| Preface | p. xv |
| Integrated DNA Biochips: Past, Present and Future | p. 1 |
| Early Developments | p. 1 |
| Formative Years | p. 2 |
| New Developments | p. 5 |
| Future and Path Forward | p. 7 |
| Integrated Molecular Analyses of Biological Samples on a Bead-Based Microarray Platform | p. 10 |
| Universal Arrays and the GoldenGate Genotyping Assay | p. 12 |
| Gene Expression Analysis with the DASL Assay | p. 15 |
| Allele-Specific Expression Analysis | p. 16 |
| DNA Methylation Analysis | p. 17 |
| Whole-Genome Gene Expression | p. 19 |
| Whole-Genome Genotyping | p. 19 |
| Integrated Microfluidic CustomArray Biochips for Gene Expression and Genotyping Analysis | p. 25 |
| Semiconductor-Based DNA Microarray | p. 28 |
| Microfluidic Cartridge | p. 30 |
| Fluidic Architecture and Operation | p. 32 |
| Micropumps | p. 32 |
| Micromixing | p. 33 |
| Microvalves | p. 35 |
| Gene Expression Assay | p. 35 |
| Subtyping Assay | p. 38 |
| Sequencing Assay | p. 40 |
| Discussion | p. 41 |
| Self-Contained, Fully Integrated Biochips for Sample Preparation, PCR Amplification and DNA Microarray Analysis | p. 46 |
| Device Design and Fabrication | p. 48 |
| Fluidic Transport | p. 49 |
| Micromixing | p. 49 |
| Microvalves | p. 52 |
| Micropumps | p. 55 |
| Sample Preparation | p. 56 |
| On-Chip DNA Amplification | p. 58 |
| DNA Microarray Detection | p. 59 |
| Pathogenic Bacteria Detection | p. 61 |
| Single Nucleotide Polymorphism Assay | p. 62 |
| Discussion | p. 62 |
| Conclusion | p. 63 |
| Integrating Sample Processing and Detection with Microchip Capillary Electrophoresis of DNA | p. 68 |
| Microchip CE of DNA | p. 69 |
| Integrating Sample Processing with Microchip CE of DNA | p. 70 |
| Integrated DNA Detectors for CE Microchips | p. 73 |
| Phase-Changing Sacrificial Materials for Polymer Microchip Analysis Systems | p. 73 |
| Integrated Plastic Microfluidic Devices for Bacterial Detection | p. 78 |
| Device Design and Fabrication | p. 79 |
| Microfluidic Valves | p. 82 |
| Screen-Printed Heaters and Electrodes | p. 83 |
| PCR Thermal Cycling | p. 83 |
| Bacterial Detection | p. 84 |
| PCR in Integrated Microfluidic Systems | p. 90 |
| PCR in Microfluidic Systems | p. 91 |
| Integrated PCR and Gel Electrophoresis | p. 91 |
| Integrated PCR and Sample Purification | p. 95 |
| Integrated PCR and Hybridization | p. 98 |
| Further Advancements in Integration | p. 98 |
| Novel Micro-PCR Methods | p. 102 |
| Integrated Nucleic Acid Analysis in Parallel Matrix Architecture | p. 107 |
| Nucleic Acid Analysis | p. 107 |
| Pneumatic Control of Microfluid | p. 107 |
| Integration and Parallelization on a Microfluidic Chip | p. 108 |
| DNA Analyses with Complex Parallelization | p. 109 |
| RNA Analyses | p. 111 |
| Matrix PCR on a Microfluidic Chip | p. 113 |
| Pico Titer Plate-Based PCR | p. 113 |
| Microfluidic Digital PCR | p. 114 |
| Microfluidic Sanger DNA Sequencing | p. 114 |
| Microfluidic DNA Sequencing-by-Synthesis | p. 115 |
| Summary and Perspective | p. 116 |
| Chip-Based Genotyping by Mass Spectrometry | p. 117 |
| MALDI Based Genotyping Methods | p. 119 |
| Chip as a Sample Positioning and Concentration Device | p. 120 |
| Chip as a Functionalized Capture Device | p. 121 |
| ESI Based Genotyping Methods | p. 123 |
| Analyzing DNA-Protein Interactions on a Chip | p. 128 |
| Approaches to Identify Cis-Regulatory Elements | p. 129 |
| Surface Plasmon Resonance-Based Assays | p. 130 |
| Using Surface Plasmon Resonance to Measure DNA-Protein Interaction | p. 131 |
| Tests Using a Spreeta Biosensor | p. 132 |
| Experimental Set Up | p. 133 |
| Measuring DNA-Protein Interactions Using the Surface Plasmon Resonance Sensor | p. 134 |
| Surface Preparation | p. 134 |
| Measurements of Double-Stranded DNA Surface Adsorption | p. 135 |
| Sensitivity of the Surface Plasmon Resonance Based Sensor | p. 135 |
| Projected Sensitivity Based on Preliminary Experiments | p. 135 |
| Surface Plasmon Resonance Is Sensitive Enough to Detect Physiologically Relevant DNA-Protein Interactions | p. 136 |
| Single Molecule DNA Detection | p. 139 |
| Single-Molecule DNA Detection Based on Use of Molecular FRET Probes | p. 141 |
| Single-Quantum-Dot-Based FRET Nanosensor for DNA Detection | p. 142 |
| Single-Molecule Fluorescence Burst Coincidence Detection | p. 143 |
| Multiplexed DNA Detection Based on Multicolor Colocalization Analysis of Quantum Dot Nanoprobes | p. 146 |
| Manipulation and Focusing of Single Molecules | p. 147 |
| Conclusion and Prospectives | p. 147 |
| Nanochannels for Genomic DNA Analysis: The Long and the Short of It | p. 151 |
| Theory | p. 154 |
| Methods: Realizations of Nanochannels | p. 162 |
| Experimental Results | p. 165 |
| Beyond Microtechnology-Nanotechnology in Molecular Diagnosis | p. 187 |
| History of Nanotechnology | p. 187 |
| Safety and Nanotechnology | p. 188 |
| Nanofabrication Methods | p. 189 |
| Selected Applications in Molecular Diagnosis | p. 190 |
| Index | p. 199 |
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