FRET - F rster Resonance Energy Transfer

FRET - Förster Resonance Energy Transfer Meeting the need for an up-to-date and detailed primer on all aspects of the topic, this ready reference reflects the incredible expansion in the application of FRET and its derivative techniques over the past decade, especially in the biological sciences. This wide diversity is equally mirrored in the range of expert contributors.

The book itself is clearly subdivided into four major sections. The first provides some background, theory, and key concepts, while the second section focuses on some common FRET techniques and applications, such as in vitro sensing and diagnostics, the determination of protein, peptide and other biological structures, as well as cellular biosensing with genetically encoded fluorescent indicators. The third section looks at recent developments, beginning with the use of fluorescent proteins, followed by a review of FRET usage with semiconductor quantum dots, along with an overview of multistep FRET. The text concludes with a detailed and greatly updated series of supporting tables on FRET pairs and Förster distances, together with some outlook and perspectives on FRET.

Written for both the FRET novice and for the seasoned user, this is a must-have resource for office and laboratory shelves.

Auteur

*Dr. Igor L. Medintz obtained his B.S. and M.S in Forensic Science, followed by a Ph.D. degree in Molecular Biology in 1998 at the City University of New York. He carried out research as a postdoctoral fellow at the University of California Berkeley as well as at U.S. Naval Research Laboratory (NRL) in Washington, D.C. Since 2004, he has been a Research Biologist at NRL where he focuses on developing chemistries to interface nanomaterials with biology and understanding how nanoparticles engage in different types of energy transfer.*

*Professor Niko Hildebrandt obtained a Diploma in Medical Physics in 2001 at the University of Applied Sciences Berlin and a Ph.D. degree in Physical Chemistry in 2007 at the University of Potsdam, where he also carried out postdoctoral research until 2008. From 2008 to 2010 he was head of the group NanoPolyPhotonics at the Fraunhofer Institute for Applied Polymer Research in Potsdam. Since 2010 he has been Full Professor at Université Paris-Sud, where he is leading the group of NanoBioPhotonics (www.nbp.ief.u-psud.fr) at the Institut d'Electronique Fondamentale with a research focus on time-resolved FRET spectroscopy and imaging for multiplexed nanobiosensing.*

Contenu
Preface xv

List of Contributors xix

Part One Background, Theory, and Concepts 1

1 How I Remember Theodor Forster 3
Herbert Dreeskamp

2 Remembering Robert Clegg and Elizabeth Jares-Erijman and Their Contributions to Fret 9
Thomas M. Jovin

2.1 Biographical Sketch of Bob Clegg 10

2.2 Biographical Sketch of Eli Jares-Erijman 11

2.3 The Pervasive Influence of Gregorio Weber 12

2.4 Contributions by Bob Clegg to Fret 12

2.5 Contributions by Eli Jares-Erijman to FRET 16

2.6 A Final Thought 18

References 19

3 Forster Theory 23
B. Wieb van der Meer

3.1 Introduction 23

3.2 Pre-Förster 23

3.3 Bottom Line 25

3.4 9000-Form, 9-Form, and Practical Expressions of the *R*06Equation 26

3.5 Overlap Integral 28

3.6 Zones 31

3.7 Transfer Mechanisms 33

3.8 Kappa-Squared Basics 34

3.9 Ideal Dipole Approximation 35

3.10 Resonance as an All-or-Nothing Effect 36

3.11 Details About the All-or-Nothing Approximation of Resonance 39

3.12 Classical Theory Completed 41

3.13 Oscillator Strength-Emission Spectrum Relation for the Donor 42

3.14 Oscillator Strength-Absorption Spectrum Relation for the Acceptor 43

3.15 Quantum Mechanical Theory 44

3.16 Transfer in a Random System 47

3.17 Details for Transfer in a Random System 48

3.18 Concentration Depolarization 51

3.19 Fret Theory 1965-2012 52

References 59

4 Optimizing the Orientation Factor Kappa-Squared for More Accurate Fret Measurements 63
B. Wieb van der Meer, Daniel M. van der Meer, and Steven S. Vogel

4.1 Two-Thirds or Not Two-Thirds? 63

4.2 Relevant Questions 65

4.3 How to Visualize Kappa-Squared? 65

4.4 Kappa-Squared Can Be Measured in At Least One Case 68

4.5 Averaging Regimes 70

4.6 Dynamic Averaging Regime 72

4.7 What Is the Most Probable Value for Kappa-Squared in the Dynamic Regime? 76

4.8 Optimistic, Conservative, and Practical Approaches 83

4.9 Comparison with Experimental Results 85

4.10 Smart Simulations Are Superior 90

4.11 Static Kappa-Squared 92

4.12 Beyond Regimes 101

4.13 Conclusions 102

References 103

5 How to Apply Fret: From Experimental Design to Data Analysis 105
Niko Hildebrandt

5.1 Introduction: Fret - More Than a Four-Letter Word! 105

5.2 Fret: Let's Get Started! 106

5.3 Fret: The Basic Concept 107

5.4 Fret: Inevitable Mathematics 112

5.4.1 Förster Distance (Or Förster Radius) 112

5.4.2 Fret Efficiency 113

5.4.2.1 Determination by Donor Quenching 113

5.4.2.2 Determination by Acceptor Sensitization 113

5.4.2.3 Determination by Donor Quenching and Acceptor Sensitization 114

5.4.2.4 Determination by Donor Photobleaching 115

5.4.2.5 Determination by Acceptor Photobleaching 115

5.4.3 Fret with Multiple Donors and/or Acceptors 116

5.5 Fret: The Experiment 118

5.5.1 The Donor-Acceptor Fret Pair 118

5.5.2 Förster Distance Determination 119

5.5.3 The Main Fret Experiment 122

5.5.3.1 Steady-State Fret Measurements 123

5.5.3.2 Time-Resolved Fret Measurements 130

5.5.3.3 Interpretation of Time-Resolved FRET Data 133

5.6 Fret beyond Förster 139

5.6.1 Time-Resolved Fret with Lanthanide-Based Donors 140

5.6.1.1 Terbium to Quantum Dot Fret Using Time-Resolved Donor Quenching and Acceptor Sensitization Analysis 141

5.6.2 BRET and CRET 147

5.6.3 Energy Transfer to Metal Nanoparticles (FRET, NSET, DMPET, NPILM, etc.) 148

5.6.4 Other Transfer Mechanisms 150

5.6.4.1 Electron Exchange Energy Transfer (Dexter Transfer) 151

5.6.4.2 Charge Transfer (Marcus Theory) 152

5.6.4.3 Plasmon Coupling 153

5.6.4.4 Singlet Oxygen Diffusion 154

5.7 Summary and Outlook 155

References 156

6 Materials for FRET Analysis: Beyond Traditional Dye-Dye Combinations 165
Kim E. Sapsford, Bridget Wildt, Angela Mariani, Andrew B. Yeatts, and Igor Medintz

6.1 Introduction 165

6.2 Bioconjugation 166

6.3 Organic Materials 171

6.3.1 Ultraviolet, Visible, and Near-Infrared Emitting Dyes 171

6.3.2 Quencher Molecules 173

6.3.3 Environmentally Sensitive Fluorophores 175

6.3.4 Dye-Modified Microspheres/Nanomaterials 179

6.3.5 Dendrimers and Polymer Macromolecules 180

6.3.6 Photochromic Dyes 182

6.3.7 Carbon Nanomaterials 186

6.4 Biological Materials 188

6.4.1 Natural Fluorophores 188

6.4.2 Nonnatural Amino Acids 190

6.4.3 Green Fluorescent Protein and Derivatives 192

6.4.4 Light-Harvesting Proteins 200

6.4.5 DNA-Based Macrostructures/Nanotechnology 201

6.4.6 Enzyme-Generated Bioluminescence 201

6.4.7 Enzyme-Generated Chemiluminescence 209

6.5 Inorganic Materials 211

6.5.1 Luminescent Lanthanide Complexes and Doped Nano-/ Microparticles 212

6.5.2 Luminescent Transition Metal Complexes 217

6.5.3 Noble Metal Nanomaterials (Gold, Silver, and Copper) 219

6.5.4 Silicon-Based Materials 222

6.5.5 Semiconductor Nanocrystals 223

6.6 Multi-Fret Systems 231

6.7 Summary and Outlook 236

References 236

Part Two Common Fret Techniques/Applications 269

7 In Vitro Fret Sensing, Diagnostics, and Personalized Medicine 271
Samantha Spindel, Jessica Granek, and Kim E. Sapsford

7.1 Introduction 271

7.2 Small Organic Molecules and Synthetic Organic Polymers 272

7.3 Carbohydrate-Lipid 273

7.4 The Biotin-Avidin Interaction 273

7.5 Proteins and Peptides 275

7.5.1 …