Recognition Receptors in Biosensors (eBook)

Preface 5
Foreword 7
Contents 9
Contributors 12
Principles of Biomolecular Recognition 17
Abbreviations 18
Symbols 18
1.1 What Is Molecular Recognition? 18
1.2 General Principles of Interaction Thermodynamics 20
1.2.1 Free Energy, Enthalpy, and Entropy in Interacting Systems 21
1.2.2 Interaction Energy in the Association of Two Semi-Rigid Molecules in the Gas Phase 22
1.3 Interaction Energies in the Gas Phase 24
1.3.1 First-Order Electrostatic Interactions Involving Permanent Charges and Multipoles 25
. 34
1.3.2 Second-Order Induction–Polarization Energy 36
1.3.3 London Dispersion 38
1.3.4 Steric Repulsion (Pauli Exclusion) and Modeling of van der Waals Forces 41
1.3.5 Charge Transfer 43
1.4 Thermodynamics of Association in the Gas Phase 44
1.4.1 Thermodynamic Contributions from Nuclear Motions 44
1.4.2 Conformational Entropy 47
1.5 Interaction Energies in the Aqueous Environment 48
1.5.1 Effects of Water on Electrostatics 48
1.5.2 Effect of Water on Induction and van der Waals Forces 49
1.5.3 Effect of Water on Thermodynamic Contributions from Nuclear Motions 51
1.5.4 Hydrophobic Effect 52
1.5.5 Interactions of Dissolved Ligands with Macromolecules in Solution 53
1.6 A Synthesis 55
1.7 Concluding Remarks 57
References 57
Surface Sensitization Techniques and Recognition Receptors Immobilization on Biosensors and Microarrays 60
Abbreviations 61
2.1 Introduction 62
2.2 Adsorption, Chemical Grafting, and Entrapment 2.2.1 From Adsorption to Grafting, a Historical Perspective 63
2.2.2 Adsorption and Grafting: Physical Chemistry and Thermodynamics 66
2.2.3 Kinetic Aspects of Adsorption, Desorption, and Grafting 68
2.2.4 Nonspecific Adsorption as a Source of Background Signal 69
2.3 Classification of the Main Immobilization Pathways 2.3.1 Specificities of Biomolecules for Chemical Coupling 70
2.3.2 Strategy of Chemical Grafting 71
2.3.3 Chemical Grafting of Native Biomolecules and Associated Surface Biofunctionalization 72
2.3.4 Immobilization of Modified Biomolecules 78
2.4 Surface Functionalization 91
2.4.1 2D Immobilization: Grafting of Monolayers 93
2.4.2 3D Immobilization: Thick Layers, Entrapment Methods 107
2.4.3 Immobilization onto Colloidal Particles 124
2.5 Concluding Remarks 133
References 134
Analytical Tools for Biosensor Surface Chemical Characterization 148
Abbreviations 149
3.1 Introduction 149
3.2 Surface Chemical Analysis 149
3.2.1 Secondary Ion Mass Spectrometry (SIMS) 150
3.2.2 X-Ray Photoelectron Spectroscopy 153
3.3 Examples 158
3.4 Cell-Based Biosensor Prototypes 158
3.4.1 Glyco-Engineering 163
3.4.2 Immunosensors 173
3.5 Concluding Remarks 182
References 182
Enzyme for Biosensing Applications 188
Abbreviations 189
4.1 Introduction 190
4.2 Biocatalysis and Enzyme Specificity 190
4.2.1 Classification of Enzymes 191
4.3 Enzyme Immobilization 194
4.3.1 Confinement Within a Semipermeable Membrane 194
4.3.2 Adsorption 194
4.3.3 Affinity Interactions 195
4.3.4 Entrapment 196
4.3.5 Cross-linking 196
4.3.6 Covalent Binding 197
4.4 Enzyme-Based Biosensors: Different Transduction Modes 4.4.1 Electrochemical Detection 198
4.4.2 Gravimetric Detection: Quartz Crystal Microbalance ( QCM), Surface Acoustic Wave ( SAW) Devices, Microcantilevers 208
4.4.3 Calorimetric Detection 209
4.4.4 Optical Detection 210
4.5 Concluding Remarks 219
References 220
Antibodies in Biosensing 232
Abbreviations 233
5.1 Introduction 233
5.2 Antibodies: An Overview 5.2.1 Immunoglobulin Expression In Vivo 234
5.2.2 Antibody Formats 234
5.2.3 Anti-Antibodies System 237
5.3 Antibodies as Biosensors: Various Technologies 237
5.3.1 Techniques Utilizing Immunoprecipitation 238
5.3.2 Radioimmunoassays 241
5.3.3 Enzymatic Immunoassays 241
5.3.4 Immunocytochemical and Immunohistochemical Assays 244
5.3.5 Flow Cytometry 245
5.3.6 Bead-Based Assays 247
5.3.7 Additional Techniques 251
5.4 Multiplexing Methodologies 252
5.4.1 ChIP-on-Chip Assays 252
5.4.2 Antibody Microarrays 252
5.4.3 Multiplexing IHC/ICC 254
5.4.4 Multispot ELISAs 255
5.5 Concluding Remarks 256
References 256
Peptides as Molecular Receptors 260
Abbreviations 260
6.1 Introduction 261
6.2 Peptides as Receptor Molecules 262
6.3 Combinatorial Chemistry 264
6.4 Dynamic Combinatorial Library 266
6.5 Phage Display Technology 269
6.6 Rational Design Approach Using Computational Methods 269
6.6.1 Molecular Mechanics 270
6.6.2 Building Blocks 272
6.6.3 Leapfrog 272
6.7 Molecular Imprinting 274
6.8 Application in Sensors 275
6.9 Future Perspective 278
6.10 Concluding Remarks 279
References 279
Carbohydrates as Recognition Receptors in Biosensing Applications 286
Abbreviations 286
7.1 Introduction 288
7.2 General Aspects of Glycochemistry 7.2.1 Introduction 290
7.2.2 Structural Aspects and Chemistry of Carbohydrates 290
7.2.3 Glycosylation Methods 295
7.2.4 Chemo-enzymatic Glycosylation Methods 297
7.2.5 Glycoconjugates 298
7.2.6 Examples of Naturally Occurring Carbohydrates 300
7.3 Biological Role 306
7.3.1 The Glycocalix and Extracellular Matrix Polysaccharides 306
7.3.2 Carbohydrates in Host–Pathogen Interactions and Metastasis 309
7.4 Carbohydrate-Based Biosensors 311
7.4.1 Obtaining Saccharide Probes 311
7.4.2 Surface Physicochemistry: Non-specific Adsorption and Immobilisation 312
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7.4.3 Transduction 325
7.5 Biosensors: Applications 7.5.1 Antibody/ Antigen 336
7.5.2 Enzyme/Carbohydrates 337
7.5.3 Carbohydrates/Lectins 338
7.5.4 Whole Cells 339
7.6 Concluding Remarks 340
References 341
Nucleic Acid Diagnostic Biosensors 353
Abbreviations 353
8.1 Introduction 354
8.1.1 Development of Nucleic Acid Diagnostics 355
8.1.2 Properties of a Diagnostic Target 355
8.1.3 DNA and RNA targets 356
8.1.4 Nucleic Acid Diagnostics Methods 356
8.1.5 Polymerase Chain Reaction 357
8.2 Biosensors 358
8.2.1 Biosensor Assay formats 358
8.2.2 Biological Recognition Elements and Immobilisation Methods 359
8.3 Biosensor Formats for Nucleic Acid Diagnostics 8.3.1 Optical Based Systems 361
8.3.2 Surface Plasmon Resonance 361
8.3.3 Piezoelectric Biosensors 363
8.3.4 Electrochemical Biosensors 364
8.3.5 Other Detection Formats 365
8.3.6 Signal Amplification 365
8.4 Microarrays 366
8.5 Use of Nucleic Acid Biosensors for Rapid Pathogen Detection 368
8.6 Future Developments 369
8.6.1 Micro and Nano Scale Biosensors 370
8.7 Concluding Remarks 370
References 371
Tissue-Based Biosensors 374
Abbreviations 375
9.1 Introduction 375
9.2 Tissue-Based Biosensors in Experimental Animals 376
9.3 Incorporating Biosensor Molecules Into Tissues 377
9.4 Biophotonics-Based Biosensors and Biosensors Based on Other Physical Outputs 378
9.5 Measuring Light Output from Bioluminescence-Based Biosensor Tissues in Living Animals 380
9.6 Tissue-Based Biosensors Based on Bioluminescence Resonance Energy Transfer ( BRET) 382
9.7 Examples of Tissue-Based Biosensors That Use BRET 9.7.1 Example 1: Vasopressin 383
9.7.2 Example 2: Rapamycin 385
9.8 Potential Uses of Tissue-Based Biosensors in Human Medicine 385
9.9 Concluding Remarks 388
References 388
Biosensing with Plants: Plant Receptors for Sensing Environmental Pollution 391
Abbreviations 391
10.1 Introduction 392
10.2 Biomonitoring 395
10.2.1 What Is Ligand–Receptor Interaction? 397
Ligand 397
Ligand Receptor Protein 397
10.2.2 The Role of Hormones in Plant Development and Stress Signaling 398
10.2.3 Receptor-Like Kinases 406
10.2.4 Cell Wall Associated Kinase and WAK-Like Kinase 409
10.2.5 Leucine-Rich Repeats: LRR-RLK Subfamily 410
10.3 Possible Implications of Ligand–Receptor Interaction Studies on Future Phytosensing Research 412
10.4 Concluding Remarks 413
Mega Plant Biotech Industry 414
References 415
Bacteriophage-Based Biosensors 422
Abbreviations 423
11.1 Introduction 424
11.2 Detection by Phage Amplification 427
11.3 Detection of Released Intracellular Components During Phage Lysis 428
11.3.1 Measurement of Adenosine Triphosphate Release 428
11.3.2 Measurement of Enzymes and Other Cytoplasmic Markers 429
11.3.3 Measurement of Phage Progeny 430
11.4 Direct Detection Through Cell Wall Recognition 11.4.1 Phage Immobilization 433
11.4.2 Affinity Detection 436
11.4.3 Fluorescently Labeled Phages 443
11.5 Indirect Detection 11.5.1 Detection Based on Inhibition of Metabolism and Growth 444
11.6 Detection by Reporter Phages 444
11.6.1 Bioluminescent Reporter Phages (lux and luc) 445
11.6.2 Fluorescent Reporter Phages ( gfp) 448
11.6.3 Colorimetric Reporter Phages ( lacZ) 449
11.6.4 Ice Nucleation Reporter Phages ( inaW) 449
11.7 Other Detection Methods Using Phages 11.7.1 Phage- Conjugated Quantum Dots 450
11.8 Conclusions and Future Remarks 450
References 451
Antibody Engineering for Biosensor Applications 457
Abbreviations 458
12.1 Antibodies – Nature’s Own Biosensor 458
12.2 Antibody Structure and Function 459
12.2.1 Immunoglobulin Gamma and the Ig Fold 459
12.2.2 Conventional and Recombinant Antibodies 463
12.2.3 The Nature of Antibody Binding 467
12.2.4 General Thermodynamic Stabilities of Antibody Scaffolds 473
12.3 Antibody Technologies 12.3.1 Conventional Antibodies 475
12.3.2 Recombinant Antibodies 479
12.3.3 Alternative Protein Scaffolds 487
12.3.4 Limitations of Protein Recognition Elements 488
12.4 Opportunities in Biosensor Development 489
12.4.1 Assay Economics 489
12.4.2 Speed of Analysis 491
12.4.3 Multiplexity of Analysis 492
12.5 The Biosensor Interface 494
12.5.1 Surface Adsorption of Antibodies – An Interface Case Study 495
12.5.2 The Necessity of Holistic Interface Development 498
12.6 Bespoke Antibody Engineering for Biosensors 500
12.6.1 Stability 500
12.6.2 Specificity 505
12.6.3 Sensitivity 507
12.6.4 Immobilization 511
12.6.5 Other Engineering Strategies for Biosensors 519
12.7 Concluding Remarks 520
References 521
Genetically Engineered Proteins as Recognition Receptors 536
Abbreviations 537
13.1 Introduction 537
13.1.1 Fluorescence in Biological Sensing 538
13.1.2 Determination of Apparent Dissociation Constant ( Kd) Using Fluorescence 539
13.2 Naturally Selected Biosensors 13.2.1 Fluorescent- Labeled Proteins as Biosensors 540
13.2.2 Genetically Modified Single Cys Biosensors 541
13.2.3 Glucose Binding Protein Biosensors 545
13.2.4 Design of GFP Fusion Biosensors 550
13.3 Designed Evolution 13.3.1 In Silico Evolution: Biosensors by Design 551
13.3.2 Computational Design Using ROSETTA 552
13.3.3 Computational Design Using DEZYMER 553
13.4 In Vivo Evolution: Receptor Proteins by Combinatorial Screening 553
13.4.1 Trp Cage Motif 554
13.4.2 g-B-Crystallin 555
13.4.3 Min-23 (a Knottin) 555
13.4.4 Scorpion Toxins and Defensins 556
13.4.5 Lipocalins 557
13.4.6 Staphylococcal Protein A Domain 557
13.4.7 Ankyrin Repeat Proteins 558
13.4.8 Green Fluorescent Protein 558
13.5 Concluding Remarks 560
References 560
Biosensing Systems Based on Genetically Engineered Whole Cells 569
Abbreviations 570
14.1 Introduction 570
14.2 Whole-Cell-Based Sensing Systems 571
14.3 Luminescent Reporter Genes 571
14.4 Advantages and Disadvantages of Whole-Cell-Based Sensing Systems 575
14.5 Bacterial Whole-Cell Sensing Systems 576
14.5.1 General Toxicants 578
14.5.2 Stress Factors 579
14.5.3 Specific Analytes or Groups of Analytes 582
14.6 Eukaryotic Whole-Cell Sensing Systems 585
14.6.1 Yeast Cells 587
14.6.2 Mammalian Cells 587
14.7 Integration of Genetically Engineered Whole-Cell Sensing Elements in Biosensors 588
14.8 Concluding Remarks 592
References 593
Photosynthetic Proteins Created by Computational and Biotechnological Approaches in Biosensing Applications 603
Abbreviations 604
15.1 The Emergence of Technology Based on Photosynthetic Proteins 604
15.2 Key Issues in Designing Photosystems-Based Biosensors 606
15.3 General Remarks on the Reaction Centers of Photosystems 610
15.4 Immobilization Procedures for Biomediator Stabilization 613
15.5 Transduction Systems 616
15.6 Electrochemical Detection of Pollutants 617
15.7 Optical Transducers for the Detection of Herbicides 622
15.8 Enhancing Biomediator Properties by Bioengineering and Bioinformatics 625
15.9 Innovative Applications of Photosystem- Based Technologies 628
15.10 Why make Photosystems-Based Biosensors for Environmental Monitoring? 631
15.11 Concluding Remarks 632
References 632
Oligonucleotides as Recognition and Catalytic Elements 635
Abbreviations 636
16.1 Introduction 637
16.2 DNA Hybridization 637
16.2.1 Melting Temperature 639
16.2.2 Melting Temperature Prediction 639
16.2.3 Effect of Mismatched Bases on Melting Temperature 643
16.2.4 Hybridization Interference Through Self-Annealing 644
16.2.5 Hybridization to Probes Immobilized on a Solid Matrix 645
16.3 Application of Oligonucleotides as Recognition Elements for Nucleotide Analysis 646
16.3.1 Original Hybridization-Based Assays 646
16.3.2 Oligonucleotides as Recognition Elements in Polymerase Chain Reaction ( PCR) 647
16.3.3 Whole Genome Amplification (WGA) Technologies 649
16.3.4 Microarray Applications 650
16.4 Oligonucleotides as Genetic Regulatory Elements 654
16.4.1 Antisense Oligonucleotides 654
16.4.2 RNA Interference (RNAi) 656
16.4.3 Ribozymes 662
16.5 Oligonucleotides as Ligands-Aptamer Binding 664
16.5.1 Aptamer Structure and Design 664
16.5.2 Aptamer Selection 667
16.5.3 Non-SELEX Selection of Aptamers 668
16.5.4 Aptamer Applications 669
16.6 Concluding Remarks 669
References 670
Aptamers: Versatile Tools for Reagentless Aptasensing 679
Abbreviations 679
17.1 Introduction 680
17.2 Some General Notes on Aptamer Technology 17.2.1 Aptamer Selection: SELEX and Automated SELEX 681
17.2.2 Aptamer Stability: Spiegelmers and Chemically Modified Aptamers 685
17.2.3 The Molecular Basis of the AptamerÒTarget Interaction. Implications in Assay Development 688
17.2.4 Advantages and Drawbacks Versus Other Biorecognition Molecules 692
17.3 Aptamers as Bio-recognition Elements in Biosensor Development 694
17.3.1 Mass-Sensitive and Resonant Aptasensors: Specificity Online 695
17.3.2 Optical Aptasensors 697
17.3.3 Electrochemical Aptasensors 703
17.3.4 Aptamer Molecular Beacons: Aptabeacons 709
17.4 Concluding Remarks 714
References 715
Phage Display Technology in Biosensor Development 727
Abbreviations 728
18.1 Introduction 728
18.2 In Vitro Selections: Peptide Phage Display 18.2.1 Introduction to In Vitro Selections 731
18.2.2 Peptide Phage Display 732
18.2.3 Phage Display Targeting Biotin-Binding Proteins 734
18.2.4 Peptide Phage Display in the Detection of Toxins 736
18.2.5 Landscape Phage and the Detection of Salmonella typhimurium 737
18.3 Antibody Phage Display 18.3.1 Introduction to Antibody Phage Display 739
18.3.2 Early Examples of Antibody Phage Display 740
18.3.3 Phage Selected Antibodies in the Detection of Toxins 741
18.3.4 Lab on a Chip Applications 742
18.4 Protein Phage Display 18.4.1 Introduction to Protein Phage Display 742
18.4.2 Protein-protein Interactions in Phage Display 743
18.4.3 Protein-DNA Interactions in Phage Display: Zinc Finger Domains 746
18.5 Concluding remarks 747
References 748
Molecularly Imprinted Polymer Receptors for Sensors and Arrays 754
Abbreviations 755
19.1 Introduction 755
19.2 Molecular Imprinting 19.2.1 Chronology 757
19.2.2 Approaches 759
19.3 Ligating Monomers 19.3.1 Inorganic 760
19.3.2 Organic Monomers 760
19.4 Polymer Morphology 19.4.1 Bulk Polymers 761
19.4.2 Polymer Films 763
19.4.3 Surface Imprinting 763
19.4.4 Soluble MIPs 764
19.5 Sensor Transduction 19.5.1 Mass Sensors 764
19.5.2 Electrochemical Sensors 767
19.5.3 Optical Sensors 768
19.6 Sensor Examples 19.6.1 Mass Sensors 769
19.6.2 Electrochemical Sensors 770
19.6.3 Optical Sensors 772
19.7 Concluding Remarks 776
References 776
Biomimetic Synthetic Receptors as Molecular Recognition Elements 779
Abbreviations 779
20.1 Introduction 780
20.2 How to Achieve High Selectivity, Affinity, and Sensitivity 781
20.3 Examples of Different Analytes 785
20.3.1 Inorganic Cations 786
20.3.2 Anion Complexes 788
20.3.3 Complexation of Aminoacids and Peptides 792
20.3.4 Complexation of Nucleotides and Nucleosides 795
20.3.5 Carbohydrate Detection 801
20.3.6 Complexation of Terpenes and Steroids 807
20.4 Concluding Remarks 809
References 810
Kinetics of Chemo/Biosensors 820
Abbreviations 820
21.1 Background 821
21.2 Introduction 821
21.3 Adsorption Models 823
21.4 Theory 825
21.4.1 Single-Fractal Analysis 826
21.4.2 Dual-Fractal Analysis 827
21.5 Illustrations 827
21.5.1 Illustration 1 828
21.5.2 Illustration 2 833
21.6 Illustration 3 837
21.7 Estimating Kinetic Parameters and Explanation of Fractal Analysis Calculations 21.7.1 Estimating Kinetic Parameters 840
21.7.2 Explanation of Fractal Analysis Calculations 841
21.7.3 Example 842
21.7.4 Physical Interpretation of Kinetic Parameters 843
References 844
Index 846