Integrated Biochips for DNA Analysis

by Liu, Robin Hui, Ph.D.; Lee, Abraham P.

• ISBN13: 9780387767581
• ISBN10: 0387767584
• Edition: 1st
• Format: Hardcover
• Copyright: 2007-12-30
• Publisher: Landes Bioscience

Summary

The objective of this book is to provide up-to-date coverage of some of the emerging developments in the field of integrated DNA biochips. It will prove a useful source of information for researchers in the field and for those who are just entering the field of biochip research.

Table of Contents

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
Table of Contents provided by Ingram. All Rights Reserved.