Inhaltsverzeichnis

Vorwort

Preface

To meet the emerging needs of genomics, proteomics, and the other omics, microarrays have become unique and important tools for high-throughput analysis of biomolecules. Microarray technology provides a highly sensitive and precise technique for obtaining information from biological samples. It can simultaneously handle a large number of analytes that may be processed rapidly. Scientists are applying microarray technology to understand gene expression, to analyze mutations and single-nucleotide polymorphisms, to sequence genes, and to study antibody-antigen interactions, aptamers, carbohydrates, and cell functions, among many other research subjects.

The objective of Microarrays is to enable the researcher to design and fabricate arrays and binding studies with biological analytes. An additional goal is to provide the reader with a broader description of microarray technology tools and their potential applications. In this edition, Microarrays is divided in two parts: Volume 1 deals with methods for preparation of microarrays, and Volume 2 with applications and data analysis. Various methods and applications of microarrays are described and accompanied by exemplary protocols. Volume 2 also covers topics related to bioinformatics, an important aspect of microarray technologies because of the enormous amount of data coming out of microarray experiments. Together, the two volumes provide useful information to the novice and expert alike.

From this point onward, I will discuss the contents of Volume I: Synthesis Methods. For readers just entering the array technology field, as well as those who are well versed, the history of microarray technology from its conception is covered in the first chapter. Surface activation chemistries and various types of matrices involved in the synthesis of microarrays are summarized in Chapters 2 and 3. As the major objective of this volume is to provide detailed synthesis methods for constructing microarrays, so the emphasis of the remaining chapters is on methods and protocols. I tried to include various types of protocols. Some may look very similar, but in fact each protocol has a unique utility based on the research problem or individual interests. Chapter 4 details array optimization processes based on numerous factors, for example, the printing quality, spot morphology, and quantification of hybridized target. Chapter 5 presents array-based comparative genomic hybridization (array CGH) and includes procedures for making bacterial artificial chromosome DNA arrays. Chapter 6 describes the 60-mer oligonucleotide probes immobilized on coated glass slides to study the effect of target concentration, retention, signal linearity, and properties of fluophores in quantitative gene expression measurements. The array production method using premodified DNA can be directly applied to construction of oligo or cDNA arrays. Such arrays can be used for detection of chromosomal abnormalities in complex genomes. Chapter 7 highlights the use of unique bifunctional reagents, NTMTA and NTPAC for building glass and plastic biochips. Chapter 8 explains the use of sensitive reagents for the determination of the functional group density in the microarray system by spectrophotometric methods. Chapter 9 illustrates the synthesis of high-density arrays using a digital microarray synthesis platform. The use of long optimized oligonucleotide probes (150-mers) for high and specific signal intensity for the measurement of gene expression is described in Chapter 10. In addition to sequence and probe length, the importance of other parameters, such as the surface of the glass slide, linkers/spacers, and the conditions for hybridization are also highlighted in Chapter 10. Chapter 11 deals with in situ synthesized oligoarrays using the Southern Array Maker (SAM) synthesizer and standard phosphoramidite chemistry. The array probes, including cystic fibrosis, were synthesized onto the flat surface of aminated polypropylene. The printing and use of the synthetic oligonucleotide probes for the detection of multiplex ligation-dependent probe amplification products is explained in Chapter 12. The synthesis and the use of grafted pyrrole oligonucleotide probes are demonstrated in Chapter 13. Chapter 14 deals with the optimization of hybridization conditions for in situ synthesized oligoarrays on plastic. Chapters 15 and 16 are devoted for the synthesis of peptide arrays. Creation of protein microarrays in microplate is described in Chapter 17. Arrays of the captured monoclonal antibodies corresponding to specific interleukins are printed down onto the bottom of the wells. A Biomek® 2000 workstation equipped with a high-density replicating tool is used for printing the low-density arrays. For higher density arrays, a microarrayer system (BioDot, Inc.) is employed. Printing the protein arrays onto specially polymer-coated glass slide while maintaining the activity and structure of the protein is described in Chapter 18. Chapter 19 focuses on the printing of cell microarrays for the functional exploration of genomes. Chapter 20 is related to suspension arrays. The oligocoated microparticles are hybridized with the target molecule. The protocol for quantification of oligohybridization complex is analyzed by a europium (111) detection system. Glyco-bead array for calculating the sugar-binding lectins is described in Chapter 21. As we all are aware that array technology is moving forward from micro to nano, Chapter 22 describes this emerging technology.

The chapter highlights the utility of nanoarrays, particularly the analysis of nanoarrays-by using label-free nucleic acids and proteins and others.

I believe this volume, Synthesis Methods, will provide valuable information to scientists at all levels, from the novice to those intimately familiar with array technology. I would like to thank all the contributing authors for providing manuscripts. My thanks are also due to colleagues for their help in completing this work. I thank John Walker for editorial guidance and the staff of Humana Press for making it possible to include large body of available microarray technologies in this volume. Finally, my thanks to my family, especially to my sweet wife Sushma Rampai, for providing all sorts of incentives to complete this project successfully.

Jang B. Rampal

Klappentext

METHODS IN MOLECULAR BIOLOGY^TM • 381

Series Editor: John M. Walker

Microarrays
Volume 7, Synthesis Methods, Second Edition
Edited by
Jang B. Rampal, PhD
Beckman Coulter, Inc., Brea, CA

Microarrays, Volumes 1 and 2, present information for designing and fabricating arrays and binding studies with biological analytes, while providing the reader with a broad range of microarray technology tools and their potential applications. The first volume deals with methods and protocols for the preparation of microarrays. The second volume details applications and data analysis, which is important in analyzing the enormous amount of data coming out of microarray experiments.

Among the topics discussed in Volume I : Synthesis Methods, are matrices in the synthesis of microarrays, array optimization processes, array-based comparative genomic hybridization, 60-mer oligonucleotide probes, bifunctional reagents NTMTA and NTPAC, and high-density arrays using digital microarray synthesis platforms. Other topics include multiplex ligation-dependent probe amplification(MLPA), hybridization conditions for in situsynthesized oligonucleotide arrays, peptide arrays, high-density replication tools (HDRT), protocols for the quantification of oligo hybridization, glyco-bead arrays, and an investigation into the emerging nanotechnology.

Volume 2: Applications and Data Analysis includes insight into processes and protocols for high-qual ity glassbased microarrays used to study nonmammalian vertebrate systems. It describes applications in DNA, peptide, antibody, and carbohydrate microarraying, oligonucleotide microarrays generated from hydrolysis PCR probe sequences, microarray platforms in clinical practice, and screening of cDNA libraries on glass slide microarrays. Authors in this volume also discuss μ Paraflo^TM biochip for nucleic acid and protein analysis, volumetric mass spectrometry protein arrays, protocols for predicting DNA duplex stabil ity on oligonucleotide arrays, and integrated analysis of microarray results.

Microarrays, Volumes 1 and 2, provide ample information to all levels of scientist, from the novice to those intimately familiar with array technology.

FEATURES

• Meticulous exploration into state-of-the-art methods and protocols for microarray technology
• Authors examine bioinformatics, an important aspect in analyzing large amounts of data that emerge during experiments

CONTENTS

Introduction: Array Technology-An Overview. Current Microarray Surface Chemistries. Nonfouling Surfaces: A Review of Principles and Applications for Microarray Capture Assay Designs. Optimization of Oligonucleotide DNA Microarray. Detection of DNA Copy Number Alterations in Complex Genomes Using Array Comparative Genomic Hybridization. Evaluating the Quality of Data From Microarray Measurements. Construction of Oligonucleotide Microarrays (Biochip Using Heterobifunctional Reagents. Choice of Polymer Matrix, Its Functionalization and Estimation of Functional Group Density for Preparation of Biochips. Methods in High-Resolution, Array-Based Comparative Genomic Hybridization. Design and Fabrication of Spotted Long Oligonucleotide Microarrays for Gene Expression Analysis. Construction of In Situ Oligonucleotide Arrays on Plastic. Detecting Ligated Fragments on Oligonucleotide Microarrays: Optimizing Chip Design, Array Multiplex Ligation-Dependent Probe

Amplification Modification, and Hybridization Parameters. Detection of Single-Nucleotide Polymorphisms in Cancer-Related Genes by Minisequencing on a Microelectronic DNA Chip. Hybridization Analysis Using Oligonucleotide Probe Arrays. In Situ Synthesis of Peptide Microarrays Using Ink-let Microdispensing. Intein-Mediated Peptide Arrays for Epitope Mapping and Kinase/Phosphatase Assays. Printing Low Density Protein Arrays in Microplates. Forward-Phase and Reverse-Phase Protein Microarray. Cell Microarray for Functional Exploration of Genomes. Quantification of Mixed-Phase Hybridization on Polymer Microparticles by Europium (III) Ion Fluorescence. Measurement of the Sugar-Binding Specificity of Lectins Using Multiplexed Bead-Based Suspension Arrays. Nanotechnology: Moving From Microarrays Toward Nanoarrays. Index.

Methods in Molecular Biology™ • 381
MICROARRAYS, VOLUME 1
SYNTHESIS METHODS, SECOND EDITION
ISBN: 978-1-58829-589-7
E-ISBN: 978-1-59745-303-5
ISSN: 1064-3745
humanapress.com

ISBN: 978-1-58829-589-7

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Index

A

AFM, 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, applications, 15, 16
- 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 fouling prevention, 74, 75
Atomic force microscopy (AFM), nanochip array detection, 429
ATRP, see Atom transfer radical polymerization

B

Background, definition, 39, 95
- protein/peptide arrays, 50, 51
- surface chemistry effects, 39, 40
Biomek high-density replicating tool, see Microplate protein microarray

C

Capillary electrophoresis, multiplex ligation-dependent probe amplification products, 255, 257, 263
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 washing, 201, 202
- 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

Cy3, fluorescence spectral characterization, 128, 130
Cy5, fluorescence spectral characterization, 128, 130
Cystic fibrosis, see In situ synthesis; Oligonucleotide probe array

D

DELFIA^® , see Oligonucleotide-coated microparticles

- 1 -O-(4, 4'-Dimethoxytrityl)-6 aminohexanol (DTAH), aldehyde determination on glass, 177
- carboxyl group determination on glass, 177
- epoxide group determination on glass, 176, 177, 182

- functional group quantification on surfaces, 168, 183
- synthesis, 173
- S-4, 4'-Dimethoxytrityl-3 mercaptopropionic acid (DMPA), amino group determination on glass, 175

- functional group quantification on surfaces, 168, 169, 178, 179
- 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 microarrays data quality analysis, array fabrication, 122, 123
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 optimization,
- 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)-2mercaptoethane

E

Electrochemical 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 signal development, 291, 292, 298
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

F

Flow cytometry, microsphere glycopeptide array analysis of lectin binding, 406-408
Fouling, see Protein fouling

Full Moon BioSystem slides, protein microarrays, 365

G

Glass 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, 170, 183

- aldehyde group generation, 171

- aminopropylation, 170

- carboxalkylation, 171

- density determination, 177

- glycidyloxypropylation, 170, 184

- hydroxyalkylation, 170

- 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

H

Heparin, 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

N

Nanochip 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 hybridization

Nonspecific binding (NSB), see also Background,

- definition, 39
- fouling, see Protein fouling

- surface chemistry considerations, 50, 51, 60
NSB, see Nonspecific binding

NTMTA, see Heterobifunctional reagents
NTPAC, see Heterobifunctional reagents

O

Oligoethylene glycol alkenethiols, protein fouling prevention, 76-78, 80
Oligonucleotide-coated microparticles, applications, 385, 386
- hybridization quantification with
- europium(III) fluorescence, DELFIA® detection, 397

- fluorescent tagging of
oligonucleotides, 395, 396
- immobilization of oligonucleotides, 394, 398
- materials, 386-388, 397, 398
- microparticle derivatization, 391, 392, 398
- mixed-phase hybridization assays, 396-398
oligonucleotide synthesis, 392-394, 398
- reagent synthesis, 15-(4, 4-dimethoxytrity loxy)12, 13-dithapentadecanoic acid, 389-391, 398
- pyridinium (4, 4- dimethoxytrityloxy) acetate, 388, 389, 398
Oligonucleotide probe array, biotin label quantification, chemiluminescent detection, 289
- colorimetric detection, 290, 296
- dot blot preparation, 288, 289
- differentiation of closely-related sequences, 281-283, 292, 293
- ELF signal development, 291, 292, 298
- hybridization, mplicon hybridization, 290, 291, 297

- factors affecting, 292

- quality control, 290, 297

- theory, 280, 281
- materials, 283-285
- polymerase Chain reaction, amplicon concentration estimation, 288, 295
- amplification, 286, 294
- electrophoresis of amplification products, 287, 295
- gel staining, 287, 295
- principles, 279, 280
- replica blot, 291
- SYBR GREEN I, destaining, 286
- staining, 285, 293, 294

P

PCR, see Polymerase chain reaction

PEG, see Polyethylene glycol

Peptide microarray, see Protein/peptide
- microarray Phosphatase, intein-mediated peptide array assays,

- blotting, 330, 331
- immunoassay, 331
- incubation conditions, 330
- ligation reaction, 330
- on-membrane assay, 331, 332
- principles, 320, 321, 328
- substrate preparation, 329, 330
PixSys, microplate protein microarray printing, 356, 358
PLL, see Polylysine

Polyethylene glycol (PEG), functional derivatives, 67, 73
- grafting, see Polymer brush

- coatings protein fouling prevention mechanisms, 66-69
- structure, 67
- surface coating, 67
Polylysine (PLL), surface chemistry, 44, 45
Polymerase chain reaction (PCR), oligonucleotide probe array, amplicon concentration estimation, 288, 295
- amplification, 286, 294
- electrophoresis of amplification products, 287, 295
- gel staining, 287, 295
- target and primer synthesis for polypropylene oligonucleotide array -construction, 242
Polymer brush coatings, fabrication of brushes, 70-73

- functional assessments of surface
- chemistries, 81, 82
- grafting density, 70-72
- grafting-from strategies, 74, 75
- grafting-to strategies, 72-74
protein fouling prevention mechanisms, 69, 70
Polymer thin film, surface chemistry, 45, 46
Polypropylene surface, DMTr determination of hydroxyl groups, 175

- functional group chemistry, 167

- functionalization, density determination, 177
- hydroxylation, 171
- materials, 169, 183
- in situ synthesis of oligonucleotide arrays, see In situ synthesis oligonucleotide

probe array, see Oligonucleotide probe array

Probe, definition, 3
- density, 95, 97, 98, 100
- loading, 38
Protein fouling, diagnostic surface selectivity, 61-65
performance benchmarks, 62-65
prevention strategies, controlled interfacial chemistries, 75-81
- overview, 65, 66
polyethylene glycol surfaces, 66-69
polymer brush coatings, fabrication of brushes, 70-73
- grafting density, 70-72
- grafting-from strategies, 74, 75
- grafting-to strategies, 72-74
- mechanisms, 69, 70
Protein/peptide microarray, forward-phase protein microarray, antibody detection, 369-371
- Full Moon BioSystem slides, 365
- humidity treatment, 369, 372
- materials, 365
pretreatment, 369, 372
printing target preparation, 369
- scanner calibration, 366-368
- glycopeptide arrays, see Glycopeptide arrays ink-jet microdispensing of peptide microarrays, cellulose membrane substrate
preparation, 302, 303, 310
- enzyme-linked immunosorbent assay antibody probing, 307, 308, 311
- materials, 300-302, 309, 310
peptide cleavage, 308, 309
peptide synthesis, 304-307, 311
printing system and set up, 303, 304, 310, 311
- intein-mediated peptide arrays, antibody specificity analysis, 316-318, 327, 328
- blotting of carrier protein-peptide
- complex, 323, 324
- epitope mapping, 316, 326, 327
- kinase assays, on-membrane assay, 332, 333
principles, 319, 333
- ligation efficiency determination, 325.335
- materials, 321, 322, 334
peptide ligation to carrier protein, 323, 335-337
phosphatase assays, blotting, 330, 331
- immunoassay, 331
- incubation conditions, 330
- ligation reaction, 330
- on-membrane assay, 331, 332
principles, 320, 321, 328
- substrate preparation, 329, 330
principles, 314-316
- sample preparation, 322, 323, 335.336
- Western blot, 325, 326
- microplate microarrays, see Microplate

protein microarray nanochip array, see Nanochip array overview and applications, 16, 17, 299, 300, 364
- reverse-phase protein microarray, antibody detection, 372
- Full Moon BioSystem slides, 365
- humidity treatment, 371
- materials, 365
pretreatment, 372
printing target preparation, 371
- scanner calibration, 366-368
- surface chemistry, capture array, 51, 52
- commercial products, 48, 49, 53
- interaction array, 52, 53
- reverse-phase array, 52
Pyridinium (4, 4-dimethoxytrityloxy) acetate, synthesis, 388, 389, 398

Q

Quill pin, microplate protein microarray printing, 348, 354, 355

R

Radio frequency glow discharge (RFGD), coating deposition, 80, 81
polypropylene derivatization, 228, 230
Reverse blot, see Oligonucleotide probe
- array RFGD, see Radio frequency glow
- discharge RNA interference, see Cell microarray

S

Saccharide microarray, see Carbohydrate microarray

SAMs, see Self-assembled monolayers

Scanning, comparative genomic hybridization arrays, 115
- high-resolution comparative genomic hybridization, 202
scanner calibration, DNA microarrays, 124, 129
- protein microarrays, 366-368
SDTB, see N -Succinimidyl-4-0-(4, 4'dimethoxytrityl)butyrate

Self-assembled monolayers (SAMs), protein fouling prevention, 76, 77, 79, 80
Single nucleotide polymorphism (SNP), clinical significance, 267, 268
- detection approaches, 268
sequencing on DNA chip, DNA extraction, 270, 276
- extended probe denaturation and revelation, 273

- fluorescent signal acquisition and analysis, 273-276
- interpretation, 274, 275
- materials, 268-270, 275, 276
- minisequencing reactions, 272, 273, 276
- overview, 268
- target extraction, 270-272
Slide, see Glass surface

Small interfering RNA, see Cell microarray

SNP, see Single nucleotide polymorphism

Southern Array Maker, polypropylene oligonucleotide array construction, 238-240, 245
Spot morphology, surface chemistry effects, 38, 39
- importance, 95
Spotting, complementary DNA or long DNA

- fragments, see Complementary

- DNA microarrays, covalent linkage, 11
- immobilization techniques, 11, 12
- noncovalent linkage, 11
- overview, 7, 8, 134, 166
- probe optimization, 98, 100
Substrates, 11, 134
- N -Succinimidyl-4-0-(4, 4'-dimethoxytrityl)butyrate (SDTB), amino group determination, glass, 176
- polypropylene, 231 functional group quantification on
surfaces, 168, 180, 183, 231
- preparation of reagent, 174
synthesis, 172
Sulfhydryls, see Mercapto group

Surface chemistry, see also Spotting,

- carbohydrate arrays, 53, 54
- DNA microarrays aldehyde surfaces, 45
- aminosilane surfaces, 42-44
- commercial arrays, 41, 42
- custom array vendors, 42, 43
- epoxide surfaces, 45
- membranes, 46, 47
- polylysine surfaces, 44, 45
- polymer thin films, 45, 46
- non-DNA array considerations, cross-reactivity, 49, 50
- nonspecific binding, 50, 51, 60
- overview, 47
structure and bioactivity preservation, 48
- overview, 37, 38
- processing parameter impact, background, 39, 40
- probe loading, 38
spot morphology, 38, 39
- prospects, 54
- protein/peptide arrays, capture array, 51, 52
- commercial products, 48, 49, 53
- interaction array, 52, 53
- reverse-phase array, 52
SYBR GREEN I, see Oligonucleotide

T

- probe array Target, definition, 3
Tissue microarray, overview and applications, 19, 20

W

Western blot, intein-mediated peptide arrays, 325, 326

Autor

Contributors

HAFID ABAIBOU • Apibio, Grenoble, France
BOGDAN V. ANTOHE • Micro-Fab Technologies, Inc., Piano, TX
IAN R. BERRY • Regional DNA Lab, Regional Genetics Service, St. James's
University Hospital, Leeds, UK
WEI-WEN CAI • Department of Molecular and Human Genetics, Houston, TX
DAVID CASTEL • CEA, DSV, DRR, Functional Genomics Department, Evry,
France
TOM S. CHAN • Beckman Coulter, Inc., Fullerton, CA
KAILASH CHAND GUPTA • Nucleic Acids Research Laboratory, Institute
of Genomics and Integrative Biology, Delhi University Campus, Delhi, India
HUA CHEN • NASA Ames Research Center, Moffett Field, CA
HUANG-TSU CHEN • Full Moon BioSystems, Inc., Sunnyvale, CA
JYOTI CHOITHANI • Nucleic Acids Research Laboratory, Institute of Genomics
and Integrative Biology, Delhi University Campus, Delhi, India
CHENG-CHUNG CHOU • Department of Life Science and Institute of Molecular
Biology, National Chung Cheng University, Chia-Yi, Taiwan, Republic
of China
CLAUS B. V. CHRISTENSEN • Department of Micro and Nanotechnology,
Technical University of Denmark, Kongens Lyngby, Denmark
PHILIPPE CLEUZIAT • Apibio, Grenoble, France
PETER J. COASSIN • Aurora BioSciences Discovery, San Diego, CA
PATRICK W. COOLE Y • Micro-Fab Technologies, Inc., Piano, TX
MICHAEL C. CRESS • Beckman Coulter, Inc., Fullerton, CA
MARIE-ANNE DEBILY • CEA, DSV, DRR, Functional Genomics Department,
Evry, France
CAROL A. DELANEY • Regional DNA Lab, Regional Genetics Service,
St. James's University Hospital, Leeds, UK
MARTIN DUFVA • Department of Micro and Nanotechnology, Technical
University of Denmark, Kongens Lyngby, Denmark
A. K. GAIGALAS • Biotechnology Division, National Institute of Standards
and Technology, Gaithersburg, MD
INCA GHOSH • New England Biolabs, Beverly. MA
XAVIER GIDROL • CEA, DSV, DRR, Functional Genomics Department, Evry,
France
PING GONG • Department of Chemical Engineering, Polytechnic University,
Brooklyn, NY
DAVID W. GRAINGER • Department of Pharmaceutics and Pharmaceutical
Chemistry, University of Utah, Salt Lake City, UT
CHARLES H. GREEF • Accelr8 Technology Corporation, Denver, CO
ALEXANDRE HO-PUN-CHEUNG • Centre de Recherche en Cancérologie, Centre
Régional de Lutte contre le Cancer Val d'Aur elle-Paul Lamarque, Parc
Euromédecine, Montpellier Cedex, France
SEIICHIRO ITO • Life Science Division, Hitachi Software Engineering Co.
Ltd., Kanagawa, Japan
KAISA KETOMÄKI • Department of Chemistry, University of Turku,
Turku, Finland
SAMVEL KOCHINYAN • New England Biolabs, Beverly, MA
PRADEEP KUMAR • Nucleic Acids Research Laboratory, Institute of Genomics
and Integrative Biology, Delhi University Campus, Delhi, India
JUN Li • NASA Ames Research Center, Mojfett Field, CA
MICHAEL J. LOCHHEAD • Accelr8 Technology Corporation, Denver, CO
HARRI LÖNNBERG • Department of Chemistry, University of Turku, Turku,
Finland
EVELYNE LOPEZ-CRAPEZ • Centre de Recherche en Cancérologie, Centre
Régional de Lutte contre le Cancer Val d'Aur elle-Paul Lamarque,
Montpellier Cedex, France
SHWETA MAHAJAN • Nucleic Acids Research Laboratory, Institute of Genomics
and Integrative Biology, Delhi University Campus, Delhi, India
ROBERT S. MATSON • Beckman Coulter, Inc., Fullerton, CA
MARK R. MCCORMICK • Nimble-Gen Systems Inc., Madison, WI
J. NOBLE • Biotechnology Group, Quality of Life Division, National Physical
Laboratory, Middlesex, United Kingdom
RAYMOND C. MILTON • Beckman Coulter, Inc., Fullerton, CA
KONAN PECK • Institute of Biomedical Sciences, Academia Sinica, Taipei,
Taiwan, Republic of China
AMANDINE PITAVAL • CEA, DSV, DRR, Functional Genomics Department,
Evry, France
JANG B. RAMPAL • Beckman Coulter, Inc., Brea, CA
GOPAL REMBHOTKAR • Nucleic Acids Research Laboratory, Institute
of Genomics and Integrative Biology, Delhi University Campus, Delhi, India
TODD A. RICHMOND • Nimble-Gen Systems Inc., Madison, WI
M. SALIT • Biotechnology Division, National Institute of Standards
and Technology, Gaithersburg, MD
M. B. SATTERFIELD • Biotechnology Division, National Institute of Standards
and Technology, Gaithersburg, MD
HARTMUT SELIGER • Arbeitsgruppe Chemische Funktionen in Biosystemen,
Universität Ulm, Ulm, Germany
REBECCA R. SELZER • Nimble-Gen Systems Inc., Madison, WI
YAXIAN SHI • Full Moon BioSystems, Inc., Sunnyvale, CA
Luo SUN • New England Biolabs, Beverly, MA
GRAHAM R. TAYLOR • Regional DNA Lab, Regional Genetics Service,
St. James's University Hospital, Leeds, UK
BHASHYAM VAIJAYANTHI • Department of Chemistry, Gargi College,
University of Delhi, Siri Fort Road, Delhi, India
LILI WANG • Biotechnology Division, National Institute of Standards
and Technology, Gaithersburg, MD
MING-QUN Xu • New England Biolabs, Beverly, MA
KAZUO YAMAMOTO • Frontier Science Bioscience, University of Tokyo,
Kashiwa Chiba, Japan
FUMIKO YASUKAWA • Life Science Division, Hitachi Software Engineering
Co. Ltd., Kanagawa, Japan
SHANSHAN ZHANG • Full Moon BioSystems, Inc., Sunnyvale, CA
YAPING ZONG • Full Moon BioSystems, Inc., Sunnyvale, CA
YUNFEI ZONG • Full Moon BioSystems, Inc., Sunnyvale, CA