DeutschesFachbuch.de : Microarrays, Volume I Synthesis Methods

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Contents
Dedication v
Preface vI
Contents of the Companion Volume xiii
Contributors xvii
1 Introduction: Array Technology-An Overview
Hartmut Seliger 7
2 Current Microarray Surface Chemistries
David W. Grainger, Charles H. G reef, Ping Gong, and Michael f. Lochhead 37
3 Nonfouling Surfaces: A Review of Principles and Applications for Microarray Capt...
Ping Gong and David W. Grainger 59
4 Optimization of Oligonucleotide DNA Microarray
Martin Dufva and Claus B. V. Christensen 93
5 Detection of DNA Copy Number Alterations in Complex Genomes Using Array Comparat...
Wei-Wen Cai 105
6 Evaluating the Quality of Data From Microarray Measurements
Lili Wang, A. K. Gaigalas, M. B. Satterfield, M. Salit, Y. long, and J. Noble 127
7 Construction of Oligonucleotide Microarrays (Biochip) Using Heterobifunctional R...
Jyoti Choithani, Bhashyam Vaijayanthi, Pradeep Kumar, and Kailash Chand Gupta 133
8 Choice of Polymer Matrix, Its Functionalization and Estimation of Functional Gro...
Shweta Mahajan, Bhashyam Vaijayanthi, Copal Rembhotkar, Kailash Chand Gupta, and Prad...
9 Methods in High-Resolution, Array-Based Comparative Genomic Hybridization
Mark R. McCormick, Rebecca R. Selzer, and Todd A. Richmond 189
10 Design and Fabrication of Spotted Long Oligonucleotide Microarrays for Gene Exp...
Cheng-Chung Chou and Konan Peck 213
11 Construction of In Situ Oligonucleotide Arrays on Plastic
Jang B. Rampai, Peter J. Coassin, and Robert S. Matson 227
12 Detecting Ligated Fragments on Oligonucleotide Microarrays: Optimizing Chip Des...
Ian R. Berry, Carol A. Delaney, and Graham R. Taylor 247
13 Detection of Single-Nucleotide Polymorphisms in Cancer-Related Genes by Miniseq...
Alexandre Ho-Pun-Cheung, Hafid Abaibou, Philippe Cleuziat, and Evelyne Lopez-Crapez ...
14 Hybridization Analysis Using Oligonucleotide Probe Arrays
Roberts. Matson and Jang B. Rampai 279
15 In Situ Synthesis of Peptide Microarrays Using Ink-Jet Microdispensing
Bogdan V. Antohe and Patrick W. Cooley 299
16 Intein-Mediated Peptide Arrays for Epitope Mapping and Kinase/Phosphatase Assay...
Ming-Qun Xu, Inca Ghosh, Samvel Kochinyan, and Luo Sun 313
17 Printing Low Density Protein Arrays in Microplates
Robert S. Matson, Raymond C. Milton, Michael C. Cress, Tom S. Chan, and Jang B. Rampa...
18 Forward-Phase and Reverse-Phase Protein Microarray
Yaping Zong, Shanshan Zhang, Huang-Tsu Chen, Yunfei Zong, and Yaxian Shi 363
19 Cell Microarray for Functional Exploration of Genomes
David Castel, Marie-Anne Debily, Amandine Pitaval, and Xavier Gidrol 375
20 Quantification of Mixed-Phase Hybridization on Polymer Microparticles by Europi...
Kaisa Ketomäki and Harri Lönnberg 385
21 Measurement of the Sugar-Binding Specificity of Lectins Using Multiplexed Bead-...
Kazuo Yamamoto, Fumiko Yasukawa, and Seiichiro Ito 407
22 Nanotechnology: Moving From Microarrays Toward Nanoarrays
Hua Chen and Jun Li 411
Index 437
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Index
AAFM, see Atomic force microscopy
Aldehydes, functional determination on glass, 177
- glass slide modification, 171
- quantification on surfaces, 168, 169
- surface chemistry, 45
Alginic acid, polymer brush coating for protein fouling prevention, 73, 74
Allele-specific oligonucleotide, see Oligonucleotide probe array
Amino group, aminopropylation of glass slides, 170
- quantification on surfaces, 168, 169, 174-176, 230, 231
Aminosilane, surface chemistry, 42-44
Analyte, definition, 3
Array comparative genomic hybridization, see Comparative genomic hybridization Array,...
- definition, 2, 3- historical perspective, 4-7- interdisciplinary development, 4
- Internet resources, 22
- prospects, 21, 22
Atom transfer radical polymerization (ATRP), polymer brush coating for protein foulin...
Atomic force microscopy (AFM), nanochip array detection, 429
ATRP, see Atom transfer radical polymerization
BBackground, definition, 39, 95
- protein/peptide arrays, 50, 51
- surface chemistry effects, 39, 40
Biomek high-density replicating tool, see Microplate protein microarray
CCapillary electrophoresis, multiplex ligation-dependent probe amplification products...
Carbohydrate microarray, glycopeptide arrays, see
- Glycopeptide arrays
- overview and applications, 17-19
- surface chemistry, 53, 54
Carbon nanotube (CNT) nanoelectrode array, advantages, 415, 416
- electrochemical detection, 422-425
- fabrication, 418, 419, 421
- nanotube features, 414, 415
- nucleic acid analysis rationale, 417, 418
- overview, 412, 414-416
- probe functionalization, 421, 422
- prospects, 430
- sensitivity of electrode, 414, 415
Carboxyl group, carboxalkylation of glass slides, 171
quantification on surfaces, 168, 169, 177
Cell microarray, functional genomics, cell transfection and fixation, 380
- image acquisition, 380, 381
- knockdown assessment, 381
- materials, 375-378, 382, 383
- microarray construction printing, 379, 380, 383, 384
- solutions, 378, 379, 383
- plasmid preparation, 378, 383
- principles, 375
- small interfering RNA preparation, 378
- transfection assessment, 381
- overview and applications, 19, 20
CGH, see Comparative genomic hybridization
CNT nanoelectrode array, see Carbon nanotube nanoelectrode array
Combinatorial library, definition, 2- formats, 3
- historical perspective, 6, 7
Comparative genomic hybridization (CGH), challenges, 106
clone-based arrays, 106
crosslinking of silanized DNA, 107, 108- fluorescence ratio normalization, 115, 116
- genomic probe labeling, chemical activation, 112, 113, 117
- random priming labeling, 113, 114, 118
- high-resolution mapping, agarose gel electrophoresis of fragmented DNA, 198, 200
- applications, 189, 190
- data analysis,
- example, 206, 208
- normalization, 204, 205
- PAIR data combination, 203, 204
- segmentation, 205, 206
- viewing data, 206
- window averaging, 205
- DNA sample quality, 208, 209- fine-tiling array design, 195- hybridization and wash...
- mask preparation for synthesis, 196
- materials, 196, 197
- Nimble-Gen microarray, access, 196
- utilization, 190, 191, 196
- Nimble-Scan-TM analysis, 203
- optimization, oligonucleotide length, 192
- probe selection, 192
- strand selection, 192
- ozone interference, 210
- sample preparation, fluorescent labeling, 200, 201, 210
- pooling and suspension, 201
- scanning, 202
- sonication of genomic DNA, 198
- tiling formats in array design, 193
- whole genome array design, 15-mer frequency determination, 194
- initial probe sets, 193, 194
- oligo uniqueness, 194, 195
- probe selection, 195
- hybridization and washing, 114, 115, 118
- image quantification, 115
- materials, 109, 110
- oligoarray construction, 108, 109
- principles of array comparative genomic hybridization, 105, 106
- printing and processing of arrays, 112, 116, 117
- scanning, 115
- silanizationof DNA, 106, 107, 110, 111, 116
- slides, cleaning, 111
- coating, 111, 112, 116
Complementary DNA microarrays, complementary DNA synthesis and labeling, 222, 223
- immobilized DNA as probes, 213, 214, 222
- materials, 215
- probe design, algorithms, 30-70-mers, 219, 220 150-mers, 216-219
- overview, 214, 215, 222
- unique sequence identification, 215, 216
- probe immobilization, 221
- probe preparation, 30-70-mers, 221, 223 150-160-mers, 220-223
- RNA extraction, 221, 222
- sensitivity, 214
- spotting, 12, 13
Copy number, see Multiplex ligationdependent probe amplification
Cy 3, fluorescence spectral characterization, 128, 130
Cy 5, fluorescence spectral characterization, 128, 130
Cystic fibrosis, see In situ synthesis; Oligonucleotide probe array
DDELFIA® , see Oligonucleotide-coated microparticles
- 1 -O-(4, 4'-Dimethoxytrityl)-6 aminohexanol (DTAH), aldehyde determination on glass...
- carboxyl group determination on glass, 177
- epoxide group determination on glass, 176, 177, 182- functional group quantificatio...
- synthesis, 173
- S-4, 4'-Dimethoxytrityl-3 mercaptopropionic acid (DMPA), amino group determination ...
- hydroxyl group determination on glass, 176
- preparation of reagent, 174
- sulfhydryl group determination on glass, 175
- synthesis, 171, 172 15-(4, 4-Dimethoxytrityloxy)-12, 13
dithapentadecanoic acid, synthesis, 389-391, 398
- 4, 4'-Dimethoxytrityl-S'-(2-thio-5-nitropyridyl)-2
- mercaptoethane (DTNPME), functional group quantification on surfaces, 168, 181, 183
- preparation of reagent, 174
- sulfhydryl group determination on glass, 176
- synthesis, 172, 173
DMPA, see S'-Dimethoxytrityl-S mercaptopropionic acid DMTr,
- amino group determination glass, 174, 175
- polypropylene, 230, 231 functional group quantification on surfaces, 168, 169, 178
- hydroxyalkyl group determination on glass, 175
- hydroxyl group determination on polypropylene, 175
- pyridinium (4, 4-dimethoxytrityloxy) acetate synthesis, 388, 389, 398
- sulfhydryl group determination on glass, 175
DNA microarray, clinical prospects, 121
- comparative genomic hybridization, see Comparative genomic
- hybridization complementary DNA or long DNA fragments, see Complementary DNA microa...
dye fluorescence spectral characterization, 128, 130
- hybridization and washing, 124, 124
- materials, 122
- scanner calibration, 124, 129
- target concentration effects on hybridization signals, 127, 129, 130
- target oligonucleotide retention, 124, 126, 129
- immobilization with heterobifunctional reagents, see Heterobifunctional reagents op...
- hybridization, 99, 101
- materials, 95-97, 99
- spotting for probe optimization, 98, 100
- standard curve construction, 98, 100
- performance parameters, 93, 94
DNA sequencing, see Single nucleotide
- polymorphism DNA silanization, see Comparative
- genomic hybridization DTAH, see 1-0-(4, 4'-Dimethoxytrityl)6-aminohexanol
DTNPME, see 4, 4'-Dimethoxytrityl-5'(2-thio-5-nitropyridyl)-2 mercaptoethane
EElectrochemical detection, carbon nanotube nanoelectrode arrays, 422-425
Element, definition, 2, 3
ELF, see Enzyme-labeled fluorescence
ELISA, see Enzyme-linked
- immunosorbent assay Enzyme-labeled fluorescence (ELF), oligonucleotide probe array ...
Enzyme-linked immunosorbent assay (ELISA), antibody probing, 307, 308, 311
- peptide assays, 313, 314
Epitope mapping, intein-mediated peptide arrays, 316, 326, 327
Epoxides, quantification on surfaces, 168, 169, 176, 177, 182
- surface chemistry, 45
Europium(III) fluorescence, see-Oligonucleotide-coated microparticles
FFlow cytometry, microsphere glycopeptide array analysis of lectin binding, 406-408
Fouling, see Protein fouling
Full Moon BioSystem slides, protein microarrays, 365
GGlass surface, functional group chemistry, 166, 167
- functional group quantification, see also specific reagents- overview, 168, 169
- reagent preparation, 171-174- functionalization of microslides, activation, 169, 17...
- aldehyde group generation, 171- aminopropylation, 170- carboxalkylation, 171
- density determination, 177- glycidyloxypropylation, 170, 184- hydroxyalkylation, 17...
- materials, 169, 183- mercaptopropylation, 170, 183, 184
Glycopeptide arrays, flow cytometry analysis, 406-408
- materials, 402, 403, 407
- microsphere coupling to glycopeptides, one-step coupling, 403, 405, 407, 408
- two-step coupling activation, 405, 408
- coupling, blocking, and storage, 405, 406, 408
- multiplexed bead-lectin binding assay, 406
- principles of lectin analysis, 401, 402
HHeparin, polymer brush coating for protein fouling prevention, 73
Heterobifunctional reagents, NTMTA, features, 135
- immobilization chemistry, 152, 153
- synthesis, 143, 144, 152, 160
- NTPAC, features, 136
- modification for array detection, 254, 255, 262, 263
- oligonucleotide probe printing, 251, 252, 254, 262
NNanochip array, enzyme assays, 429, 430
- overview, 412, 417
- prospects, 430
- protein detection, advantages, 425
- antibody immobilization and hybridization, 428, 429
- detection, 429
Nano-Arrayer, 425
- surface modification, 426-428
Nanotechnology, see also Carbon
nanotube nanoelectrode array; Nanochip array, definition, 412, 413
nanoarray rationale, 413, 414
Nimble-Gen microarray, see Comparative genomic hybridizationNonspecific binding (NSB)...
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