Microarray Technology and Its Applications (eBook)

Preface 6
Acknowledgements 9
Contents 11
List of Contributors 17
General Microarray Technologies 23
1 Array Formats 24
1.1 Introduction 24
1.2 Reasons to Use Arrays 25
1.3 Arrays for Nucleic Acid Analysis 27
1.4 Protein Arrays 29
1.5 The ArrayPlateTM 30
1.6 Conclusion 40
References 41
2 Biomolecules and Cells on Surfaces – Fundamental Concepts 44
2.1 Introduction 44
2.2 Types of Immobilization 44
2.3 DNA Immobilization on Surfaces 49
2.4 Protein Immobilization on Surfaces 53
2.5 Carbohydrate Immobilization 57
2.6 Immobilization of Cells on Surfaces 59
2.7 Conclusions 62
References 63
3 Surfaces and Substrates 66
3.1 Introduction 66
3.2 DNA Microarrays 67
3.3 Protein Microarrays 71
3.4 Conclusion 76
References 77
4 Reagent Jetting Based Deposition Technologies for Array Construction 83
4.1 Introduction 83
4.2 Reagent Jetting – Technology Overview 83
4.3 Thermal Jet Based Dispensing 85
4.4 Piezo Jet Based Dispensing 87
4.5 Solenoid Jet Based Dispensing 88
References 91
5 Manufacturing of 2-D Arrays by Pin- printing Technologies 93
5.1 Introduction 93
5.2 Definition of ‘Contact’ Pin–Printing 93
5.3 Overview of Different Pin Technologies 94
5.4 Other System Components and Environmental Factors 99
5.5 Pin Printing Process 101
5.6 Example of a High Throughput Pin–Printing System for Manufacturing of 2D Arrays – the Corning GENII System 104
5.7 Conclusion 106
References 107
6 Nanoarrays 109
6.1 Introduction 109
6.2 Passive Nano–scale Arrays 111
6.3 Computational Nanoarrays 125
6.4 Dynamic Nanoarrays 129
6.5 Conclusion 135
References 135
7 The Use of Microfluidic Techniques in Microarray Applications 139
7.1 Introduction 139
7.2 Biochannel Hybridization Arrays 140
7.3 Chips with Cavitation Microstreaming Mixers – Kinetics Studies 148
7.4 Integrated Microfluidic Reactors for DNA Amplification and Hybridization 155
7.5 Summary and Conclusions 162
References 162
8 Labels and Detection Methods 166
8.1 Introduction 166
8.2 Fluorophore Labelling and Detection Methods 167
8.3 Enhanced Fluorescence-Based Assays 170
8.4 Phosphor Reporters 173
8.5 Electrochemical Detection 175
8.6 Metal Nanoparticle Labels and Metal Thin Films for Microarrays 178
8.7 Conclusions 191
References 193
9 Marker-free Detection on Microarrays 199
9.1 Introduction 199
9.2 Imaging Ellipsometry and Imaging Surface Plasmon Resonance on Biochips 199
9.3 Intrinsic UV Fluorescence for Chip Analysis of Rare Proteins 208
9.4 Genetic Diagnostics with Unlabelled DNA 215
References 222
DNA Microarrays 226
10 Analysis of DNA Sequence Variation in the Microarray Format 227
10.1 Introduction 227
10.2 Principles of Genotyping 229
10.3 Performing the Assays in Practice 233
10.4 Conclusion 238
References 239
11 High Sensitivity Expression Profiling 244
11.1 Introduction 244
11.2 Oligonucleotide Expression Arrays 245
11.3 cDNA-based Expression Arrays 254
11.4 Appendix 259
References 260
12 Applications of Matrix-CGH (Array-CGH) for Genomic Research and Clinical Diagnostics 266
12.1 Introduction 266
12.2 Technical Aspects 268
12.3 Applications 271
References 275
13 Analysis of Gene Regulatory Circuits 279
13.1 Introduction 279
13.2 An Experimental Protocol for Genome Wide Location Analysis 282
13.3 Example: Identifying the Target Genes of Human E2F4 287
13.4 Summary 289
References 289
Protein Microarrays 291
14 Protein, Antibody and Small Molecule Microarrays 292
14.1 Introduction 292
14.2 Protein Microarrays 293
14.3 Antibody Microarrays 296
14.4 Peptide and Other Synthetic Arrays 300
References 303
15 Photoaptamer Arrays for Proteomics Applications 309
15.1 Introduction 309
15.2 Overview of Photoaptamer Discovery and High Throughput Production 310
15.3 Using Photoaptamer Microarrays 313
15.4 Discussion 315
References 317
16 Biological Membrane Microarrays 321
16.1 Introduction 321
16.2 Biospecific Binding Studies Using Membrane Microarrays 325
16.3 Conclusions 330
References 331
Cell & Tissue Microarrays
17 Use of Reporter Systems for Reverse Transfection Cell Arrays 334
17.1 Introduction 334
17.2 Reporter Systems for Reverse Transfection 336
17.3 Reagents and Protocols 343
References 344
18 Whole Cell Microarrays 345
18.1 Introduction 345
18.2 The Need 346
18.3 The Solution 346
18.4 Challenges and Opportunities for Cellular Micrroarrays 351
References 353
19 Tissue Microarrays for Miniaturized High- Throughput Molecular Profiling of Tumors 354
19.1 Introduction 354
19.2 The TMA Technology 355
19.3 The Representativity Issue 355
19.4 TMA Applications 358
19.5 Future Directions 360
19.6 Protocol 361
References 363
20 Application of Microarray Technologies for Translational Genomics 370
20.1 Introduction 370
20.2 High Throughput Clinical Target Validation Using Tissue Microarrays 372
20.3 Examples of Studies Integrating DNA and Tissue Microarray Technologies for the Rapid Clinical Translation of Genomic Discoveries 374
20.4 High Throughput Characterization of Gene Function Using Live Cell Microarrays 377
20.5 Conclusions 379
References 381
Index 384