Index

3D immobilization, 55 3DLinkTM, 218

Abimed GmbH, 289 AC voltammetry, 124

Accelr8 Technology Corporation, 51 acoustic microstreaming, 74, 92, 120,

128–130, 132, 134, 135 adsorption, 25–27, 30, 33–35, 37, 47–50,

52–54, 93, 168, 183, 218, 241, 336, 340

biomolecule, 26, 45, 167 DNA, 29, 32, 301 electrostatic, 30, 33 oligonucleotide, 30, 231 passive, 159, 166, 218

protein, 27, 33–35, 39, 53–55, 93, 338, 339

adsorption isotherms, 26, 28, 30 Advanced Array Technology, 149, 167 A ymax, 288

A ymetrix, 4, 6, 46, 47, 73, 75, 103, 214, 218, 220, 222, 275, 288, 289

AFM, 75, 94–100, 103–105, 184 AIMS Scientific, 289

allele specific oligonucleotide (ASO), 213–216, 218, 222

Amersham Biosciences, 121, 130, 218, 220, 230, 272, 281, 282

APC Inc., 129

Apogent Discoveries, 46

aptamers, 279, 286, 297, 298, 300–303 array

antibody, 8, 16, 279, 283–286

cDNA, 6, 66, 152, 165, 230, 239–243, 253, 254, 284, 286, 366, 367

DNA, 4–6, 8, 32, 45, 46, 48, 49, 55, 119, 128–130, 147, 168, 169, 229, 253–255, 259, 260, 265–268, 271–274, 281, 283, 284, 288, 309, 310, 324, 341, 345, 361, 363, 365

dynamic, 90 e ciency, 4 passive, 90, 101

protein, 8, 32, 33, 45, 50–53, 55, 80, 104, 191–193, 197, 279–281, 283, 284, 305, 309, 310, 316, 324, 345

reverse transfection, 325, 326, 328–332

scan, 4, 5

small molecule, 53, 279 survey, 4, 5

synthetic, 287

tissue, 4, 89, 258, 345–349, 351–354, 362–367, 370, 371

array format, 3, 6, 131, 211, 212, 214–218, 222, 279, 286, 297, 298, 300, 303, 324, 327, 368

array-CGH, 251, 252 array-of-arrays, 4, 212, 213, 217

arrayed primer extension (APEX), 216 ArrayPlateTM, 4, 5, 9, 11–16, 18–20 ASAPTM, 70

BD Biosciences, 51 bead-based array, 6–8, 215

beads, 3, 6, 7, 50, 109, 112–115, 153, 154, 268–270, 287, 298–300

376 Index

paramagnetic, 120 Beckton Dickenson, 340 Biacore, 168, 183

binding constants, 314, 316 biochannel devices, 120, 121, 123, 124,

126

BioDisk Synthesizer, 289 biomolecule attachment, 23, 45

biomolecule immobilization, 23, 39, 41, 45, 91

biosensors, 109, 115 Biosignal Packard, 313

capillary pin-printing, 76, 77, 80 carbohydrate arrays, 24, 36

Cartesian Technologies, 9, 70, 313, 332, 342

cavitation microstreaming, 128–135 cell immobilization, 23, 38–41, 324 cell-based arrays, 38, 41, 63, 89, 324,

330, 337, 338, 340–343, 362, 368–371

cell-based screening, 335, 342 chromatin immunoprecipitation (ChIP),

265, 266, 269, 270, 272, 273 Ciphergen Biosystems Inc., 51 cis-regulatory elements, 265 Clontech, 46, 124

CMTTM4K Cancer arrays, 242 CodeLinkTM, 121, 218, 220, 230,

233–235, 238, 240 comparative genomic hybridization,

251, 252, 256, 257, 259, 260 computational nanoarrays, 105 computing on surfaces, 106–108 contact pin-printing, 73

Corning Inc., 46, 75, 77, 84–86, 230, 241, 242, 272, 325, 327, 329, 332

covalent attachment, 25, 27, 30, 32, 33, 35–37, 47–49, 52–56, 99, 193, 216, 218, 231, 299, 302, 303

CoverWell Incubation Chambers, 327, 332

degenerate–oligonucleotide–primed– PCR (DOP–PCR), 253, 256

dendrimers, 147, 149, 151, 152, 172

detection limits, 36, 149, 152, 155, 158, 162–164, 166–168, 170, 172, 173, 184, 190

dip pen nanolithographyTM, 54, 75, 96–104

direct nanopipet deposition, 96 disposable pin-printing, 79 DLVO theory, 26

DNA computing, 105–108, 115

DNA immobilization, 28, 30, 32, 265, 268, 273

DNA polymerase, 138, 215–217, 220, 271, 272

dose dependency, 316 DuroTM, 129

dynamic range, 85, 86, 148, 149, 157, 162, 163, 165, 166, 172, 236, 237, 240

electrochemical detection, 3, 120, 123, 124, 128, 132, 147, 149, 156–158, 173

electrokinetic valves, 136 electronic array, 5, 7

electrostatic interactions, 24–27, 29, 30, 33, 34, 39, 47, 194, 312

ELISA, 4, 8–10, 12, 16, 18, 19, 284–286, 305

ellipsometry, 181, 183, 184, 189, 190 EP3, 182

epitope mapping, 289

Erie Scientific Company, 46 eSensorTM, 7, 123–125, 131, 134 Eurogentec, 340

expression microarray, 86, 119, 229, 230, 232, 235, 239, 275, 283, 369

expression profiling, 14, 170, 212, 255, 279

Fast Slides, 281 Ferrocene, 7, 157, 158 fiber optic array, 7, 50

fiber optic capillary printing, 77, 78 flourescence in situ hybridization, 153,

251–253, 258, 259, 345–347, 349, 350, 362, 363, 370

fluorescence recovery after photobleaching (FRAP), 311, 312

fluorophore, 98, 147–149, 151–155, 158, 160, 162, 172, 218–220, 242, 281, 282, 285

ganglioside microarray, 313, 317–319 GAPSTM Slides, 46, 51, 53, 85, 241, 312, 313, 315, 327–329, 332

gels, 8, 41, 49, 51, 55, 56, 96, 137, 138, 140, 181, 195, 266, 269, 280, 284, 305, 312

gene silencing, 370

GeneChip R , 4, 214, 217, 218, 220, 222 genetic diagnostics, 197, 204

Genicon Sciences Corporation, 165, 166 Genisphere, 151, 172

genome wide location analysis, 265–268, 275

GenomicDevices & Diagnostics, 340 GenoSpectra, 77, 78

Genova Pharmaceuticals, 324 glass substrate, 46–48, 51, 53, 241

gold nanoparticles, 98, 100, 103, 149, 159–165, 167, 168, 170–174

gold substrate, 49, 51, 54, 56, 98, 104, 154, 157

GPCR, 53, 54, 309, 311–317, 319 Grace BioLabs, 327, 332 Greiner, 281

haptens, 159, 229–231

High Throughput Genomics (HTG), 4, 9, 11, 12

Hitachi Genetic Systems, 76 Hitachi x-cut pin printing, 76 HTS Biosystems, 51

Human Genome Project, 371 hybridization kinetics, 7, 119, 120, 123,

125, 126, 128, 131, 132, 134, 167, 186, 232, 240, 243

Hydra R 600, 124, 132 Hydrogel, 7, 51, 136, 281

hydrophobic attraction, 26, 28, 29, 34, 51, 312

I–Elli2000, 181, 182, 190 Illumina, 7

imaging devices, 114 immunohistochemistry (IHC), 345, 346,

350–352, 365

Index 377

Innovadyne Technologies Inc., 70

Instrumedics, 354, 364

Intavis, 289

ligation-mediated PCR (LM–PCR), 265, 266, 271, 273

Light Machines, 129

lipids, 24, 38, 53, 86, 310–312, 317, 318, 368, 369

Loctite, 129

Luminex, 6

marker-free detection, 181 matrix-assisted laser desorption /

ionization mass spectrometry (MALDI–MS), 181, 197, 198

matrix-CGH, 251–259

membrane bound molecules, 309, 319 membrane microarrays, 55, 310–313,

318, 319

metal nanoparticle, 147, 148, 159–162, 165, 167, 169, 171

Metrigenix, 46

micro–Total Analysis Systems ( TAS), 119

micro-fabricated pin array, 75 micro-machined pin, 77 microfluidic valve, 64, 68–71, 119,

136–140

microfluidics, 55, 70, 102, 109, 119, 125, 135, 138, 142, 279, 285, 286

microlithography, 89, 91 microtitre ELISA, 285 microwells, 55, 93, 285, 286 Mie theory, 160

molecular motors, 109–113, 115 Molecular Probes, 281

Motorola Labs, 7, 119, 123, 124, 130–132, 149, 157, 218, 230, 233

MotorolaLabs, 121

mRNA assay, 9, 13, 14, 16–18, 20

nanoarray, 89–92, 96–99, 101–105, 109, 113–115

protein, 54 NanoChip R , 7

Nanofilm Technologie, 182, 183, 189, 190

nanografting, 94, 95

378 Index

nanolithography, 91, 95, 101 nanoparticle, 96, 103, 149, 159–164,

166–169, 171–174

Nanosphere Inc., 149, 163, 164, 167, 173 non-specific binding, 23, 47, 50, 52, 98,

105, 149, 155, 184, 193, 235, 298, 317

nuclease protection assay (NPA), 9, 10, 13–15

oligonucleotide expression, 230 oligonucleotide ligation assay (OLA),

214, 215, 218 on-chip PCR, 120 onco chip, 257

Operon Technologies, 122, 130, 138 optical coding, 153

Panomics, 51

PDMS, 55, 120, 121, 213

Peltier thermal electrical devices, 136, 139

peptide array, 51, 52, 181, 197, 287–290 peptide libraries, 287, 288

peptide nucleic acid (PNA), 24, 181, 197, 198, 200–204, 214

PerkinElmer Life Sciences Inc., 51, 67, 138, 220, 281, 313

phosphor reporters, 147, 154 photo-bleaching, 153, 311, 312 photoaptamer, 297, 298, 300–305 photoaptamer array, 297, 301, 303, 304 photolithography, 47, 53, 73, 91, 218 piezo jet dispensing, 64, 67, 68, 74 piezoelectric (PZT) transducer, 129–131 plasmon resonant particles (PRPs), 166 Pluronics phase change valves, 137–140 PNA microarray, 202, 203

polymerase chain reaction (PCR), 6, 7, 105–107, 120, 122–124, 126, 132, 136–140, 142, 149, 151, 157, 158, 164, 197, 212, 215, 216, 220, 222, 229, 230, 239, 242, 243, 253, 255, 256, 265, 266, 270–273, 280, 283, 297, 298, 300, 340, 345

Polysciences Inc., 353 power generation, 90, 113

printed circuit board (PCB), 131, 157

protein immobilization, 32, 33, 50, 52–55, 192, 193, 195, 197, 260, 284, 299, 301, 302, 311, 316, 317

protein-protein binding, 191

QuadPerm, 327

quality control, 12, 83, 85, 184, 230, 280, 301, 351

Quantum Dot Corporation, 154

quill pin-printing, 75–77, 80, 81, 312, 313

reagent jetting, 63–65, 68, 69, 71 resonant light scattering (RLS), 161,

165, 166, 172

reverse transfection, 324–326, 328, 330–332, 341, 368

ring and pin-printing, 75

RNA in-situ hybridization (RNA-ISH), 345–347, 362, 363

rotary motors, 109–111, 113

scanning probe microscopy (SPM), 92, 96, 103–105, 181

Scatchard analysis, 317

scatter-based detection, 160, 163, 164, 170

Schleicher & Schuell, 281

Seashell Corporation, 166 SELEX, 297–302

self-assembled monolayer (SAM), 7, 30, 40, 49, 54, 94, 200, 312

semiconductor quantum dots (QDs), 149, 152–154, 173

sensitivity, 5, 8, 16–20, 32, 33, 36, 45, 55, 56, 76, 115, 147–149, 151, 154–156, 158, 159, 162, 165–168, 170, 172, 184, 189, 195, 285, 302, 303, 305, 341

Serial analysis of gene expression (SAGE), 7

Sigma–Genosys, 9–11, 268, 270–272, 289, 332

signal transduction, 159, 284, 313, 325 silicon substrate, 48, 53

silver enhancement, 149, 159, 161–165, 167, 170–172

single base extension (SBE), 216

single nucleotide polymorphism (SNP), 7, 91, 119, 120, 123, 131, 142,

147–149, 151, 154, 158, 163, 164, 172, 173, 197, 198, 211–220, 222

single nucleotide primer extension (SNE), 215–217, 219

single-cell comparative genomic hybridization (SCOMP), 253, 256

solenoid jet dispensing, 64, 68–71, 74 solid pin-printing, 74, 75, 80, 81 SomaLogic, 299

SPBIOTM Microarray Station, 76 SPOT, 288, 289

SpotBotTM Personal Microarrayer, 122, 138

stealth pin-printing, 76, 77, 79 steric e ects, 155, 166, 167, 282

surface plasmon resonance (SPR), 3, 45, 49, 51, 54, 149, 159–161, 167–169, 181, 183–185, 189, 190, 282

surface-enhanced Raman scattering (SERS), 149, 169, 170, 173

SurModics, 46, 121, 218

Taqman, 239, 240

Index 379

TeleChem International Inc., 51, 52, 76, 77, 79, 122, 332, 333

thermal jet dispensing, 64, 65

time correlated single photon counting (TCSPC), 191, 196

time–of–flight secondary ion mass spectrometry (TOF–SIMS), 181, 198–204

titanium dioxide substrates, 51, 54 transcription factors, 211, 265, 267, 268,

275

translational genomics, 361, 362, 368, 371

Universal Protein Stain, 301, 303

van der Waals forces, 25–28, 30, 155 virus, 99, 103, 323, 336 VP–Scientific, 79

Xenopore, 46

Zyomyx Inc., 51, 54