Microarrays / Hans-Joachim Müller, Thomas Röder.

Format:

Book

Author/Creator:

Müller, Hans-Joachim.

Contributor:

Röder, Thomas.

Series:

Experimenter series

The experimenter series

Language:

English

Subjects (All):

DNA microarrays.

Oligonucleotide Array Sequence Analysis.

Protein Array Analysis.

Medical Subjects:

Oligonucleotide Array Sequence Analysis.

Protein Array Analysis.

Physical Description:

xv, 212 pages : illustrations ; 26 cm.

Place of Publication:

Burlington, MA : Elsevier Academic Press, [2006]

Summary:

Microarray technology allows us to answer many questions about gene expression and drug-target screening by employing high-throughput screening. This can be accomplished much more quickly and economically than ever before with the new technology. This new technology, however, is still relatively unfamiliar, so comprehensive specialized knowledge is helpful and sometimes necessary for an assessment of which application can and should be used.

This book dedicates itself to microarrays with clear and understandable explanations and an overview of the presently available hardware, biochips and software. Separate chapters cover the different requirements for DNA and protein chips as well as spotters and scanners.

Readers will appreciate helpful hints and reasoned analysis about requirements for furnishing or expanding their own microarray laboratory. In addition to high-throughput screening, patent search and the requirements of a "clean room" are discussed. A comprehensive glossary and company directory are included.

Contents:

1.2 Design and development of microarrays 3

2 Applications 7

2.1 Scientific problems 7

2.2 The pharmaceutical goal 10

2.3 The demands of biotechnical companies 12

3 Technology 15

3.1 Protein microarrays 15

3.1.1 Gene and protein expression 15

3.1.2 Protein sundries: from molecule to biochip 24

3.1.3 Protein chips 42

3.2 Nucleic acid microarrays 57

3.2.1 Hybridization probes 57

3.2.2 Minimal quantities of RNA-7; What to do? 63

3.2.3 Production of DNA microarrays 70

3.3 Microarray detection 76

3.3.1 Light and radiation 76

3.3.2 Luminescent fluorophore T 78

3.3.3 High-energy laser light 84

3.3.4 Microarray scanner: Mode of operation 86

3.3.5 Operating mode of microarray imagers 90

3.3.6 Dynamic range 92

3.3.7 Pixels and spots 93

3.4 Microarray marking systems 94

3.4.1 Tyramide-signal amplification 94

3.4.2 Dendrimers 95

3.4.3 Quantum dots 96

3.4.4 Chemiluminescence 99

3.4.5 Radioactivity 100

3.4.6 Time-resolved fluorescence 100

4 Instrumentation and Software 105

4.1 Microarray spotters 106

4.1.1 Mechanical contact spotting 110

4.1.2 Piezo-dispenser technology 111

4.1.3 Grids and spots 115

4.2 Digitizing: The microarray scanner 115

4.2.1 The microarray imager 116

4.2.2 The microarray scanner 117

4.3 Microarray software and documentation 117

4.3.1 Documentation of microarray experiments 119

4.3.2 Design of the experiment 120

4.3.3 Validation of the results 121

4.3.4 Microarray software 123

4.3.5 Comparison of expression data 129

4.3.6 Advanced analysis 131

4.4 Additional laboratory equipment and Laboratory requirements for microarray applications 136

4.4.2 Additional helpful laboratory equipment 136

4.5 Clean-room technology 137

4.5.1 Cleanliness classes 137

4.5.2 Clean-room systems 138

5 Execution of the Microarray Experiment 141

5.1 Isolation and preparation of nucleic acids 141

5.1.1 Isolation of RNA 141

5.1.2 mRNA isolation from eukaryotes 142

5.1.3 mRNA isolation from bacteria 142

5.1.4 Specimen fabrication with the aid of cDNA synthesis 143

5.1.5 Hybridization on the DNA biochip 144

5.1.6 Preamplification with T7-RNA polymerase 144

5.1.7 Fabrication of the microarray samples 146

5.1.8 Quantification, inspection, reliability 147

5.1.9 Hybridization of the samples 147

5.1.10 Poly (L-lysine) coating 149

5.2 Protein array protocols 149

5.2.1 Protein array buffers 150

5.2.2 Verification with antibodies 152

5.2.3 Protein kinase array: Verification with [superscript 33]P 153

6 High-Throughput Screening 155

6.1 Laboratory automation 156

6.1.1 Laboratory automation software 158

6.1.2 Preparation of samples 160

6.1.3 Analysis and reporting 160

6.2 Drug-target screening 164

6.3 Clinical chemistry and genetic screening 164

7 Database Research and Patents 169

7.1 Database research 169

7.2 Patents 170

7.2.1 Patent research 171

7.2.2 Patent-protected technologies 177

7.3 Brands and trademarks 183

8 Prospects for the Future 185

8.1 Technical developments 185

8.2 Requirement profiles 186

8.3 The end of the end 189

9.1 Common buffers 191

9.1.1 Spotting- and washing buffers 191

9.1.2 Block solutions 191

9.1.3 Hybridization solutions 192

9.2 Formula for the calculation of the annealing temperature of oligonucleotides 192

9.2.1 Formula for oligonucleotides up to 15 bases 192

9.2.2 Formula for oligonucleotides from 20 to 70 bases 192

9.3 Molar specifications and calculations 192

9.3.1 Definition of a mole 192

9.3.2 Definition of molar mass and molarity 192

9.3.3 Picomolar quantities for nucleic acids 193

9.3.4 Definition of the dalton unit 193

9.3.5 Picomolar quantities for proteins and peptides 194

9.4 Calculation of the microarray spot surface area 194

9.5 Calculation of the microarray spot density 195

9.5.1 Spot density based on center-to-center distance 195

9.5.2 Spot density based on the number of absolute spots per cm[superscript 2] 195

9.6 Calculation of fluorophore or target density 195

Company Register 197.

Notes:

Includes bibliographical references and index.

ISBN:

0120885433

OCLC:

61451512

Publisher Number:

9780120885435