Integrated Biochips for DNA Analysis

Cover -- CONTENTS -- Preface -- 1. Integrated DNA Biochips: Past, Present and Future -- Early Developments -- Formative Years -- New Developments -- Future and Path Forward -- 2. Integrated Molecular Analyses of Biological Samples on a Bead-Based Microarray Platform -- Universal Arrays and the GoldenGate174; Genotyping Assay -- Gene Expression Analysis with the DASL174; Assay -- Allele-Specific Expression Analysis -- DNA Methylation Analysis -- Whole-Genome Gene Expression -- Whole-Genome Genotyping -- 3. Integrated Mierofluidic CustomArray Biochips for Gene Expression and Genotyping Analysis -- Semiconductor-Based DNA Microarray -- Microfluidic Cartridge -- Fluidic Architecture and Operation -- Micropumps -- Micromixing -- Microvalves -- Gene Expression Assay -- Subtyping Assay -- Sequencing Assay -- Discussion -- 4. Self-Contained, Fully Integrated Biochips for Sample Preparation, PCR Amplification and DNA Microarray Analysis -- Device Design and Fabrication -- Fluidic Transport -- Micromixing -- Microvalves -- Micropumps -- Sample Preparation -- On-Chip DNA Amplification -- DNA Microarray Detection -- Pathogenic Bacteria Detection -- Single Nucleotide Polymorphism Assay -- Discussion -- Conclusion -- 5. Integrating Sample Processing and Detection with Microchip Capillary Electrophoresis of DNA -- Microchip CE of DNA -- Integrating Sample Processing with Microchip CE of DNA -- Integrated DNA Detectors for CE Microchips -- Phase-Changing Sacrificial Materials for Polymer Microchip Analysis Systems -- 6. Integrated Plastic Microfluidic Devices for Bacterial Detection -- Device Design and Fabrication -- Microfluidic Valves -- Screen-Printed Heaters and Electrodes -- PCR 'Thermal Cycling -- Bacterial Detection -- 7. PCRin Integrated Microfluidic Systems -- PCR in Microfluidic Systems -- Integrated PCR and Gel Electrophoresis -- Integrated PCR and Sample Purification -- Integrated PCR and Hybridization -- Further Advancements in Integration -- Novel Micro-PCR Methods -- 8. Integrated Nucleic Acid Analysis in Parallel Matrix Architecture -- Nucleic Acid Analysis -- Pneumatic Control of Microfluid -- Integration and Parallelization on a Microfluidic Chip -- DNA Analyses with Complex Parallelization -- RNA Analyses -- Matrix PCR on a Microfluidic Chip -- Pico Titer Plate-Based PCR -- Microfluidic Digital PCR -- Microfluidic Sanger DNA Sequencing -- Microfluidic DNA Sequencing-by-Synthesis -- Summary and Perspective -- 9. Chip-Based Genotyping by Mass Spectrometry -- MALDI Based Genotyping Methods -- Chip as a Sample Positioning and Concentration Device -- Chip as a Functionalized Capture Device -- ESI Based Genotyping Methods -- 10. Analyzing DNA-Protein Interactions on a Chip -- Approaches to Identify Cis-Regulatory Elements -- Surface Plasmon Resonance-Based Assays -- Using Surface Plasmon Resonance to Measure DNA-Protein Interaction -- Tests Using a Spreeta Biosensor -- Experimental Set Up -- Measuring DNA-Protein Interactions Using the Surface Plasmon Resonance Sensor -- Surface Preparation -- Measurements of Double-Stranded DNA Surface Adsorption -- Sensitivity of the Surface Plasmon Resonance Based Sensor -- Projected Sensitivity Based on Preliminary Experiments -- Surface Plasmon Resonance Is Sensit.