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516

MAKI SHIOTA, MAKOTO MIYAGISHI AND KAZUNARI TAIRA

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About the Editors

Professor Mauro Ferrari is a pioneer in the fields of bioMEMS and biomedical nanotechnology. As a leading academic, a dedicated entrepreneur, and a vision setter for the Nation’s premier Federal programs in nanomedicine, he brings a three-fold vantage perspective to his roles as Editor-in-Chief for this work. Dr. Ferrari has authored or co-authored over 150 scientific publications, 6 books, and over 20 US and International patents. Dr. Ferrari is also Editor-in-Chief of Biomedical Microdevices and series editor of the new Springer series on Emerging Biomedical Technologies.

Several private sector companies originated from his laboratories at the Ohio State University and the University of California at Berkeley over the years. On a Federal assignment as Special Expert in Nanotechnology and Eminent Scholar, he has provided the scientific leadership for the development of the Alliance for Cancer Nanotechnology of the National Cancer Institute, the world-largest medical nanotechnology operation to date. Dr. Ferrari trained in mathematical physics in Italy, obtained his Master’s and Ph.D. in Mechanical Engineering at Berkeley, attended medical school at The Ohio State University, and served in faculty positions in Materials Science and Engineering, and Civil and Environmental Engineering in Berkeley, where he was first tenured. At Ohio State he currently serves as Professor of Internal Medicine, Division of Hematology and Oncology, as Edgar Hendrickson Professor of Biomedical Engineering, and as Professor of Mechanical Engineering. He is Associate Director of the Dorothy M. Davis Heart and Lung Research Institute, and the University’s Associate Vice President for Health Science, Technology and Commercialization.

Dr. Mihri Ozkan is currently an Assistant Professor in the Department of Electrical Engineering at UC-Riverside with a research focus in nanotechnology and its applications in biology and engineering. She received her Ph.D. degree in the Department of Electrical and Computer Engineering at UC-San Diego and her M.S. degree in the Department of Materials Science and Engineering at Stanford University. She has over four years of industrial experience including at Applied Materials, Analog Devices and at IBM Almaden Research Center. Her awards and honors include “Emerging Scholar Award of 2005” by the American Association of University Women, “Invited participant of Kecks Future Initiative“ (2005) by the National Academy of Science, “Regents Faculty Excellence Award” (2001 and 2004), “Visionary Science Award” (2003), “Technical Ingenuity Award” (2003), “Research Leadership Award” (2003), “Selected US team member in US-Japan Nanotechnology Symposium” (2003), and “Best graduate student awards” from the Materials

520

ABOUT THE EDITORS

Research Society, the Society of Biomedical Engineering and Jacobs School of Engineering (1999, 2000, 2001). Dr. Ozkan’s research is recognized as “frontier research” by the

Virtual Journal of Nanoscale Science & Technology (edited by Dr. David Awschalom) and featured many times in public newspapers, on the cover of journals, online news sites and newsletters. She is an active board member and treasurer in the International Society for BioMEMS and Biomedical Nanotechnology. Her editorial activities include the Journal of Sensors and Actuators B and the Journal of Biomedical Microdevices. She holds more than 25 patent disclosures and about 8 US-patents.

Professor Michael J. Heller began his position at University of California, San Diego in July 2001. He has a joint appointment between the department’s of Bioengineering and Electrical and Computer Engineering (ECE). His experience (academic and industrial) includes many areas of biotechnology and biomedical instrumentation, with particular expertise in DNA synthesis, DNA microarray diagnostics and optoelectronic based biosensor technologies. Dr. Heller has been the co-founder of three high-tech companies: Nanogen, Nanotronics and Integrated DNA Technologies. Dr. Heller’s most recent work involved the development of an integrated microelectronic array based system for genotyping, genetic and infectious disease diagnostics, protein analysis, cell separations and for nanofabrication applications. Dr. Heller has a respectable publication record, and has been an invited speaker to a large number of scientific conferences and meetings related to DNA microarrays, biosensors, lab-on-a-chip devices, bio-MEMS and nanotechnology. He has over 30 issued US patents related to microelectronic chips, microarrays and integrated devices for DNA hybridization, miniaturized sample to answer diagnostic devices, biosensors, genomics, proteomics, nanotechnology and nanofabrication, nano-based DNA optical storage and for fluorescent energy transfer in DNA nanostructures. Dr. Heller has been a panel member for the NAS(NAE) Review of National Nanotechnology Initiative 2001–2002; the NAS(NAE)—Engineer for the 2020 - 2001/2002; the White House (OSTP) National Nanotechnology Initiative 1999/2000; and has also been involved in a number of NSF Nanotechnology Workshops.

Index

AbetaP-mediated toxicity, modulator of, 89 Acetonitrile, 164, 170, 359

Acrylamide polymers, 61 β-actin, 32, 413, 421

Active microelectronic array hybridization technology, 141

Acute lymphoblastic leukemia (ALL), Affymetrix microarray, 40, 513

Acute myeloid leukemia (AML), 40 Advanced array technology, 360 Affymetrix GeneChip arrays, 42

Affymetrix GeneChip microarrays, 37–38, 44 profiling of transcripts in human cancer cell lines,

44

Affymetrix microarrays, 37, 40, 43 applications of, 40

ALP-labeled anti-digoxigenin antibody, 443 Aminopropyltriethoxysilane, 170 Aminosilane, 61, 170

Amplification

ligation rolling-circle, 449

nucleic acid sequence-based, 404, 408

plots for serial dilutions of GAPDH target, 33 Amplified, biotin labeled RNA (aRNA), 38 Anomalous positive DEP effect, 113

Anti permissive molecules, 61

Antibodies, 6, 9, 14, 18, 48, 50–51, 128–130, 132, 195, 214–216, 219–220, 222–224, 227, 300–301

Antibody-modified ion channel switches, 50 Antibody production, 50

Antigen, 48

APMA gated Na+ ion channels, 72, 83 APMA-gated channels, 73

Apoptosis, 69, 79–80, 84, 87–88, 91, 93, 118, 425–426, 514

condensation of chromatin due to, 84, 86, 91 inducement of, 118

induction of, 425 slow onset of, 87 vs. necrosis, 84, 88

Apoptotic bundles, 80, 83–84, 86

Applied Biosystems 7900HT sequence detection system, 25

assay

precision of, 33 reproducibility of, 34

data analysis, real-Time, 31, 35

standard curve method, 31 threshold cycle value, 31

Aptamers, 50, 129

ARE See AU rich element

Array architecture, general principles of, 172 “Arrays of microarrays”, 24

Arrays. See specific arrays

Assembly, 66

Atomic force microscopy, 163, 219–221, 297, 462 biotin-streptavidin system with, 290

covalent protein

Shiff base formation, 290 poly His tagged proteins

poly-His-Ni 2+ specific interaction, 290 ATP Synthase, as molecular motor, 459

Attenuated total reflection–Fourier transform infrared spectroscopy, 163

AU rich element (ARE), 416

model of mRNA degradation, 417 Autofinish, software for generating additional

sequence data, 378, 385

Autoimmune disorders, protein arrays for diagnosis of, 133

Aziridine polymerization, 173, 181

Bacillus anthracis, sensitivity study for, 18 Bacterial DNA, identification of, 17

Basepair sequences, relative binding coefficients of, 488

B-cell library, 41 Beadedarray, 449 Benzoin ethyl ester, 165 Benzophenone, 165

522

BeWo trophoblasts, 122 Biacore, 50, 162, 221

Bio compact disk assay, 360 Bio-CD workstation, 361

Biochemical Oxygen Demand (BOD) sensor, 53 Biochip technologies, 95

Biological agents, rapid identification of, 10, 15–16

Biological toxins for biological warfare applications cholera toxin B (CTB), 14

staphylococcal enterotoxin B(SEB), 14 Biological warfare agents, rapid identification of, 4,

15–16

Biological weapons, threat of, 98 Biomarker identification, 127 Biomimetic receptors, 49

Biomineralization, biological self assembly of, 461 Biomolecular activity by nanoparticle antennas,

control of

ATP synthase as molecular motor, 459

complex hybrid structures, biological self assembly of, 461

DNA as medium for computation, 463 nanomechanical devices, light powered, 463 nanoparticles as antennas for controlling

biomolecules, 465

dehybridization of DNA oligonucleotide reversibly by RFMF heating of nanoparticles, 471

determination of effective temperature by RFMF heating of nanoparticles, 469

selective dehybridization of DNA oligos by RFMF heating of nanoparticles, 471

technical approach, 468 Biomolecules, diverse population of, 127

Bioparticles, 16, 63, 104, 107, 113, 118–119 intrinsic physico-chemical properties of, 119

Bioparticles, dielectric polarizability of, 107 Bioreceptor component classification of, 48 Bioreceptors, 48, 95

Biosensing System, 66 Biosensors

affinity, 48 antibody based, 50 catalytic, 48

cell based, 52 characteristics of, 49 definition of, 47–48 enzyme-based, 51–52

fluorescence based cell biosensors, 53–54 ion channels, 51

IUPAC definition of, 47–48 nucleic acid based, 49, 51 properties of, 48

resonant mirror-based biosensor (Lab Systems), 50

INDEX

surface plasmon resonsance biosensor (BIAcore), 50

tissue based, 49–50 use in

defense applications, 49 environmental, 49–52, 66 medical, 49 toxicological, 49

Biothreat defence, 104 Biotin molecules, 144, 443 Black Hole QuencherTM, 28

BLAST, sequence search tool, 391, 406 Blood

DEP spectrum of, 116–117 screening diagnostics test, 409

Blood cells human, 122

TWD theoretical model for manipulation, separation and characterization of, 119

Boc-chemistry, 188

“Bottom-up” process, 138–139, 146–147 Bristol-8 B lymphoblastoid cells, 122 Brownian force, 63

Bubble generation pumps, 330

Cancer cells, 104, 109, 118–119, 122–123, 286, 300, 408

DEP spectrum of, 116–117

TWD theoretical model for manipulation, separation and characterization of, 119

CapB gene, sensitivity study for, 18

Capillary electrophoresis, 312, 331, 374, 382, 449; See also Electrophoresis

constant denaturant, 449 Capillary valving techniques, 340

Carbohydrate–lectin interactions, 297 Carbon nanotubes, 137–139, 146–147 Carbonate, N, N-disuccinimidyl, 173 6-Carboxyfluorescein

2, 7-dimethoxy-4, 5-dichloro-, 26 hexacholoro-, 26

tetrachloro-, 26

Carboxylate, N-succinimidyl-trans-4- (maleimidylmethyl)cyclohexane-1–170

Carboxytetramethylrhodamine6-, 28 CD applications, 339

automated cell lysis, 344

enzyme-linked immunosorbant assays, 341 capillary valving on CD, 336, 340–341

burst frequency, 70, 332, 336–337 critical burst condition, 336

cellular based assays, 342

integrated nucleic acid sample preparation, 356 analytical measurements, 332, 359

multiple parallel assays, 341

INDEX

PCR amplification, 356 MALDI MS analysis, 358

CD centrifugal microfluidic platform, 338 CD fluid propulsion, 333

CD photo detector, 360 Cell

dielectric properties of, 12, 56, 61, 63–64 dielectrophoretic (DEP) force, 12

Cell activation, 116

Cell adhesion and growth, 61

Cell based biosensors, 52, 57, 96, 98 Cell bursting, 120, 122

selective, 124 Cell culture

neuron, 59, 67 primary osteoblast, 68

Cell cultures, neuroblastoma, 88, 121

Cell death, 64, 80, 83, 88, 91, 114–115, 422 Cell differentiation, 68

Cell line, H19-7, from ATCC, 65

Cell manipulation on a CMOS chip, 109 Cell networks, ordered, 61

Cell patterning techniques by bio-microelectronic circuits, 60 microfabrication schemes, 60 micro-contact printing (µCP), 61 topographical method, 60

Cell penetrating peptides (CPP), 420, 423–424 Cell physiometry tools based on dielectrophoresis,

103–123 dielectrophoresis, 104–107

dielectric polarizability of bioparticles, 107 dynamics of interfacial polarization, 107–112 surface charge effects, 113–116

other physiometric effects, 116–118 traveling wave dielectrophoresis (TWD),

118–120

controlling possible DEP-induced damage to cells, 120–123

Cell separation, 12, 61, 63, 121, 145–146 dielectrophoretic, 12, 61

Cell therapeutics, 103

Cell types, parameters for dielectrophoretic patterning, 65

Cell-based assays, 54

Cell-based biosensors, 52, 57, 96, 98 Cell-based functional genomics, 156 Cellular delivery techniques

endocytic, 419–421, 423–425 non-endocytic, 419–422, 426

Cellular metabolism based biosensors, 55 cytosensor microphysiometer, 55

in cancer research, 55

microfabrication technology used in, 55, 65 microfluidics, 55

523

Cellular microorganism based sensors, 52 in environmental treatment processes

biochemical oxygen on demand, 52 Cellular proteins, diversity of, 127 Cellular sensors, impedance based, 56

electric cell-substrate impedance sensing (ECIS) technique, 56

noninvasive assay of cultured cell adhesion, 56 Cellulose, amino derivatization of, 189 Centrifuge based fluidic platforms, 329

CD applications, 339

automated cell lysis on CD, 344 CD Platform for ELISA, 223, 340

cellular based assays on CD platform, 342 integrated nucleic acid sample preparation and

PCR amplification, 356

modified commercial CD/DVD drives in analytical measurements, 365–359

multiple parallel assays, 341

sample preparation for MALDI MS Analysis, 358

two-point calibration of an optode-based detection system, 339

compact disc or micro-centrifuge fluidics, 333 simple fluidic function, 334

mixing of fluid, 334 packed columns, 339 valving, 318, 331

volume definition (metering) and common distribution channels, 338

Cervical carcinoma cells, separation from blood, 145 Charged coupled device (CCD), man-made, 138–139,

146

Chemical agents, selection of, 69 Chemical agent sensing, 58, 70

signature pattern for control experiments, 70 Chemical analytes, visualization of physiological

changes due to effect of ethanol on neurons, 80 ethanol on osteoblasts, 80

hydrogen peroxide on neurons, 83 hydrogen peroxide on osteoblasts, 84 pyrethroid on neurons, 86

pyrethroid on osteoblasts, 88 EDTA on neurons, 89 EDTA on osteoblasts, 91

Chemical microarrays, 289–292, 296, 298, 300–302 applications, 300

cell-binding studies, 300

cell signaling, 230, 298, 300, 302 diagnostic studies, 301

drug discovery, 302 characterization, 299

post-translational modification, 297–299, 324 Chemical warfare agents, VX and soman (GD), 57

524

Chip assembly, 66–67

Chips designed for particles and or biomolecular microseparations, 5

Chromatogram DNA sequencer, 376

Chronic myelogenous leukemia, causes of, 502, 509 Clark-type probe for dissolved oxygen, 53 Clausius-Mosotti factor, 105

Clone cluster, construction of tiling path of, 371 Clone insert end sequencing, 370

Clone library, retrieving sequence-ready clones from, 369–370, 375

Clones. See also Source clones CMOS, 14, 156

400-site chip, 16

cell manipulation on, 109 fabrication technology, 138

second generation developed at Nanogen, 17 CMOS array, electronic assay for fl-SEB and fl-CTB

on, 14

CODIS. See Combined DNA index system Coherent surfaces, stepwise synthesis on, 185 Colorectal tumors, allelic imbalance in, 411 Combined DNA index system, 10 Complementarity determining regions (CDRs), 224 Complementary metal-oxide-semiconductor

field-effect transistors, See CMOS

Complex hybrid structures, biological self assembly of, 461

“Consensus rot”, 376

“Consensus” sequence, in shotgun sequencing, 372, 375

Contact printing process, peptide arrays of contact tip deposition printing, 200

dip-pen nanolithography, 173, 200, 202 micro contact printing, 61, 173, 200 pin-and-ring printing, 200, 202

Contig, sequence overlap, 366, 372 Cosmids, 368, 372, 386, 394 Counterions

field-induced fluctuations and mobility of, 116 relaxations, 113–114, 116

CSF1PO, STR loci, 11

CTE-ribozyme sequence coupled to RNAhelicase, 514

Cytosensor Microphysiometer R , principle of, 506

DABCYL, 28

Dark QuencherTM, 28, 31

DELFIA fluorescence enhancement solution, 442 Deoxyribose nucleic acid (DNA), structure of

Watson-Crick B-form, 479

DEP behavior of cell suspensions, monitoring of, 114

DEP effect, anomalous positive, 113–114 DEP field-flow fractionation technique, 118

INDEX

DEP separation for U937 and PBMC mixture, procedure of, 13

DEP spectrum of mammalian cells, 117 DEP traps, 109

by extruded quadrupolar traps, 109 by high-density electrode arrays, 109 by zipper electrodes, 109

positive and negative, principle of generation of, 62 DEP. See also Dielectrophoresis

selective separation and detection of bacteria by, 115

Detection probes hybridization probes, 30 hydrolysis probes, 26 molecular beacon probes, 30 scorpion probes, 30

Diagnostic applications, DNA genotyping, 141

Diaminocyclohexane, 1, 2-plasma deposition of, 165 Dielectric dispersions, (α- and β-, 114 Dielectrophoresis, 70, 103, 145; See also DEP

behavior through electrophoresis, 111 forces, 12–14

frequency-dependent behavior of, 107, 108, 112 Dielectrophoresis for cell patterning, 61

basis of dielectrophoresis, 62 dielectric properties of cells, 64 effect of electric fields on cells, 64 microelectrodes, dielectrophoresis, 64

Differential display, 23

Diffuse large B-cell lymphoma (DLBCL), 41 Digoxigenin-labeled PCR product, 443 Digoxigenin-tailed specific probe, 443 Diketonate, β-, 443

Dipole moment, 107 induced, 110

Dip-Pen nanolithography/scanning probe lithography, 173

Displacement flux densities, 108 DNA

constructs, 137

elastic properties, effect of sequence on, 494 filament, kinetics of deformation of, 489–491 flexibility, experimental techniques, 492 hybridization, 31

hyperchromicity, 469

intercalating dyes, ethidium bromide and SYBR Green, 25

labeling of targets and amplification,

by single fluorophore experimental designs, 37 by two fluorophore experimental designs, 39

medium for computation, 463 nanocomponents and other nanofabrication

applications using EFAD devices, 137–156 probes, 4

INDEX

thermodynamic measurements of, 484 basepair dependent, 488

twist of, rotational and translational parameters, 489 DNA analyses, 318

fragment separations, 318 sample purification, 318 sequencing, 324 integration of PCR, 322

DNA analysis, fluorescent lanthanide labels with time-resolved fluorometry in, 443

DNA hybridization assay, 448–451

forensic analysis, implementation of SNP assays in, 11

rapid, 16

lanthanide fluorescent complexes and labels, 438 time-resolved fluorometry of lanthanide complexes,

441

DNA genotyping diagnostic applications, Nanogen microelectronic arrays, 141

DNA hairpin dehybridization, 469

DNA hybridization assays, 144, 442–444 DNA inserts

“genome equivalents” of, 368 of source clone, 374

DNA micro spot-array hybridization assays, 360 DNA microarray technologies, 3–4, 14

for measuring gene expression, 24 DNA oligos, dehybridization by RFMF

heating, 471

DNA-protein interactions, influence of basepair sequence on, 494

generalized deformations of objects, 481

double helix and structure atlas of DNA, sequence dependent bending of, 485

double helix elastic constants, sequence dependent aspects to, 484

sequence dependent elasticity, some experimental consequences, 486

phage, 434 binding specificity and DNase I cutting rates, 486

nucleosome formation, sequence and temperature dependence, 491–492

DNase II endonuclease in endocytic pathway, 425 cDNA arrays, 42

comparison with oligonucleotide microarray expression profiles, 44

microscale printing of DNA, 36 preparation of sample, 36 printing of PCR products, 35

cDNA microarrays, profiling of transcripts in human cancer cell lines, 44

dsDNA molecule, deformation of backbone of, 483 Drug development, 452

Drug discovery, 103

Dulbeco modified eagle medium (DMEM), 68

525

Dye (s)

DNA intercalating ethidium bromide, 25 SYBR Green, 25

Hoechst, 79–82, 84, 86, 88, 90, 93, 95, 97 fluorescent reporter dye, 26, 28

quencher dye, 26, 28

reporter, wavelength shifting, 408 trypan blue, 65

“Eberwine” strategy, 39 EDTA

on neurons, visualization of physiological changes due to effect of, 93–95

on osteoblasts, visualization of physiological changes due to effect of,80

EDTA sensing, 76

single neuron sensing, 76 single osteoblast sensing, 76

Eigen vectors, 71, 73

Elastomers, polydimethylsiloxane (PDMS), 61, 202

Electric cell-substrate impedance sensing (ECIS), 56 Electric field array devices, DNA nanocomponents

and other nanofabrication applications, 137 active microelectronic array hybridization

technology, 140–141, 144–145, 147 electric field assisted nanofabrication process,

146–153

integration of optical tweezers for manupilation of live cells, 146

Electrical sensing, 50, 52, 65 Electrical sensing cycle, 70 ElectroCaptureTM assay, 18

PKA assay, 18–19

Electrofusion and electroporation, limitations in, 124 Electrokinesis, 109

Electrokinetic pumping, 312

Electron paramagnetic resonance (EPR), to study DNA flexibility, 484

Electronic assay for fl-SEB and fl-CTB on CMOS array, 14

Electronic hybridization, 7, 11

Electronic microarray technology, applications in genomics and proteomics 3–18

applications, 5

single nucleotide polymorphisms (SNPs)-based diagnostics, 10–11

forensic detection, 3, 10–12

gene expression profiling, 9, 12–13 cell separation, 12, 61

electronic immunoassays, 14 electronic microarray technology and

applications, miniaturization of, 14–18 proteomics in, 18

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