Fluorescent Analogs of Biomolecular Building Blocks E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 870

Veröffentlichungsjahr: 2016

Beschreibung

Fluorescent Analogs of Biomolecular Building Blocks focuses on the design of fluorescent probes for the four major families of macromolecular building blocks. Compiling the expertise of multiple authors, this book moves from introductory chapters to an exploration of the design, synthesis, and implementation of new fluorescent analogues of biomolecular building blocks, including examples of small-molecule fluorophores and sensors that are part of biomolecular assemblies.

Leseprobe

TABLE OF CONTENTS

TITLE PAGE

COPYRIGHT

LIST OF CONTRIBUTORS

PREFACE

1 FLUORESCENCE SPECTROSCOPY

1.1 FUNDAMENTALS OF FLUORESCENCE SPECTROSCOPY

1.2 COMMON FLUORESCENCE SPECTROSCOPY TECHNIQUES

1.3 SUMMARY AND PERSPECTIVE

REFERENCES

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

2.4 SUMMARY AND PERSPECTIVE

REFERENCES

3 POLARIZED SPECTROSCOPY WITH FLUORESCENT BIOMOLECULAR BUILDING BLOCKS

3.1 TRANSITION MOMENTS

3.2 LINEAR DICHROISM

3.3 MAGNETIC CIRCULAR DICHROISM

3.4 FÖRSTER 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 (FRET)

3.10 SINGLE-MOLECULE FLUORESCENCE-DETECTED LINEAR DICHROISM (FLD)

REFERENCES

4 FLUORESCENT PROTEINS: THE SHOW MUST GO ON!

4.1 INTRODUCTION

4.2 HISTORICAL SURVEY

4.3 PHOTOPHYSICAL PROPERTIES

4.4 PHOTOCHEMICAL REACTIONS

4.5 ION SENSITIVITY

4.6 RELATION MICROSCOPY–SPECTROSCOPY FOR FLUORESCENT PROTEINS

4.7 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

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

5.3 APPLICATION OF FLUORESCENT BUILDING BLOCKS IN PROTEINS

5.4 CONCLUSIONS

5.5 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

6 FLUOROMODULES: FLUORESCENT DYE–PROTEIN COMPLEXES FOR GENETICALLY ENCODABLE LABELS

6.1 INTRODUCTION

6.2 FLUOROMODULE DEVELOPMENT AND CHARACTERIZATION

6.3 IMPLEMENTATION

6.4 CONCLUSIONS

6.5 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

7 DESIGN OF ENVIRONMENTALLY SENSITIVE FLUORESCENT NUCLEOSIDES AND THEIR APPLICATIONS

7.1 INTRODUCTION

7.2 SOLVATOCHROMIC FLUORESCENT NUCLEOSIDE ANALOGS

7.3 FLUORESCENTLY LABELED NUCLEOSIDES AND OLIGONUCLEOTIDE PROBES: COVALENT ATTACHMENT OF SOLVATOCHROMIC FLUOROPHORES ONTO THE NATURAL BASES

7.4 NUCLEOSIDES WITH DUAL FLUORESCENCE FOR MONITORING DNA HYBRIDIZATION

7.5 APPROACH FOR DEVELOPING ENVIRONMENTALLY SENSITIVE FLUORESCENT (ESF) NUCLEOSIDES

7.6 BASE-SELECTIVE FLUORESCENT ESF PROBE

7.7 MOLECULAR BEACON (MB) AND ESF NUCLEOSIDES

7.8 SUMMARY AND FUTURE OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

8 EXPANDING THE NUCLEIC ACID CHEMIST'S TOOLBOX: FLUORESCENT CYTIDINE ANALOGS

8.1 INTRODUCTION

8.2 DESIGN AND CHARACTERIZATION OF FLUORESCENT C ANALOGS

8.3 IMPLEMENTATION

8.4 CONCLUSIONS

8.5 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

9 SYNTHESIS AND FLUORESCENCE PROPERTIES OF NUCLEOSIDES WITH PYRIMIDOPYRIMIDINE-TYPE BASE MOIETIES

9.1 INTRODUCTION

9.2 DISCOVERY, DESIGN, AND SYNTHESIS OF PYRIMIDOPYRIMIDINE NUCLEOSIDES

9.3 IMPLEMENTATION

9.4 CONCLUSIONS

9.5 PROSPECTS AND OUTLOOK

REFERENCES

10 FÖRSTER RESONANCE ENERGY TRANSFER (FRET) BETWEEN NUCLEOBASE ANALOGS – A TOOL FOR DETAILED STRUCTURE AND DYNAMICS INVESTIGATIONS

10.1 INTRODUCTION

10.2 THE TRICYCLIC CYTOSINE FAMILY

10.3 DEVELOPMENT OF THE FIRST NUCLEIC ACID BASE ANALOG FRET PAIR

10.4 CONCLUSIONS

10.5 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

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

11.3 IMPLEMENTATION

11.4 CONCLUSIONS

11.5 PROSPECTS AND OUTLOOK

REFERENCES

12 DESIGN AND PHOTOPHYSICS OF ENVIRONMENTALLY SENSITIVE ISOMORPHIC FLUORESCENT NUCLEOSIDES

12.1 INTRODUCTION

12.2 DESIGNING ENVIRONMENTALLY SENSITIVE EMISSIVE NUCLEOSIDES

12.3 TWO ISOMORPHIC ENVIRONMENTALLY SENSITIVE DESIGNS

12.4 PROBING ENVIRONMENTAL SENSITIVITY

12.5 RECENT ADVANCEMENTS IN ISOMORPHIC FLUORESCENT NUCLEOSIDE ANALOGS

12.6 SUMMARY

12.7 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

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

13.3 IMPLEMENTATION

13.4 CONCLUSIONS

13.5 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

14 FLUORESCENT C-NUCLEOSIDES AND THEIR OLIGOMERIC ASSEMBLIES

14.1 INTRODUCTION

14.2 DESIGN, SYNTHESIS, CHARACTERIZATION, AND PROPERTIES OF FLUORESCENT C-GLYCOSIDE MONOMERS

14.3 IMPLEMENTATION OF FLUORESCENT C-GLYCOSIDE MONOMERS

14.4 OLIGOMERS OF FLUORESCENT C-GLYCOSIDES: DESIGN, SYNTHESIS, AND PROPERTIES

14.5 IMPLEMENTATION OF FLUORESCENT C-GLYCOSIDE OLIGOMERS

14.6 CONCLUSIONS

14.7 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

15 MEMBRANE FLUORESCENT PROBES: INSIGHTS AND PERSPECTIVES

ABBREVIATIONS

15.1 INTRODUCTION

15.2 NBD-LABELED LIPIDS: MONITORING SLOW SOLVENT RELAXATION IN MEMBRANES

15.3 -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

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

16.5 CONCLUSIONS

16.6 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

17 FLUORESCENT NEUROTRANSMITTER ANALOGS

17.1 INTRODUCTION

17.2 DESIGN AND OPTICAL PROPERTIES OF FLUORESCENT NEUROTRANSMITTERS

17.3 APPLICATIONS OF FLUORESCENT NEUROTRANSMITTERS

17.4 CONCLUSIONS

17.5 PROSPECTS AND OUTLOOK

ACKNOWLEDGMENTS

REFERENCES

INDEX

END USER LICENSE AGREEMENT

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Guide

Cover

Table of Contents

Preface

Begin Reading

List of Illustrations

1 FLUORESCENCE SPECTROSCOPY

Figure 1.1 A simplified Jablonski diagram not including higher singlet excited states than S

1

.

Figure 1.2 Absorption (dashed lines) and fluorescence (solid lines) spectra of 5-(thiophen-2-yl)-6-aza-uridine in water (black) and dioxane (gray). Annotations illustrate the most important parameters that can be obtained. The difference in Stokes shift in water and dioxane reveals the environmental polarity sensitivity of this isomorphic fluorescent nucleoside.

Note:

Stokes shifts are typically reported in energy units, commonly cm

−1

.

2 NATURALLY OCCURRING AND SYNTHETIC FLUORESCENT BIOMOLECULAR BUILDING BLOCKS

Figure 2.1 Naturally occurring fluorescent biomolecular building blocks.

Figure 2.2 Examples of noncovalent, polar head group, on-chain, chain-end, and in-chain fluorescent membrane probes.

Figure 2.3 Examples of emissive amino acid analogs 7azaTrp (

16

), 1PyrAla (

17

), NBDAla (

18

), 51dansylAla (

19

), 6DMNA (

20

), and Aladan (

21

).

Figure 2.4 Selected examples of fluorescent nucleoside surrogates.

3 POLARIZED SPECTROSCOPY WITH FLUORESCENT BIOMOLECULAR BUILDING BLOCKS

Figure 3.1 Schematic showing the molecular fixed (lower case

x

,

y

,

z

) and laboratory coordinate systems (upper case , , ). The projection of the transition moment, , on the molecule axis is shown by the angles , , and .