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Book Details
Abstract
Surface plasmon resonance (SPR) plays a dominant role in real-time interaction sensing of biomolecular binding events and with the biosensor field expanding more applications are being found. In response to the market, an update to the original title which was published in 2008 is now appropriate. With over fifty percent of the material being updated, this book provides a total system description including optics, fluidics and sensor surfaces.
Spanning theory, instrumentation and applications, it covers all the relevant issues for the practicing researcher. Unlocking the potential for SPR by showing highly exciting and unique opportunities for unraveling the functional relationships of complex biological processes, it is intended for a wide audience. A comprehensive and accessible source it contains expanded tutorial details to inspire students and guide them in this technology.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover\r | Cover | ||
| Contents | xix | ||
| Foreword to the 1st Edition | v | ||
| Foreword to the 2nd Edition | x | ||
| Preface to the 1st Edition | xiii | ||
| Preface to the 2nd Edition | xv | ||
| Chapter 1 Introduction to Surface Plasmon Resonance | 1 | ||
| 1.1 Introduction to Surface Plasmon Resonance | 1 | ||
| 1.2 What is a Biosensor? | 2 | ||
| 1.2.1 A Simple Experiment | 3 | ||
| 1.2.2 From Dip to Real-time Measurement | 4 | ||
| 1.3 How to Construct an SPR Assay | 5 | ||
| 1.3.1 The Steps of an Assay | 5 | ||
| 1.3.2 Concentration Determination | 9 | ||
| 1.3.3 Determination of Kinetic Parameters | 11 | ||
| 1.3.4 Basics of Instrumentation | 12 | ||
| 1.4 Kinetics of Biomolecular Interactions | 13 | ||
| 1.4.1 Mass Transport-controlled Kinetics | 14 | ||
| 1.4.2 Calibration-Free Concentration Analysis (CFCA) | 16 | ||
| 1.4.3 Interaction-controlled Kinetics\r | 17 | ||
| 1.4.4 Equilibrium Analysis | 19 | ||
| 1.5 Buffer Solutions for Measuring the Analysis Cycle\r | 20 | ||
| 1.5.1 Baseline or System Buffier\r | 20 | ||
| 1.5.2 Regeneration Buffer\r | 21 | ||
| 1.6 SPR-based Immunoassays | 22 | ||
| 1.6.1 Direct Assay | 22 | ||
| 1.6.2 Competition Assay | 22 | ||
| 1.6.3 Inhibition Assay | 24 | ||
| 1.6.4 Sandwich Assay with Secondary Antibody and Signal Enhancers | 24 | ||
| 1.7 How to Read This Book | 25 | ||
| 1.8 Questions | 25 | ||
| References | 26 | ||
| Chapter 2 History and Physics of Surface Plasmon Resonance | 27 | ||
| 2.1 Introduction | 27 | ||
| 2.2 History | 29 | ||
| 2.2.1 Early History of SPR Biosensors | 29 | ||
| 2.2.2 History of SPR Biosensors After 1990 | 30 | ||
| 2.3 Surface Plasmon Theory | 31 | ||
| 2.3.1 The Evanescent Wave | 31 | ||
| 2.3.2 Surface Plasmon Dispersion Equations; Resonance | 33 | ||
| 2.3.3 Excitation of Surface Plasmons | 35 | ||
| 2.3.4 Surface Plasmon Properties | 37 | ||
| 2.3.5 Choice of Experimental Parameters | 39 | ||
| 2.3.6 Optimizing SPR Imaging Performance | 42 | ||
| 2.4 SPR Instrument Optics | 46 | ||
| 2.4.1 Fixed Angle | 47 | ||
| 2.4.2 Fan-shaped Beam | 48 | ||
| 2.4.3 Scanning Angle | 50 | ||
| 2.4.4 Grating Coupler | 51 | ||
| 2.4.5 Fiber-based SPR Sensors | 51 | ||
| 2.4.6 Other Optical Systems | 54 | ||
| 2.4.7 SPR Imaging Instruments | 55 | ||
| 2.5 Concluding Remarks | 56 | ||
| 2.6 Questions | 57 | ||
| References | 58 | ||
| Chapter 3 Surface Plasmon Resonance Instruments | 60 | ||
| 3.1 Introduction | 60 | ||
| 3.2 The Cornerstones of SPR Technology | 62 | ||
| 3.3 General Optical Requirements for SPR Instruments | 63 | ||
| 3.4 SPR Liquid Handling Systems | 65 | ||
| 3.4.1 Cuvette Systems | 66 | ||
| 3.4.2 Flow Systems | 68 | ||
| 3.5 SPR Instruments: State of the Art | 71 | ||
| 3.5.1 Examples of Fan-shaped Beam SPR Instruments | 71 | ||
| 3.5.2 Examples of Fixed- and Scanning-angle SPR Instruments | 78 | ||
| 3.5.3 Examples of Other Label-free Biosensing Instruments | 84 | ||
| 3.5.4 Examples of SPR Imaging Instruments | 89 | ||
| 3.6 Biacore SPR Systems of GE Healthcare | 97 | ||
| 3.6.1 Biacore T100, T200, and S200 | 98 | ||
| 3.6.2 Biacore A100/4000 | 100 | ||
| 3.6.3 Biacore 8K | 101 | ||
| 3.7 Conclusions | 102 | ||
| 3.8 Questions | 103 | ||
| References | 103 | ||
| Chapter 4 SPRpages – Getting a Feeling for the Curves\r | 106 | ||
| 4.1 Introduction | 106 | ||
| 4.2 The Exponential | 106 | ||
| 4.3 A Curve | 108 | ||
| 4.3.1 Baseline | 108 | ||
| 4.3.2 Association | 109 | ||
| 4.3.3 Steady State | 109 | ||
| 4.3.4 Dissociation | 109 | ||
| 4.3.5 Response Units | 109 | ||
| 4.3.6 Equilibrium and Saturation | 110 | ||
| 4.3.7 Rmax Value | 110 | ||
| 4.3.8 Curve Response | 112 | ||
| 4.3.9 Req value | 112 | ||
| 4.3.10 Time to Reach Equilibrium | 113 | ||
| 4.4 Curve Examples | 114 | ||
| 4.4.1 Curve Shape | 114 | ||
| 4.4.2 Exponential Curve | 114 | ||
| 4.4.3 Mass Transport Limitation (MTL) | 116 | ||
| 4.4.4 Biphasic Curves | 118 | ||
| 4.4.5 Drift, Jumps and Spikes | 119 | ||
| 4.5 Experimental Setup | 121 | ||
| 4.5.1 Analyte Concentration Range | 121 | ||
| 4.5.2 Blank Injections | 122 | ||
| 4.5.3 Multi-cycle Kinetics | 122 | ||
| 4.5.4 Single-cycle Kinetics | 122 | ||
| 4.5.5 Equilibrium Analysis | 123 | ||
| 4.5.6 Fast Kinetics | 125 | ||
| 4.5.7 Decaying Surface | 125 | ||
| 4.6 Sensorgram Quality | 127 | ||
| 4.7 The Affinity Plot; Getting a Feeling for the Numbers | 128 | ||
| 4.8 Curve Fitting | 128 | ||
| 4.8.1 Residual Plot | 130 | ||
| 4.8.2 Local and Global Fitting | 131 | ||
| 4.8.3 Deviations from a 1 : 1 Interaction | 131 | ||
| 4.9 Interaction Validation | 132 | ||
| 4.10 Publications | 132 | ||
| 4.10.1 Evaluating Published Results | 133 | ||
| 4.10.2 Minimal Requirements for Describing a Biosensor Experiment | 134 | ||
| 4.11 SPR Simulation | 135 | ||
| 4.11.1 Different Analyte Concentration (Same Kinetics) | 136 | ||
| 4.11.2 Different Association Rate (Different Affinity) | 137 | ||
| 4.11.3 Different Dissociation Rate (Different Affinity) | 137 | ||
| 4.11.4 Different Kinetics (Same Affinity) | 139 | ||
| 4.11.5 Different Injection Times (Same Kinetics) | 140 | ||
| 4.11.6 Different Dissociation Times (Same Kinetics) | 140 | ||
| 4.12 Questions | 141 | ||
| 4.13 Glossary | 146 | ||
| References | 147 | ||
| Chapter 5 Detailed Analysis of Kinetic Binding Traces with Distributions of Surface Sites | 149 | ||
| 5.1 Introduction | 149 | ||
| 5.2 The Physical Picture | 151 | ||
| 5.3 Calculating Surface Site Distributions | 153 | ||
| 5.3.1 Basic Principle | 153 | ||
| 5.3.2 Mass Transport Limitation | 155 | ||
| 5.3.3 Higher Order Reaction Schemes | 157 | ||
| 5.4 Experimental Design | 158 | ||
| 5.4.1 Information Content | 158 | ||
| 5.4.2 Effect of Sensor Surface\r | 161 | ||
| 5.4.3 Ligand Immobilization Process | 161 | ||
| 5.4.4 Analyte Purity | 164 | ||
| 5.5 Conclusions | 167 | ||
| 5.6 Questions | 167 | ||
| Acknowledgements | 168 | ||
| References | 168 | ||
| Chapter 6 Surface Chemistry in SPR Technology | 171 | ||
| 6.1 Introduction | 171 | ||
| 6.1.1 Interaction Mechanisms on Biosensor Surfaces | 172 | ||
| 6.1.2 The Surface Structure: Between Evanescent Field and Analyte Diffusion | 175 | ||
| 6.2 The Metal Layer of SPR Sensor Chips | 180 | ||
| 6.3 Adhesion Linking Layers for Noble Metals, Inorganic Dielectrics, and Plastics | 183 | ||
| 6.3.1 Adhesion Linking Layers for Noble Metal Surfaces | 184 | ||
| 6.3.2 Adhesion Linking Layers for Inorganic Dielectrics | 186 | ||
| 6.3.3 Adhesion Linking Layers for Plastics and Carbon Surfaces | 186 | ||
| 6.4 Bioinert Matrices | 187 | ||
| 6.4.1 Non-specific Adsorption of Biomolecules | 187 | ||
| 6.4.2 Functionalization Strategies for Ultralow-fouling Two-dimensional Surfaces | 189 | ||
| 6.4.3 Bioinert Hydrogels | 192 | ||
| 6.5 Choosing the Optimal Nanoarchitecture | 194 | ||
| 6.5.1 Two-dimensional Surfaces | 195 | ||
| 6.5.2 Three-dimensional Hydrogels | 197 | ||
| 6.6 Coupling Procedures for Ligand Immobilization | 202 | ||
| 6.6.1 Adsorptive Immobilization | 202 | ||
| 6.6.2 Covalent Immobilization | 203 | ||
| 6.6.3 Covalent Activation Chemistries | 208 | ||
| 6.6.4 Immobilization via Molecular Linkers | 225 | ||
| 6.6.5 Immobilization of Membrane Proteins | 234 | ||
| 6.6.6 Overview and Selection of Immobilization Chemistries | 238 | ||
| 6.7 Considerations for Spatially Resolved Immobilization | 242 | ||
| 6.8 Conclusions and Outlook | 247 | ||
| 6.9 Questions | 248 | ||
| References | 249 | ||
| Chapter 7 Fragment and Low Molecular Weight Compound Analysis | 255 | ||
| 7.1 Introduction | 255 | ||
| 7.2 Assay Formats for Low Molecular Weight Analysis | 256 | ||
| 7.2.1 Direct Binding Assay (DBA) | 256 | ||
| 7.2.2 Solution Competition or Inhibition in Solution Assay (ISA) | 258 | ||
| 7.2.3 Surface Competition Assay (SCA) | 258 | ||
| 7.2.4 Selection of Assay Format | 258 | ||
| 7.3 Methodology | 261 | ||
| 7.3.1 Immobilization of Proteins | 262 | ||
| 7.3.2 Immobilization of Small Molecules | 266 | ||
| 7.3.3 Protein Activity | 267 | ||
| 7.3.4 Compound Solubility and Concentrations in Screening | 268 | ||
| 7.3.5 Compound Refractive Index Increment | 268 | ||
| 7.3.6 Buffer Selection\r | 268 | ||
| 7.3.7 Sample Preparation | 269 | ||
| 7.3.8 Solvent Correction | 270 | ||
| 7.3.9 Z', Positive and Negative Controls\r | 271 | ||
| 7.4 Target Considerations | 272 | ||
| 7.4.1 GPCRs | 272 | ||
| 7.4.2 Kinases | 273 | ||
| 7.5 Fragment Screening Workflow | 274 | ||
| 7.5.1 Fragment Libraries | 274 | ||
| 7.5.2 Clean Screen | 274 | ||
| 7.5.3 Binding Level Screen | 276 | ||
| 7.5.4 Data Analysis – Report Points and Curve Shapes\r | 276 | ||
| 7.5.5 Affinity Screen | 282 | ||
| 7.5.6 Affinity Analysis | 282 | ||
| 7.5.7 Site Specificity – Use of Blocked or Saturated Targets\r | 285 | ||
| 7.6 Hit to Lead Workflow | 287 | ||
| 7.6.1 Off-rate Screening\r | 287 | ||
| 7.6.2 Lead Optimization | 288 | ||
| 7.7 Tips | 290 | ||
| 7.8 Questions | 290 | ||
| References | 292 | ||
| Chapter 8 Combined Antibody Characterization: High-throughput Ranking, Binning, and Mapping\r | 295 | ||
| 8.1 General Introduction | 295 | ||
| 8.2 Affinity Ranking | 296 | ||
| 8.2.1 Experiment 1: Affinity Ranking of Human IgG Binding Hepatitis C Virus E2 Protein | 297 | ||
| 8.2.2 Experiment 2: Affinity Ranking of Rabbit IgG Binding MHC–Peptide Complexes | 303 | ||
| 8.2.3 Conclusions on Affinity Ranking and Outlook | 307 | ||
| 8.3 Epitope Binning | 307 | ||
| 8.3.1 Experiment 3: Epitope Binning of Antibodies Binding the Respiratory Syncytial Virus (RSV) Glycoprotein | 309 | ||
| 8.3.2 Conclusions on Epitope Binning and Outlook | 312 | ||
| 8.4 Epitope Mapping | 313 | ||
| 8.4.1 Experiment 4: Epitope Mapping of Anti-RSVG Antibodies Using a Library of Overlapping Peptides\r | 313 | ||
| 8.4.2 Experiment 5: Mapping the Epitope of Anti-human Parecho Virus Antibody AM | 18 | ||
| with Alanine Scanning SPR | 320 | ||
| 8.4.3 Conclusions on Epitope Mapping and Outlook | 323 | ||
| 8.5 General Conclusions and Outlook | 324 | ||
| 8.6 Questions | 324 | ||
| References | 325 | ||
| Chapter 9 Treating Raw Data: Software for SPR Applications | 328 | ||
| 9.1 Introduction | 328 | ||
| 9.2 Software Tools for Designing and Executing Experiments | 329 | ||
| 9.2.1 General Considerations | 329 | ||
| 9.2.2 Pre-assay Studies | 331 | ||
| 9.2.3 Software Tools for Pre-assay Planning | 331 | ||
| 9.2.4 Takeaways for SPR Study Design and Execution | 333 | ||
| 9.3 Data Analysis | 333 | ||
| 9.3.1 Data Output | 333 | ||
| 9.3.2 Data Analysis Software Packages | 333 | ||
| 9.4 Fundamental Data Processing Techniques | 335 | ||
| 9.4.1 Introduction | 335 | ||
| 9.4.2 Normalization/Calibration | 335 | ||
| 9.4.3 Excluded Volume Correction | 335 | ||
| 9.4.4 Referencing | 336 | ||
| 9.4.5 Blank Subtraction | 337 | ||
| 9.4.6 x-Scale Alignment | 337 | ||
| 9.4.7 y-Scale Zeroing | 337 | ||
| 9.5 Example of Competitive Epitope Binning Data Analysis | 338 | ||
| 9.5.1 Introduction | 338 | ||
| 9.5.2 Epitope Binning Experimental Design | 339 | ||
| 9.5.3 Preprocessing of Data Using SPRint | 340 | ||
| 9.5.4 Epitope Characterization Using Epitope Binning 2.0 | 344 | ||
| 9.6 Example of Kinetic Data Analysis | 349 | ||
| 9.6.1 Introduction | 349 | ||
| 9.6.2 Experimental Design | 349 | ||
| 9.6.3 Preprocessing of Data Using SPRint | 349 | ||
| 9.6.4 Global Kinetic Analysis in Scrubber 2.0 HT | 350 | ||
| 9.7 Conclusions | 354 | ||
| 9.8 Questions | 354 | ||
| Acknowledgements | 355 | ||
| References | 355 | ||
| Chapter 10 Biolayer Interferometry (Octet) for Label-free Biomolecular Interaction Sensing | 356 | ||
| 10.1 Introduction to Biolayer Interferometry (BLI) | 356 | ||
| 10.2 BLI Platforms | 358 | ||
| 10.3 BLI Biosensors | 359 | ||
| 10.3.1 Biosensor Selection | 361 | ||
| 10.3.2 Regeneration of Biosensors | 365 | ||
| 10.4 Basics of Binding Kinetics Using BLI | 367 | ||
| 10.4.1 Relationship Between Req, Rmax, and KD | 370 | ||
| 10.5 Data Acquisition and Analysis on the Octet | 370 | ||
| 10.5.1 Data Acquisition on the Octet | 370 | ||
| 10.5.2 Data Analysis on the Octet | 372 | ||
| 10.6 Determination of Affinity Constants Using BLI | 378 | ||
| 10.6.1 Ligand Surface Immobilization | 378 | ||
| 10.6.2 Binding Kinetics | 379 | ||
| 10.6.3 Setting Up Kinetics Assays Using BLI | 380 | ||
| 10.6.4 Protein Quantitation on the Octet | 384 | ||
| 10.7 Emerging Applications | 389 | ||
| 10.7.1 Octet Use in Epitope Binning | 389 | ||
| 10.7.2 Octet in Virus Titer Studies | 391 | ||
| 10.7.3 Analysis of FcRn–Antibody Interactions Using the Octet\r | 393 | ||
| 10.8 Questions | 396 | ||
| References | 397 | ||
| Chapter 11 Strategies for Building Protein–Glycosaminoglycan Interaction Networks Combining SPRi, SPR, and BLI | 398 | ||
| 11.1 Introduction | 398 | ||
| 11.2 A Roadmap to Build Protein–Glycosaminoglycan Interaction Networks\r | 400 | ||
| 11.3 Identification of Biomolecular Interactions by Surface Plasmon Resonance Imaging | 401 | ||
| 11.4 Building and Functional Analysis of Protein–Glycosaminoglycan Interaction Networks | 403 | ||
| 11.5 Contextualization of the Interaction Network with Kinetic Parameters and Affinity | 407 | ||
| 11.5.1 Kinetic and Affinity Data Available in Interaction Databases | 407 | ||
| 11.5.2 Kinetics and Affinity Calculated by Bio- Layer Interferometry | 407 | ||
| 11.6 Conclusion | 411 | ||
| 11.7 Abbreviations | 411 | ||
| 11.8 Questions | 412 | ||
| Acknowledgements | 412 | ||
| References | 412 | ||
| Chapter 12 Future Trends in SPR Technology | 415 | ||
| 12.1 Introduction | 415 | ||
| 12.2 Trends in SPR Instrumentation | 417 | ||
| 12.2.1 Nanoparticle-based Localized SPR (LSPR) | 417 | ||
| 12.2.2 SPR Imaging | 419 | ||
| 12.3 Trends in Fluidics | 420 | ||
| 12.3.1 Microarray Spotting on SPR Sensor Chips | 421 | ||
| 12.3.2 Gradient Printing for Multiplex Sensing | 424 | ||
| 12.4 Trends in Sensor Surfaces | 426 | ||
| 12.4.1 SensEyes® Sensor: Easy2Spot | 427 | ||
| 12.4.2 SensEye Protein A/G, SensEye Anti-IgG, and Fixit Protocol\r | 428 | ||
| 12.5 Hyphenated SPR Technology | 430 | ||
| 12.5.1 SPR-MS | 430 | ||
| 12.5.2 Other Hyphenated SPR Techniques | 431 | ||
| 12.5.3 Implementation of ''Lab-on-a-Chip'' Devices for SPR Systems | 432 | ||
| 12.5.4 Electrochemical SPR (E-SPR) Application | 434 | ||
| 12.6 Prospects for SPR-based Point-of-care Devices | 435 | ||
| 12.6.1 Point-of-care Theranostics | 436 | ||
| 12.6.2 Signal Enhancement Cascade for Boosting the Dynamic Range | 437 | ||
| 12.7 Trends in Measuring Reliable Kinetic Parameters | 439 | ||
| 12.7.1 Affinity Ranking with the Interpolation Method | 440 | ||
| 12.7.2 Affinity Ranking with the Interpolated Distribution Analysis Method | 444 | ||
| 12.8 SPRi Cytometry | 446 | ||
| 12.8.1 Label-free Cell Membrane Antigen Profiling | 447 | ||
| 12.8.2 Quantifying the Ratio of Surface Antigens per Cell Population | 452 | ||
| 12.8.3 Extracellular Vesicle Monitoring Using SPRi | 459 | ||
| 12.8.4 Affinity Ranking of Cell Surface Antigens on Living Cells | 463 | ||
| 12.8.5 Quantifying the Production Rate of Molecules per Individual Cell | 465 | ||
| 12.8.6 Microwell Cell Selection Using SPRi: the McSPRinter | 467 | ||
| 12.9 Conclusions | 474 | ||
| 12.10 Questions | 475 | ||
| References | 475 | ||
| Appendix Questions and Answers | 479 | ||
| Subject Index | 508 |