1;Preface;6 2;Acknowledgements;9 3;Contents;11 4;List of Contributors;17 5;General Microarray Technologies;23 5.1;1 Array Formats;24 5.1.1;1.1 Introduction;24 5.1.2;1.2 Reasons to Use Arrays;25 5.1.3;1.3 Arrays for Nucleic Acid Analysis;27 5.1.4;1.4 Protein Arrays;29 5.1.5;1.5 The ArrayPlateTM;30 5.1.6;1.6 Conclusion;40 5.1.7;References;41 5.2;2 Biomolecules and Cells on Surfaces - Fundamental Concepts;44 5.2.1;2.1 Introduction;44 5.2.2;2.2 Types of Immobilization;44 5.2.3;2.3 DNA Immobilization on Surfaces;49 5.2.4;2.4 Protein Immobilization on Surfaces;53 5.2.5;2.5 Carbohydrate Immobilization;57 5.2.6;2.6 Immobilization of Cells on Surfaces;59 5.2.7;2.7 Conclusions;62 5.2.8;References;63 5.3;3 Surfaces and Substrates;66 5.3.1;3.1 Introduction;66 5.3.2;3.2 DNA Microarrays;67 5.3.3;3.3 Protein Microarrays;71 5.3.4;3.4 Conclusion;76 5.3.5;References;77 5.4;4 Reagent Jetting Based Deposition Technologies for Array Construction;83 5.4.1;4.1 Introduction;83 5.4.2;4.2 Reagent Jetting - Technology Overview;83 5.4.3;4.3 Thermal Jet Based Dispensing;85 5.4.4;4.4 Piezo Jet Based Dispensing;87 5.4.5;4.5 Solenoid Jet Based Dispensing;88 5.4.6;References;91 5.5;5 Manufacturing of 2-D Arrays by Pin- printing Technologies;93 5.5.1;5.1 Introduction;93 5.5.2;5.2 Definition of 'Contact' Pin-Printing;93 5.5.3;5.3 Overview of Different Pin Technologies;94 5.5.4;5.4 Other System Components and Environmental Factors;99 5.5.5;5.5 Pin Printing Process;101 5.5.6;5.6 Example of a High Throughput Pin-Printing System for Manufacturing of 2D Arrays - the Corning GENII System;104 5.5.7;5.7 Conclusion;106 5.5.8;References;107 5.6;6 Nanoarrays;109 5.6.1;6.1 Introduction;109 5.6.2;6.2 Passive Nano-scale Arrays;111 5.6.3;6.3 Computational Nanoarrays;125 5.6.4;6.4 Dynamic Nanoarrays;129 5.6.5;6.5 Conclusion;135 5.6.6;References;135 5.7;7 The Use of Microfluidic Techniques in Microarray Applications;139 5.7.1;7.1 Introduction;139 5.7.2;7.2 Biochannel Hybridization Arrays;140 5.7.3;7.3 Chips with Cavitation Microstreaming Mixers - Kinetics Studies;148 5.7.4;7.4 Integrated Microfluidic Reactors for DNA Amplification and Hybridization;155 5.7.5;7.5 Summary and Conclusions;162 5.7.6;References;162 5.8;8 Labels and Detection Methods;166 5.8.1;8.1 Introduction;166 5.8.2;8.2 Fluorophore Labelling and Detection Methods;167 5.8.3;8.3 Enhanced Fluorescence-Based Assays;170 5.8.4;8.4 Phosphor Reporters;173 5.8.5;8.5 Electrochemical Detection;175 5.8.6;8.6 Metal Nanoparticle Labels and Metal Thin Films for Microarrays;178 5.8.7;8.7 Conclusions;191 5.8.8;References;193 5.9;9 Marker-free Detection on Microarrays;199 5.9.1;9.1 Introduction;199 5.9.2;9.2 Imaging Ellipsometry and Imaging Surface Plasmon Resonance on Biochips;199 5.9.3;9.3 Intrinsic UV Fluorescence for Chip Analysis of Rare Proteins;208 5.9.4;9.4 Genetic Diagnostics with Unlabelled DNA;215 5.9.5;References;222 6;DNA Microarrays;226 6.1;10 Analysis of DNA Sequence Variation in the Microarray Format;227 6.1.1;10.1 Introduction;227 6.1.2;10.2 Principles of Genotyping;229 6.1.3;10.3 Performing the Assays in Practice;233 6.1.4;10.4 Conclusion;238 6.1.5;References;239 6.2;11 High Sensitivity Expression Profiling;244 6.2.1;11.1 Introduction;244 6.2.2;11.2 Oligonucleotide Expression Arrays;245 6.2.3;11.3 cDNA-based Expression Arrays;254 6.2.4;11.4 Appendix;259 6.2.5;References;260 6.3;12 Applications of Matrix-CGH (Array-CGH) for Genomic Research and Clinical Diagnostics;266 6.3.1;12.1 Introduction;266 6.3.2;12.2 Technical Aspects;268 6.3.3;12.3 Applications;271 6.3.4;References;275 6.4;13 Analysis of Gene Regulatory Circuits;279 6.4.1;13.1 Introduction;279 6.4.2;13.2 An Experimental Protocol for Genome Wide Location Analysis;282 6.4.3;13.3 Example: Identifying the Target Genes of Human E2F4;287 6.4.4;13.4 Summary;289 6.4.5;References;289 7;Protein Microarrays;291 7.1;14 Protein, Antibody and Small Molecule Microarrays;292 7.1.1;14.1 Introduction;292 7.1.2;14.2 Protein Microarrays;293 7.1.3;14.3 Antibody Microarrays;296