Contributors |
Preface |
Volumes in Series |
A Method in Enzymology for Measuring Hydrolytic Activities in Live Cell Environments / Beverly Z. Packard ; Akira Komoriya1: |
Protease Substrate Design |
Protease Specificity / 2: |
Cell-Permeable Fluorogenic Probes / 3: |
Conclusions / 4: |
References |
Heterogeneity of Fluorescence Determined by the Method of Area-Normalized Time-Resolved Emission Spectroscopy / N. Periasamy |
Introduction |
TRES and TRANES Methods |
TRES and TRANES Spectra of Simple Cases |
Physical Significance of TRANES and Isoemissive Point |
TRES and TRANES of Fluorophores in Microheterogeneous Media / 5: |
Fluorescence in Microheterogeneous and Biological Media: Special Cases / 6: |
Acknowledgment |
Multiparametric Probing of Microenvironment with Solvatochromic Fluorescent Dyes / Andrey S. Klymchenko ; Alexander P. Demchenko |
"Universal" and "Specific" Noncovalent Interactions |
The Methodology of Multiparametric Approach with Application of 3-Hydroxyflavone Dyes |
Correlations of Spectroscopic Data with Solvatochromic Variables |
Algorithm for Multiparametric Probing Based on Parameters of Absorption and Dual Emission |
Application of Multiparametric Probing |
Limitations of the Multiparametric Approach |
Concluding Remarks / 7: |
Site-Selective Red-Edge Effects |
Molecular Disorder and the Origin of Red-Edge Effects |
The Principle of Photoselection |
Ground-State Heterogeneity |
The Magnitude of Red-Edge Excitation Fluorescence Shift and Its Connection with Dielectric Relaxations |
Red-Edge Effect with High Resolution in Time |
Red-Edge Effects in Excited-State Reactions |
Fluorescent Probes for Optimal Observation of Red-Edge Effects / 8: |
Peculiarities of the Red-Edge Effects of Indole and Tryptophan / 9: |
Fluorescence Approaches to Quantifying Biomolecular Interactions / Catherine A. Royer ; Suzanne F. Scarlata10: |
Fluorescence Observables |
Designing a Fluorescence Experiment |
Forster Resonance Energy Transfer Measurements of Transmembrane Helix Dimerization Energetics / Mikhail Merzlyakov ; Kalina Hristova |
Challenges in Quantitative Measurements of Interactions Between TM Helices in Bilayers |
Bilayer Platforms for Measuring TM Helix Interactions Using FRET |
FRET Due to Random Colocalization of Donors and Acceptors (Proximity FRET) |
FRET Efficiencies and Energetics of TM Helix Dimerization |
Biological Insights from FRET Measurements |
Conclusion |
Application of Single-Molecule Spectroscopy in Studying Enzyme Kinetics and Mechanism / Jue Shi ; Joseph Dertouzos ; Ari Gafni ; Duncan Steel |
Experimental Considerations |
Sample Preparation |
Instrumentation |
Data Analysis of Single-Molecule Trajectories |
Additional Considerations |
Summary |
Ultrafast Fluorescence Spectroscopy via Upconversion: Applications to Biophysics / Jianhua Xu ; Jay R. Knutson |
Basic Concepts |
Upconversion Spectrophotofluorometer and Experimental Considerations |
Ultrafast Photophysics of Single Tryptophan, Peptides, Proteins, and Nucleic Acids |
Summary and Future Directions |
Use of Fluorescence Resonance Energy Transfer (FRET) in Studying Protein-induced DNA Bending / Anatoly I. Dragan ; Peter L. Privalov |
Preparation of Labeled DNA Duplexes |
Fluorescence Resonance Energy Transfer |
FRET in Studying Large Protein-Induced DNA Bends |
Dependence of the Protein-induced DNA Bend on the Forces Involved in Binding |
FREt in Studying Small Protein-Induced DNA Bends |
Fluorescent Pteridine Probes for Nucleic Acid Analysis / Mary E. Hawkins |
Pteridine Analog Characteristics |
Procedures for Oligonucleotide Synthesis with Pteridine Analogs |
Characterization of Pteridine-Containing Sequences |
Applications |
Acknowledgments |
Single-Molecule Fluorescence Methods for the Analysis of RNA Folding and Ribonucleoprotein Assembly / Goran Pljevaljcic ; David P. Millar11: |
Labeling Methods |
Single-Molecule Fluorescence Detection Methods |
Diffusion Single-Pair FRET for RNA Based Systems |
Total Internal Reflection Fluorescence (TIRF) for RNA Based Systems |
Application 1: Folding of the Hairpin Ribozyme |
Application 2: Assembly of the Rev-RRE Complex |
Using Fluorophore-Labeled Oligonucleotides to Measure Affinities of Protein-DNA Interactions / Brian J. Anderson ; Chris Larkin ; Kip Guja ; Joel F. Schildbach12: |
Definitions of Fluorescence Anisotropy and Intensity |
Advantages of Fluorescence Measurements |
Disadvantages of Fluorescence Measurements |
Designing the Oligonucleotide |
Designing the Experiment |
Competition Assays for Determining Specificity |
Identifying Small Pulsatile Signals within Noisy Data: A Fluorescence Application / Michael L. Johnson ; Leon S. Farhy ; Paula P. Veldhuis ; Joseph R. Lakowicz13: |
Methods |
Results |
Discussion |
Determination of Zinc Using Carbonic Anhydrase-Based Fluorescence Biosensors / Rebecca Bozym ; Tamiika K. Hurst ; Nissa Westerberg ; Andrea Stoddard ; Carol A. Fierke ; Christopher J. Frederickson ; Richard B. Thompson14: |
Principles of CA-Based Zinc Sensing |
Transducing Zinc Binding as a Fluorescence Change |
"Free" Versus Bound Zinc Ion: Speciation |
Metal Ion Buffers |
Kinetics |
Applications: Ratiometric Determination of Free Zinc in Solution |
Preparation of Apocarbonic Anhydrase |
Intracellular Sensing with TAT Tag |
Intracellular Sensing with an Expressible CA Sensor |
Instrumentation for Fluorescence-Based Fiber Optic Biosensors / Hui-Hui Zeng ; Daniel Ohnemus ; Bryan McCranor ; Michele Cramer ; James Moffett15: |
Introduction and Rationale for Fluorescence-Based Fiber Optic Sensors |
Basic Principles of Fiber Optics for Fluorescence Sensors |
Optics and Mechanics of Fluorescence-Based Fiber Optic Sensors |
Mounting and Alignment of the Instrument |
Standards for Ratiometric and Lifetime-Based Fiber Optic Fluorescence Sensors |
Construction of Fiber Optic Probes |
Zn[superscript 2+] Probe |
Cu[superscript 2+] Probe |
Use of Fiber Optic Probes for Discrete Samples |
Operating Issues: Noise, Background, Thermal Drift, and Mode Hopping |
Field and Shipboard Use |
Author Index |
Subject Index |