Micro-Nano Technology for Genomics and Proteomics BioMEMs - Ozkan
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Electronic microarray technology (cont.) overview of, 4
nanochip array and nanochip workstation 5–6, 16
nanochip electronic microarrays, capabilities of, 8
Electronic microarrays applications of, 8
cell separation, 12, 61, 63, 121, 145–146 forensic detection, , 3, 10–12
gene expression profiling, 41–42 molecular diagnostics, 10
Electronic multiplexing, 10 Electronic pumps
dielectrophoretic, 312 electrohydrodynamic, 312 electrokinetic, 312
Electroosmotic fluid flow, 106 Electro-osmotic pumping, 312 Electrophoresis
capillary, constant denaturant, 449 gel
denaturing gradient, 449 temperature gradient, 449
Electrophoresis-based detection technologies, for sequencing, 382
ELISA. See Enzyme linked immunosorbant assay Environmental chamber, 66
Enzyme linked immunosorbant assay (ELISA), 50, 340
Enzyme-based biosensors, 51
Enzymes, 48, 51–52, 96, 137–138, 140, 163, 173, 204
Epitope mapping
B-cell, peptide arrays by, 298 multipin technology
anti-β endorphin, 285
monoclonal antibodies, 128, 214–215 polyclonal serum, 224
Epoxy-modified surfaces, chemistry of, 193 Ethanol, 71
ethylene diamene tetra acetic acid (EDTA), 70 hydrogen peroxide, 69
on neurons, visualization of physiological changes due to effect of, 80–82
on osteoblasts, visualization of physiological changes due to effect of, 81, 83–84
pyrethroid, 69 Ethanol sensing, 71
single neuron sensing, 71 single osteoblast sensing, 71
Ethidium bromide and SYBR Green, DNA intercalating dyes, 24
5 -Exonuclease activity of Taq DNA polymerase, 28 Export of tRNAs in Xenopus oocytes, 504
INDEX
Extra cellular multiple-site recording probes, 59 Extracllular potential based biosensors, 58
microelectrode array technology, 60 signature patterns of specific chemical
agent, 60
Extruded quadrupolar traps, 109
FAMTM, 26
FarWestern analysis, 133
Fast Fourier Transformation (FFT) analysis, 65, 69
Fetal cells
DEP behavior of, 118 in maternal blood, 145
FFT. See Fast Fourier Transformation analysis Fibroblast growth factor, basic (bFGF), 68 Field effect transistors (FET), 61
Field flow fractionation, 109
Field-induced cell destruction, on set of, 124 Filter Binding assay, radioactive, 19 Fingerprinting, restriction digest 376
FISH. See Fluorescence in situ hybridization FLAG epitope peptides, 171
FLAG-tag, 194
Fluid flow, synchronized pulses of, 109 Fluo-3, 80
Fluorescence based cell biosensors, 53 fluorescence imaging, 54 fluorescent reagents
fluorescence resonance energy transfer, 28, 54 green fluorescent protein, 54
Fluorescence biosensor, 54
Fluorescence DNA hybridization assay, 442 Fluorescence energy transfer techniques (FRET), 54 Fluorescence in situ hybridization (FISH), 370 Fluorescence polarization (FP) PKA assay,
antibody-based, 19
Fluorescence polarization anisotropy (FPA), 484 Fluorescence resonance energy transfer (FRET), 28,
30, 54, 296, 408, 429, 443 Fluorescence spectroscopy, 54, 470–472 Fluorescence–kinetic detection methods, 25
gene, 33
Fluorescent competitive allele specific polymerase chain reaction, 449
Fluorescent detection system, 144 Fluorescent reporter dye, 26
Fluorophore with non-overlapping emission curves, 410
Fluorophore, 37 acceptor/donor, 30–31, 55
Fluorosilanes, 61 Forensic DNA profile
database of, 10 polymorphic STR loci, 10
INDEX
Forster resonant energy transfer mechanism, 146
process, 139
Fourier transformation (FFT) techniques, 65 “Frequency modulation”, 69
FRET. See Fluorescence resonance energy transfer FUN effect, 123
Fungal pathogens in Candida dubliniensis, 429
GABAA activation, 76
GAPDH target, amplification plots for serial dilutions of, 33
Gene chip sequencing arrays, 452 Gene detection, in vitro, 403
allele discrimination, 409 mutation detection, 409 pathogen detection, 408
Gene expression analysis TaqMan hydrolysis probes in, 29
Gene expression analysis, application of technologies for, 23
Gene expression of phage, 486 Gene expression profiling methods
with cDNA arrays, 41
with oligonucleotide arrays, 42
Gene expression profiling utilizing microarray technology and RT-PCR, 23
amplification efficiency of target/reference genes, 32, 34
analytical sensitivity and dynamic range, 33–34 cDNA arrays, 35–36
comparative threshold method, 31 microarrays, 32
printed oligonucleotide microarrays, 36Real-Time PCR (RT-PCR), 23–25
qualification of gene panels using RT-PCR, 32 real-time RT-PCR summary, 32 reproducibility and precision, 34
standard curve method, 31–32 technology platforms, 35
Gene expression, posttranscriptional, regulation of, degradation of mRNA, 421
Gene fluorescent detection of, 3 Gene sequencing, shotgun, 378–389 GeneChip microarrays, 37
General purpose interface bus (GPIB) control, 67 Genes, identification of, using hybrid ribozymes, 513 Genetic marker, clones cluster of, 370
Genetic variation, detection of, 449
Genome project coordination, challenges for, 394 after Celera, 392
before Celera, 386 during Celera, 388
Genome sequencing pipeline, 369 Genomic DNA, haplotype structure of, 452
527
Genomics and proteomics, application of electronic microarray technology in, 3–18
Genomics, nanochip technology application in, examples of, 4
Genotyping analysis, 145
Genotyping, TaqMan hydrolysis probes in, 29 Glass surface modification/activation via starbust
dendrimer coating, 179
Glass surfaces, multistep functionalization of, 194 Glyceraldehydes-3-phosphate dehydrogenase
(GAPDH), 32 Goniometry, 163
Gyrolab MALDI SP1 sample preparation CD, 358
H19-7 cell line from ATCC, 65
H19-7 cells, 67–68 Hagen–Poiseuille equation, 335
Hairpin nanoprobes for gene detection, 403 in vitro gene detection, 408
pathogen detection, 408
mutation detection and allele discrimination, 409 living cell RNA detection, 418
cellular delivery of probes, 419 intracellular probe stability, 419 intracellular mRNA detection, 411, 428
nanoprobe design issues for homogeneous assays, 405
intracellular RNA targets, 411 cytoplasmic and nuclear RNA, 411 RNA secondary structure, 418 opportunities and challenges, 431
Hairpin probe design, 408
Hammerhead ribozyme, catalytic domain of, 498, 508 Haplotyping, 452
HapMap, 452
Harvester fluorophore, 408
HCV diagnostic applications, TaqMan hydrolysis probes in, 29
Heterogeneous nuclear ribonucleoproteins, 411 HEXTM, 26
High throughput phenotyping, 156
High throughput screening (HTS) situations, 18, 54 High-density electrode arrays, 109
High-density oligonucleotide arrays, 449
High-risk patients, identification by gene expression profiling, 41
High-throughput screening (HTS) kinase assays, 18 HIV diagnostic applications, TaqMan hydrolysis
probes in, 29
HnRNPs. See Heterogeneous nuclear ribonucleoproteins
Hoechst dye, 79–80
Homogeneous DNA hybridization assay, 443 “Hostboards”, 140
HPLC technology, denaturing, 449
528
HTS. See High-throughput screening kinase assays Human cancer cell lines (the NCI-60 panel), 44 Human disease and drug development, SNPs role, and
haplotypes in, 447
detection of genetic variation, 449 disease gene mapping, 450
drug development, 452 evolution, 450 haplotypes, 452
SNP discovery, 448 Human genetic diversity, 452
Human genome sequencing, approaches in construction of chromosome tiling paths, 379 data sharing, 379
Human genome, research network for large-scale sequencing of, 389
Human genome, sequencing, 365
approaches used to sequence human genome, 365 overview, 366
strategy used for sequencing source clones, 368 construction of the chromosome tiling paths,
379
data sharing, 379
challenges for systems integration, 365 methodological challenges for sequencing source
clones:, 1990–1997, 381
challenges for sequencing the entire human genome:, 1998–2003, 386
are there lessons to be learned from the human genome project?,395
Hybridization probes acceptor/donor fluorophore, 30 quanti probe, 31
Hybridization probes, 30–31 Hydrogen peroxide sensing, 72
single neuron sensing, 71 single osteoblast sensing, 71
Hydrolysis probes, 26, 28
IL-1, expression levels of, increased, after LPS treatment, 14
Immobilization of peptides chemoselective, 194 non-selective, 191
Immunoassays electronic, 14
electric field driven, 14 Immunohistochemistry, 77
in situ synthesized oligonucleotide microarrays, 37
Insulin-like growth factor receptor (IGF-IR), human type I, 68
Integrated circuit (IC) technology, 95 Interfacial Polarization, dynamics of, 107 International Prognostic Indicator, 41
INDEX
Intracellular potential based biosensors, 57 chemical warfare agents
soman (GD), 57 VX, 57
Ion channel switches, antibody-modified, 50 Ion channels biosensors, 50
Ion-selective optode detection, 339 Irradiation with UV-light, 193 Irradiation, 182
JOETM, 26
“Knock down” effect in-vivo, 70
“Lego” blocks for nanofabrication, 147 “Lymphochip”, 41
“Pick & Place” fabrication process, 137 “SELEX” for systematic evolution of ligands by
exponential enrichment, 129 “Top-down” process, 138
Lanthanide fluorescent, complexes\labels of, 438 Laser excitation sources, 144
LDPS. See light directed peptide synthesis LED arrays, 189
Leica SP2 UV confocal microscope, 78 Leiden, 10
Leukemia classification, 40 Library screening, 286, 369 Library types, 203
de novo approaches, 203
protein sequence-derived libraries, 204 Ligands
aromatic amine derivative-type, 440 chlorosulfonylated tetradentate β-diketone-type,
439 LightCyclerTM, 31
Light-directed peptide synthesis (LDPS), 187–188 Limit of detection (LOD), 34
Limit of quantitation (LOQ), 34 Lipopolysaccharide-mediated differentiation, 12 Lithography, Dip-Pen nanolithography/scanning
probe, 58
Magnetic tweezers, 467
MALDI. See Matrix-assisted laser desorption ionization sample preparation Maleimidylhexanoate, N-succinimidyl-6-, 170 Maleimidylpropionate, N-succinimidyl-3-, 170
Mapped clones for sequencing, 370 Mapping source clones, strategies for clone insert end sequencing, 370
fluorescence in situhybridization, 370 library screening, 286, 369 restriction digest fingerprinting, 370
Mapping, 131, 162–163
INDEX
Mapping, disease gene, 450 Mass spectrometry, 130
MassARRAY system, by Sequenom 449 Matrix-assisted laser desorption ionization sample
preparation, 287–288
Maxizyme, active/inactive conformation of, 508 Maxizyme, allosterically controllable, design of 509 Maxizymes, 508
design of, 509 generality of, 512
inactivation of oncogene, 510 shortened hammerhead ribozymes, 508
Maxizyme-transduced BV173 cells, 512 Maxwell stress tensor, 107
Maxwell–Wagner interfacial polarization, 107 Mechanical pumps
bubble generation, 312 osmotic pressure, 312 pneumatic pressure, 312 syringe drive, 312 thermal expansion, 312
MeCP2 mutations associated to Rett syndrome, 10 Medical diagnostics, 95, 103
Melting curve single nucleotide polymorphism (MCSNP), 449
Membrane capacitance, 110 Membranes,
acrylic-acid-modified 166 methylester-modified membrane, 166
MEMS (Micro-Electromechanical Systems), 156 MEMS devices
high density data storage devices, 140
Mendelian disorders, identification of disease genes, 447
Methacrylate polymers, 61
MGB EclipseTM (Epoch Biosciences) probe, 31 Michael addition, 170
Micro total analysis systems, 357
Microarray analysis of mRNA stability in yeast, 417 Microarray and fluidic chip for extracellular sensing,
47
antibody based biosensors, 50–51 biosensing system, 51
cell based biosensors, 52 cell culture, 67
neuron culture, 67–68 primary osteoblast culture, 68
cell patterning techniques, 60
cellular metabolism based biosensors, 55 cellular microorganism based sensors, 52 chemical agents, selection of, 65
ethanol, 69
hydrogen peroxide, 69 pyrethroid, 70
ethylene diamene tetra acetic acid (EDTA), 70
529
chemical agent sensing, 70
signature pattern for control experiments, 70–71
dielectrophoresis for cell patterning, 61 dielectrophoresis, basis of, 62 dielectrophoresis, microelectrodes and, 63–64
EDTA sensing, 76 single neuron sensing, 71
single osteoblast sensing, 71 electrical sensing cycle, 70 ethanol sensing, 71
single neuron sensing, 71 single osteoblast sensing, 71
environmental chamber, 66 enzyme based biosensors, 51–52
experimental measurement system, 67–68 extra-cellular potential based biosensors, 59–60 fluorescence based cell biosensors, 53–54 hydrogen peroxide sensing, 73
single neuron sensing, 73–74 single osteoblast sensing, 74–75
impedance based cellular sensors, 55–57 intracellular potential based biosensors, 57–58 ion channel biosensors, 51
nucleic acid based biosensors, 51 physiological changes due to effect of chemical
analytes, visualization of, 80 ethanol on neurons, 80–82 ethanol on osteoblasts, 81, 83–84
hydrogen peroxide on neurons, 83, 85–86 hydrogen peroxide on osteoblasts, 85, 87–89 pyrethroid on neurons, 88–91
pyrethroid on osteoblasts, 91–93 EDTA on neurons, 89
EDTA on osteoblasts, 91 pyrethroid sensing, 74
single neuron sensing, 71 single osteoblast sensing, 71
immunohistochemistry, 77 signal processing, 68
Microarray system, compact disc-based fiber-optic microarray biosensor, 295 immunoassays, 14
piezoelectric inkjet applicator, 295 Microarray technologies, application of, 1
electronic, applications in genomics and proteomics, 3–18
Microarrays applications, 40 cDNA arrays, 35
in situ synthesized oligonucleotide, 37 protein interaction, 224
spotting techniques, 132 printed oligonucleotide, 36
Micro-centrifuge fluidics, 333
530
Micrococcus lysodeikticus, DEP frequency response for, 114–115
Micro-contact printing (µCP), for promoting cell adhesion, 61
Microelectrodes, 63 Microelectronic arrays
for bioresearch, 137
for DNA clinical diagnostics, 140 Microelectronic arrays, applications of, 145 Microelectronic arrays, by Nanogen, for DNA
genotyping diagnostic applications, 141 Microelectronic MEMS devices, heterogeneous
integration of, 140 Microfluidic channel networks, 181 Microfluidic devices
biomedical, 351
clinical diagnostic applications, 351 Microfluidics propulsion techniques, 331 Microlithography, 146
Microlocations, 14 Micromanipulators, 67
Microorganisms, immobilised mixed culture of, 16, 52
Micro-patterning
contact printing techniques, 173 micro-mirror mediated patterning, 181 photolithografic technologies, 179
Microspheres, 147–149 MicrozoomTM optical probe, 66
Miniaturized electronic microarray system, 16 Miniaturized quantitative cell-based assays, 349 Minor groove binder (MGB), 31
Molecular beacon probes configuration, 30
point mutations detection by, 30 polymorphisms detection by, 30 probe-target duplex, 30
Molecular beacons, components of fluorophore, 30
loop, 30 stem, 30 quencher, 412
Molecular gene therapy and gene discovery, engineered ribozymes, efficient tools for, 505
Molecular probes, nanostructured, 4 Motherboards, 140, 147
MPC. See mini-Pepscan cards
MRNA, expression of, inhibition by ribozyme, 512
MRNA, secondary structure, computational programs to predict, 424
Multiarray-based biochip technology, 93 Multiplex hybridization analysis, 11 Multiplex PCR-amplified DNA, 360
INDEX
Multistep functionalization glass surface, 173
pretreated titan surfaces, 168 Myc-tag, 195
Nano chip rmicroarray, 100-site, 4 NanoChip array
assays format, 9 capabilities of, 8 cartridge of, 16 fabrication of, 4–5 permeation layer of, 5 workstation of, 5
NanoChip microarray, active hybridization technology and passive hybridization technologies, 4
Nanochip technology application in genomics, examples of, 11
NanoChipTM cartridge, 7, 143 assembly, 143
NanoChipTM molecular biology workstation, 143 NanoChip workstation, 7–8
Nanoelectronics applications for, 138
nanoelectronic devices, 138 Nanofabrication,
bottom-up processes for, 138–139 DNA chips, 142
Electric field assisted process, 146
Nanogen’s 400-site NanoChiparray and cartridge, 16 Nanogen’s electronic microarray technology, 5 Nanogen’s microelectronic DNA chip device, 8 Nanogen’s Nanochip Workstation, 8
Nanogen’s portable electronic microarray detection, 10, 16
Nanomechanical devices, light powered, 463 Nanoparticles, 137
Nanoparticles, as antennas, 465 solution phase synthesis of, 466 with reactive ligands, 468
Nanoparticles, DEP behavior of, 116 Nanoparticles, in controlling biomolecules, 473
dehybridization of DNA by RFMF heating of nanoparticles, 471
determination of effective temperature by RFMF heating of nanoparticles, 469
selective dehybridization of DNA by RFMF heating of nanoparticles, 471
technical approach, 468 Nanoparticles, RFMF heating of, 467
Nanoprobe design issues for homogeneous assays, 405 Nanoprobes for imaging, sensing and therapy, 401 Nanospheres, 140, 147–148
DNA sequence, 140 production of, 140
Nanotubes, 137–138, 146–147
INDEX
Nanowires, 137
NASBA. See Nucleic acid sequence-based amplification
Necrosis, 84, 88, 224–225, 231 Neuroblastoma cell cultures, 88
Neuronal cultures on microelectrode array, 59 Neuron-EDTA frequency spectrum, 78 Neuron-ethanol frequency spectrum, 72 Neuron-hydrogen peroxide frequency spectrum, 74 Neuron-pyrethroid frequency spectrum, 76
Neurons and osteoblasts, parameters for positive and negative DEP for, 65
NMDA gated channels, 73–74, 83, 86 activation of, 73–74, 86
NMDA gated channels, 83, 86
NMDA receptor gated Cl− and Na+ ion channels, 76 NMDA receptors
N-methyl-d-aspartate (NMDA) receptor dependent, 80
Non contact printing, peptide arrays of by piezoelectric device piezoelectric ink-jets, 204
Non-fluorescent (“dark”) quencher, 28 Northern blotting, 23, 403, 422
Nuclear magnetic resonance (NMR), to study DNA flexibility, 287, 459, 465, 509
Nuclease invader technique, 449 Nuclease mutation detection method, 449 Nucleic acid based biosensors, 51 Nucleic acid fragmentation, 93
Nucleic acid probes, microscale printing of, 36 Nucleic acids, 48, 139, 167, 404, 409, 418, 420–421,
423, 425 Nucleosome formation, 491
Nucleosome reconstitution, 491–492 NUX cleavage site, 513
NUX triplet, 510
OBOC (one-bead one-compound) peptide libraries, 284
encoded, OBOC small molecule combinatorial libraries, 287–288
combinatorial library methods and chemical microarray techniques, 283
OBOC peptide libraries, 283–284 Oligocarbamates, 188
Oligonucleotide (ODN) probes, 419–420 Oligonucleotide microarray expression profiles, 44 Oligonucleotide microarray, 36–37, 39, 43–44, 200,
228, 299
Oligonucleotide microarrays, in situ synthesized Affymetrix GeneChipmicroarrays, 37–38, 42, 44 manufacture by light-directed method, 37
Oligonucleotide microarrays, methods for production of, 39
531
Oligonucleotide probes, microinjection of, 30, 36–37, 144, 404–405, 418–419
OligoWalk Probe/RNA interactions tools, 418 Oncogene, inactivation of, 512
One step grafting procedure, 167
One-bead one-compound (OBOC) combinatorial libraries to chemical microarrays, 287
chemical microarray, application of, 297 cell-binding studies, 300
diagnostic studies, 301
drug discovery and cell signaling, 300 non-biological applications, 304 post-translational modification, enzyme-substrate
and inhibitor studies, 299 protein binding studies, 298
detection methods in chemical microarrays, 299 detection methods to identify post-translational
modification of proteins, 299 identification and characterization of bound
proteins, 296
encoded OBOC small molecule combinatorial libraries, 287
peptide and chemical microarrays, 289 OBOC peptide libraries, 284
CD, microfluidics, fiber optic microarray, multiplex beads, 295
immobilization methods for pre-synthesized libraries, 289
in situ synthesis of microarrays, 292 One-bead one-compound. See OBOC
Optical tweezers, integration of, for manipulation of live cells, 153
Ordered cell networks, 61 Organic quencher molecules, 408 Osmotic pressure pumps, 312
Osteoblast-EDTA frequency spectrum, 79 Osteoblast-ethanol frequency spectrum, 73 Osteoblast-hydrogen peroxide frequency spectrum, 75 Osteoblast-pyrethroid frequency spectrum, 77 Osteoblasts and neurons, parameters for positive and
negative DEP for, 66 Osteoblasts, 87
Oxidized silicon wafers, 142 Oxygen electrode, Clark-type, 53
Oxygen, dissolved, Clark-type probe for, 53
PACs (P1 artificial chromosomes), 368 Paired mismatch (or MM), 37
Parasites, TWD theoretical model for manipulation, separation and characterization of, 119
Pathogen isolation, two-level-stacked microlaboratory, 16
Pathogens, rapid identification of, 16 Patterned surfaces, generalization of, 173, 181 PBFI ester, staining with, 88
532
PBFI, AM ester of, 88
PCR amplicon, biotinylated, 8–9, 143 PCR amplicons, 143
PCR cycle number, 28 PCR cycle number, 28
Pentafluorophenylesters, 167 Pentanedione, 5-(4”-chlorosulfo-1’,
1”-diphenyl-4’-yl)-1, 1, 1, 2, 2-pentafluoro-3, 5-(CDPP), 443
Peptide arrays in proteomics and drug discovery, 161 applications of, 161
antibodies, 162
application of peptide arrays: miscellaneous, 228 enzyme-substrate and enzyme-inhibitor
interactions, 226 peptidomimetics, 231 protein-protein interactions, 224
assays for, 224 read-out, 219 screening, 215
generation of, 128
coherent surfaces and surface modification, 163–178
generation of micro-structured surfaces, 173 peptide array preparation, 182
techniques for array production with pre-synthesized peptides, 200
library types, 200
de novo approaches, 210
protein sequence-derived libraries, 204 Peptide arrays, 182
architectures
gel pad arrays of, 172
gold electrodes arrays of, 56–57 assays, 215
read-out, 219 screening, 215
cell binding, 300 micro-structured surfaces, 173 preparation, 173
chemoselective reactions, 196 contact printing, 61, 173, 200 non contact printing, 129, 200
pre-synthesized peptides, 200 screening 215
surface modification, 163 Peptide arrays, applications of
4 α-helix bundle mini-protein of, 217, 229 antibodies, 162
antibody paratope mapping of, 224 bibliography of, 162, 231, 265 chaperone activity, 225 characterization of peptide ligand, 229 DNA binding, 228
enzyme-inhibitor interactions, 226
INDEX
enzyme–substrate interactions, 95 linear epitopes, 222
metal ion binding peptides, 229 optimization of peptidic ligands, 229 peptide ligands, 210–211, 213
polyclonal antibody epitope mapping, 224 protein interaction domain-ligand interactions,
206
Peptide arrays, read out of, chemoluminescence, 162, 219 chromogenic, 162, 219 fluorescence, 162, 219 label-free, 162, 219 radioactivity, 130, 162, 219
Peptide libraries
split-mix synthesis method, 283–284, 289
Peptide ligands, de novo approaches for identification of, 211
combinatorial library, 231, 285 random scan, 285
Peptide microarrays, 163, 197, 199, 221, 226–228, 230
immobilization methods, 289
in situ synthesis, 185, 191, 200, 289
Peptide nucleic acids (PNAs) nucleotide analogs, 167, 190, 228
Peptide sequence,
combinatorial explosion of 210
Peptide synthesis on coherent surfaces, principle of, 186
Peptide
SPOT synthesis 162–163, 190–192 Peptide/ligand interaction, 171 Peptidomimetrics, 266
Perfect match (or PM) features, 37, 431 Periodic granular rimming flow, 350 Phage 434 binding specificity, 486 Phage, gene expression of, 478 Phage-display libraries, 128
Phil’s revised assembly program (Phrap), 376, 385
Phil’s Revised Editor (Phred), 376 Phosphorylation, 18, 173, 220–221, 227 Photo-induced graft copolymerization, 165 Photolithographic masks, 178 Photolithography for patterning of surface free
energies, 183 Photolithography techniques, 61
Photolithography, “topdown” process of, 147 Photonic crystals, 153
Photoresist coatings, 178 Photosensitizers, 165 Phrap score, 377, 386
Phrap. See Phil’s revised assembly program Phred. See Phil’s Revised Editor
INDEX
Physiometric Effects, 118 PhysioNetics, 111
PKA assay, 18–19 PKA inhibitors, 19
Plastic devices, 312, 314, 316 microfluidic devices, 311 direct fabrication, 316
laser ablation, 316 mechanical machining, 316
replication casting, 316
compression molding, 316 embossing, 316
injection molding, 316
Plastic microfluidic devices for DNA and protein analyses, 315 detection, 316
DNA analyses, 318
integrating PCR and DNA fragment separations, 318
DNA sequencing, 320
DNA sample purification, 321 materials, 312
electrokinetic pumping, 312 plastic devices, 312
device fabrication, 316 pumping and detection, 316
protein analyses, 311
enzymatic digestion for protein mapping, 324 isoelectric focusing for studying protein
interactions, 323, 326 Pneumatic pressure pumps, 312 Polarizability factor, 108, 119 Polarization, double layer, 107 Polyethylene, 162, 165, 167, 170, 284 Poly-L-Lysine, 61, 181
Poly-lysine coated glass slides, 173 Polymers, amino modified, 162
Polymers, methacrylate and acrylamide, 61 Polymorphism discrimination assays, 31 Polymorphism
restriction fragment length, 449 single strand conformational, 449
Polymorphism, melting curve single nucleotide, 449 Polypropylene, 162, 165–166
Polystyrene, 147, 165 Polyurethane films, 164
Power spectral density analysis, 68–69
Printed cDNA microarrays, methods for production of, 39
Printed oligonucleotide microarrays manufacturing of synthetic DNA, 139 pre-synthesized DNA probe, 36 synthetic oligonucleotide probes, 36
Probe-target binding, 406
Probe-target hybridization kinetic rate, 406
533
Probe-target hybridization, thermodynamic parameters of, 407
Protein analyses, 311 enzymatic digestion, 324 isoelectric, 323
Protein chip array, 298
Protein interactions, detection by ELISA-based sandwich approach, 130
surface plasmon resonance method, 130, 162, 296, 299
rolling circle amplification method, 130, 449 Protein microarrays, 127
for analysis of proteins involved in recombination & DNA repair
protein expression microarrays, 130–132 protein interaction arrays, 132–133
generation of, 128 proteins, 128 antibodies, 128–129 surface chemistry, 129
microarray production, 129 detection, 130
protein arrays,133
Protein microarrays, classification of, 127 Protein sequence-derived libraries
amino acid substitution, 206–207, 209 combinatorial deletion, 208 cyclization scans, 208
duotope scan, 204, 206 hybritope scan, 204 overlapping peptides, 204 substitutional analysis, 207–208 trancation, 208
types of, 210
Protein synthesis, localization of mRNPs in, 414 Protein-DNA interactions, 132
Protein-DNA specificity, levels of, 478 Protein-protein interactions, 224 Proteins, 128
Proteins, ARE binding, 422 Proteins, bound, detection of
grating couplers, 296
label-free optical techniques, 296 reflectometry, 296
surface plasmon resonance, 296 Proteins, fluorescence, 55
Proteomic analysis by protein array, concept of, 127 Proteomics and genomics, application of electronic
microarray technology in, 3–18 Proteomics, applications in, 18 Prothrombin, 10
Psoralen, crosslinker agent, 152 Pyrethroid sensing, 75
single neuron sensing, 75 single osteoblast sensing, 76
534
Pyrethroid, visualization of physiological changes due to effect of
on neurons, 88–91
on osteoblasts, 91, 91–93
Pyroccocus furious crystal structure, 131 Pyrrole-modified peptides, electrochemical
copolymerization of, 197
Qiagen quantiprobeTM, 27 Qiagen, 31 QuantiProbeTM, 31
Quantitative assay of specific RNA target, 29 Quantum dots, 137–140
Quantum dots, 140
Quick Spin protein desalting column, 345
RAD51B-histone interactions, 133 Reactive oxygen species, 84 Reads
misassembled, 376 overlapping, 376 shotgun, 376
Real time RT-PCR, 31
Real-time PCR, mechanism of, 32
Reciprocal chromosomal translocations, 502, 513 Recombinant his-tagged proteins, 129
Reporter dyes, wavelength shifting, 408
Resonant mirror-based biosensor (Lab Systems), 50 Restriction digest fingerprinting, 370
Restriction enzymes, 370, 478
Restriction fragment length polymorphism (RELP), 449
Reverse transcription-polymerase chain reaction (RT-PCR), 23
RFLP See Restriction fragment length polymorphism RFMF heating of nanoparticles, 469
RFMF heating of nanoparticles, determination of effective temperature by, 469
Ribozyme expression systems, 499, 515 functional analysis of genes, 497 gene therapy, 497
pol III system, 499
Ribozyme, subcellular localization of, 501 Ribozymes into cells, methods for introduction of, 506 Ribozymes
administration of, 498–499 RNA-protein hybrid, 498, 505
Ribozymes, as therapeutic agents, 515
Ribozymes, engineered, efficient tools for molecular gene therapy and gene discovery, 505
maxizymes, allosterically controllable ribozymes, 508
allosterically controllable maxizyme, design of, 509
maxizyme technology, generality of, 512
INDEX
oncogene, inactivation in mouse model, 512 hybrid ribozymes, identification of genes using,
513–514
shortened hammerhead ribozymes as dimers, 508 methods for introduction of ribozymes into cells,
497–499
ribozyme expression systems, 499 higher-order structure, and their activity,
relationship between, 149, 499 Pol III system, 499–500
subcellular localization and efficacy, 501 tRNA-ribozymes, export from nucleus to
cytoplasm, mechanism of, 504 RNA-protein hybrid ribozymes, 505
accessibility to ribozymes of their target mRNAs, 505
hybrid ribozymes that efficiently cleave their target mRNAs, 505
Ribozymes, secondary structures of, 500 Ribozymes, subcellular localization and efficacy of,
499, 501
factors affecting efficacy, 507 RMS power, 69
RNA constructs, 137
RNA detection, living cell, 411 cellular delivery of probes, 419 intracellular probe stability, 419, 424 intracellular RNA detection, 434
RNA polymerase T7, mediated amplification of, 12, 38
RNA processing, RNases roles in, 412–413 RNA protection, 23
RNA study
ABI Prism 7900HT SDS, 32 analytical sensitivity, 33
limit of detection (LOD), 34 limit of quantitation (LOQ), 34
bias percentage 33
RNA targets, intracellular, 411
RNA viral load tests testing, TaqMan hydrolysis probes in, 29
RNA, secondary structure of, 418
RNA: DNA duplexes, detection of, 37–38 RNAm localization in nucleus, 413–414 RNAm, splicing of, 412–413 RNA-protein hybrid ribozymes, 505
RNAs, functional, in cultured cells, activities of, 511 Rolling circle amplification (RCA), 130, 449 RRNA pre-transcripts, degradation of, 426
Saccharomeyces cerevisiae, proteome of, 128 SBFI, AM ester of
Scanning force microscopy, to study DNA flexibility, 484
ScorpionTM Primer/Probes, 26, 30
INDEX
Screen-sequence-screen-sequence approach for clone cluster, 370
Secondary ion mass spectroscopy, 163 Sensitizers, 165
Separation buffer, 65, 68
Sequence data, hierarchical approach of assembly, reconstructing sequences, 373 finishing, filling gaps of, 367, 378 mapping, source clone, 378
sequencing, raw data, 366–367
Sequence dependent elasticity, experimental consequences of, 486
Sequence dependent
aspects to double helix elastic constants, 484 bending of double helix
structure atlas of DNA, 485
Sequence-ready clones, retrieving from clone library, 369
Sequencing by hybridization, 382 Sequencing human genome, approaches in
construction of chromosome tiling paths, 385 data sharing, 385
Sequencing of human genome, large-scale, research network for, 389
Sequencing source clones, methodological challenges, 381
Sequencing source clones, strategy used for, 368, 381–382, 386, 388
Sequencing technologies, revolutionary, 382 Sequencing, 382
Serial analysis of gene expression (SAGE), 23, 403 Short tandem repeat (STR) forensics analysis, 137 Short tandem repeats (STRs), 10
Short tandem repeats, 10
Shotgun sequence reads generation from source clone, generic procedures for
base-calling, 374, 378, 382 data curation, 374 detection, 374 fragmentation, 372 sequencing, 372
size selection, 373
source clone DNA preparation, 372 subcloning, 373
template DNA preparation, 373
Shotgun sequencing of gene, 372–373, 375, 381–383, 386
Shotgun sequencing, basic framework of level of redundancy, 383
read length, 372
robots for DNA template preparation, 385 sequencing reactions, 368, 373
template, 383
Signal processing, 60, 68–69
Signature pattern for single osteoblast, 75
535
Signature pattern vector (SP), 69 Signature pattern vector (SPV) of cell, 70
Signature patterns of cell based biosensors, 52 Signature patterns of specific chemical agent, 52, 60 Signature Patterns, 47, 52, 60, 65, 98
Silicon wafers, transformation into mercapto-modified surfaces, 197
Silicon, oxidized, 170
Single fluorophore experimental design, 38 Single nucleotide polymophisms (SNPs), 10 Single nucleotide polymorphism, 405, 409, 412 Single nucleotide polymorphisms (SNPs), 23, 448
Single platinum micro-electrode pad on the NanoChip rmicroarray, 6
Single strand conformational polymorphism (SSCP), 449 SNP discovery, 448
SNP genotyping analysis, 145 SNP genotyping, 30
SNP identification technique, 449
SNP. See Single nucleotide polymophisms, 10 SNP-IT, robotic version of, 449
SNPs, diseases associated with, 10, 447 SODA. See synthesis on defined areas
Soman and VX (GD), chemical warfare agents, 57 Source clone DNA preparation, 372, 374
Source clone, gaps of, 393 Source clones acquisition, 368 Source clones
strategies for mapping of
clone insert end sequencing, 370 FISH, 370, 372, 378
library screening, 286, 369–371 restriction digest fingerprinting, 370–371
Spearman rank correlation coefficient, 42–43 SPOT concept, application of, 189
SPOT synthesis, 167
SPOT synthesis, 162, 167, 189–190, 210, 214, 219, 222–223, 225–227, 230–231, 298
SPOT. See spot synthesis of peptides SSCP. See Single strand conformational
polymorphism
Stacked microlaboratory, fabrication of stacked structure, 15–16
Stainless steel foils, 171
Stainless steel foils, functionalization of, 171 Staphylococcus enterotoxin a (SEA) and b (SEB), 14,
17
Starbust dendrimer coating, 179 Stem cells
DEP spectrum of, 116, 122 DEP behavior of, 113–116
Stem sequences, 30 fluorescent PCR primers, 30
hairpin loop probe structure, 30 SNP genotyping, 30, 145