling
13.4 Conclusions
13.5 Prospects and Outlook
Acknowledgments
References
Chapter 14 Fluorescent C-Nucleosides and their Oligomeric Assemblies
14.1 Introduction
14.2 Design, Synthesis, Characterization, and Properties of Fluorescent C-Glycoside Monomers
14.2.1 Design of Fluorescent C-Glycoside Monomers
14.2.2 Synthesis of Fluorescent C-Glycoside Monomers
14.2.3 Characterization and Properties of Fluorescent C-glycoside Monomers
14.3 Implementation of Fluorescent C-Glycoside Monomers
14.3.1 Environmentally Sensitive Fluorophores
14.3.2 Pyrene Nucleoside in DNA Applications
14.4 Oligomers of Fluorescent C-Glycosides: Design, Synthesis, and Properties
14.4.1 Design of Fluorescent C-Glycoside Oligomers
14.4.2 Synthesis of Fluorescent C-Glycoside Oligomers
14.4.3 Characterization and Properties of Fluorescent C-Glycoside Oligomers
14.5 Implementation of Fluorescent C-Glycoside Oligomers
14.5.1 ODFs as Chemosensors in the Solution State
14.5.2 ODFs as Sensors in the Solid State
14.5.3 Alternative Designs of Oligomeric Fluorescent Glycosides
14.5.4 General Conclusions: Oligomers of Fluorescent C-glycosides
14.6 Conclusions
14.7 Prospects and Outlook
Acknowledgments
References
Chapter 15 Membrane Fluorescent Probes: Insights and Perspectives
Abbreviations
15.1 Introduction
15.2 NBD-Labeled Lipids: Monitoring Slow Solvent Relaxation in Membranes
15.3 $n$-AS Membrane Probes: Depth-Dependent Solvent Relaxation as Membrane Dipstick
15.4 Pyrene: a Multiparameter Membrane Probe
15.5 Conclusion and Future Perspectives
Acknowledgments
References
Chapter 16 Lipophilic Fluorescent Probes: Guides to the Complexity of Lipid Membranes
16.1 Introduction
16.2 Lipids, Lipid Bilayers, and Biomembranes
16.3 Lipid Phases, Phase Separation, and Lipid Ordering
16.4 Fluorescent Probes for Membrane Studies
16.4.1 Fluorescently Labeled Lipids
16.4.2 Environment-Sensitive Membrane Probes
16.4.3 Specialized Techniques Using Fluorescent Probes to Investigate Membrane Properties
16.5 Conclusions
16.6 Prospects and Outlook
Acknowledgments
References
Chapter 17 Fluorescent Neurotransmitter Analogs
17.1 Introduction
17.1.1 Structure of Neurotransmitters
17.1.2 Regulation of Neurotransmitters
17.1.3 Native Fluorescence of Neurotransmitters
17.1.4 Fluorescent Histochemical Techniques
17.2 Design and Optical Properties of Fluorescent Neurotransmitters
17.2.1 Early Examples
17.2.2 Recent Examples
17.3 Applications of Fluorescent Neurotransmitters
17.3.1 Probing Binding Pockets with Fluorescent Neurotransmitters
17.3.2 Imaging Transport and Release of Fluorescent Neurotransmitters
17.3.3 Enzyme Substrates
17.4 Conclusions
17.5 Prospects and Outlook
Acknowledgments
References
Index
Supplemental Images
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