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Fluorescent Analogs of Biomolecular Building Blocks : Design and Applications.

By: Contributor(s): Material type: TextTextPublisher: Newark : John Wiley & Sons, Incorporated, 2016Copyright date: ©2016Edition: 1st edDescription: 1 online resource (475 pages)Content type:
  • text
Media type:
  • computer
Carrier type:
  • online resource
ISBN:
  • 9781119179344
Subject(s): Genre/Form: Additional physical formats: Print version:: Fluorescent Analogs of Biomolecular Building BlocksDDC classification:
  • 572.33
LOC classification:
  • QP519.9.F56 -- F58 2016eb
Online resources:
Contents:
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.
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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.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.

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