John Wiley & Sons - 2004 - Analysis of Genes and Genomes

αsatellite, 150 α-amanitin, 51

α-complementation, 121, 122 α-helix, 16, Appendix 1.2

β-galactosidase, 44, 120, 224

β-globin gene, 175

β-mercaptoethanol, 284

γ -endotoxin, 355

2-deoxyguanosine, 387

2-deoxyribose, 7, 9

2µ yeast DNA replication origin, 222

5-enolpyruvylshikimate-3-phosphate synthase (EPSPSase), 357

7-methyl guanosine, 55

Ace1p, 268

Acetolactate synthase, 345

Activation domain (AD), 218, 220, 244 Adaptors, 187

ADE2, 145

Adenine, 7

Adeno-associated Virus (AAV), 371, 372 Adenovirus, 369 – 371, 398

adenoviral vectors, 370, 375 Affymetrix , 318

Agarose, 93

agarose gel, 89, 103, 156, 165 agarose plugs, 98

Agrobacterium tumefaciens, 341, 342, 343 – 346, 355

AIDS, 374

Alanine scanning mutagenesis, 250 Alcohol dehydrogenase (ADH1), 222, 265 Alcohol oxidase, 268

Alkaline lysis, 106 Alkaline phosphatase, 214

Allele, 1

Allele-specific PCR, 175 Alternative splicing, 58 Ampicillin, 122

ampicillin resistance, 117, 141 Amplified library, 191

Amylose, 282 Anchored primers, 315

Anchored oligo-dT primers, 194 Annealing, 155, 161

annealing temperature, 21, 165 Antibiotic, 113

Antibiotic resistance, 86 Antibody, 103, 164, 211, 325 Anticodon, 61

Antigen, 211, 325 Antisense, 329 Antisense RNA, 355

AOX1, 268

Applications of PCR, 181

Arabidopsis thaliana, 350 Arber, Werner, 66 Arbitrary primers, 315

ARS1, 143

Artificial chromosomes, 143 Astbury, William, 10

attB, 39, 129 attP, 39, 129

Autographa californica nuclear polyhedrosis virus (AcNPV), 269

Auxin, 343

Avidin, 202

Bacillus thuringiensis, 355

γ -endotoxin, 356 cry operon, 354 cry1Ac, 356

460 INDEX

Bacmid, 272

Bacterial artificial chromosomes (BACs), 148, 305

Bacterial conjugation, 110 Bacterial transformation, 84

Bacterial transposon, see Tn10, Tn5, Tn7 Bacteriophage, 66

Bacteriophage λ, 17, 111, 127, 186, 189 cohesive (cos) ends, 135, 148, 296

in vitro packaging, 134 libraries, 209l lysogenic pathway, 129 lytic pathway, 129

plaques, 126, 189, 209, 214 λPL promoter, 260 repressor, 17, 260

vectors, 126

insertional vector, 133, 141 replacement vector, 133, 141 λEMBL4, 133

λgt11, 134

λZAP, 134, 141, 214 Bacteriophage P1, 146 Bacteriophage T2, 5 Bacteriophage φX174, 296 Baculovirus, 269, 270, 378 Bait, 224

Baltimore, David, 192 Base pairs, 14 Bermuda Principle, 306

BigdyeTM terminators, 300, 302 Binary vectors, 345 Bioinformatics, 311, 324 Biolistic, 348, 352

Biotin, 201, 202, 203 Blastocoele, 381

Blastocyst, 379, 381, 384, 393 Bleomycin, 123, 376

Blue – white screening, 121, 134 Blunt-ended, 187

Border sequences, 343 Brown, Patrick, 318

Caenorhabditis elegans, 330 Caesium chloride, CsCl, 105 Calcium phosphate, 364

calcium phosphate precipitation, 364

Cancer, 400

Cassette mutagenesis, 240, 241, 252 Catabolite repression, 46

Cationic lipids, 365

Cationic liposomes, 365, 366 Cauliflower mosaic virus (CaMV), 346,

348, 349

35S promoter, 273, 358

cDNA, 164, 192, 197, 198, 203, 308 libraries, 183, 185, 191, 198, 199, 216,

224

directional cloning, 196 Celera Genomics, 306 Cell cycle, 35

checkpoints, 36 Cell membrane, 363

CEN4, 143

Centromere, 143, 289, 307 Chargaff, Erwin, 9, 76 Chargaff’s rules, 9, 12, 76

Charge per unit length of DNA, 91 Charged to alanine scanning mutagenesis,

251

Chemical transfection, 363 Chemical transformation, 85, 86 Chip-on-chip, 326

Chitin, 284

Chitin-binding domain (CBD), 284 Chloramphenicol, 61, 116, 119, 123 Chloroplast, 350

transformation, 350, 351 Chlorsulphuron, 345

CHO cells, 362 Chorionic villi, 173 Chromatid, 27 Chromatin, 24, 26

modifying complexes, 49 remodelling complexes, 49

Chromatin immunoprecipitation (ChIP), 325

Chromosome, 289 chromosome walking, 304

cI, 131

Clarke and Carbon formula, 190 Clone, 66, 394

Clone contigs, 304

Cloning, 78

in plants, 341 PCR products, 175 strategies, 183 vectors, 111, 297

Co-integration vectors, 345 Codon, 59

codon usage, 61, 263 Cohesive (cos) ends, 75, 127 Coiled-coil, 246

colE1, 114, 116 colicin E1, 114 ori, 141, 144 plasmid, 115

Complementary base pairing, 193, 206 Complementation screening, 217 Conditional knock-out, 388 Conservative replication, 30

Contigs, 304

Contour-clamped homogeneous electric field electrophoresis, 97

Copper homeostasis, 268

cos site, See Bacteriophage λ, cohesive ends Cosmid vectors, 135

Coulson, Alan, 296

Coupled transcription/translation systems, 337

Cre, 347, 352, 359 expression, 390

recombinase, 125, 146 – 148, 359, 388, 390

Crick, Francis, 12 Cro protein, 131

CTD of RNA polymerase II, 53 Cultured animal cell lines, 361

CUP1, 268

Cy3, 319, 321, 325

Cy5, 319, 321, 325 Cyclin, 36

Cyclin-dependent kinase, 36 Cystic fibrosis, 289, 383, 397 Cytokinin, 343

Cytological map, 289

Cytomegalovirus (CMV) immediate early promoter, 272, 378

Cytosine, 9

INDEX 461

Dam methylase, 250 Dam methylation, 72 Dcm methylation, 73 Degeneracies, 209

Delayed fruit ripening, 354 Delbruck,¨ Max, 37 Denaturation, 155, 161

Deoxynucleotide triphosphates (dNTP), 194, 234

Deoxyribonucleotides, 7 Dicer, 331

Dicotyledonous plants, 342 Dideoxynucleotide triphosphates (ddNTP),

296, 297, 300 Differential display, 315 Digoxigenin, 209

Dihydrofolate reductase, DHFR, 377 Direct DNA transfer, 366

Direct injection, 367 Directed evolution, 255 Disulphide bond, 213, 255 Dithiothreitol, 284

DNA, 2, 80, 93

A-form, 11

B-form, 11

base pairing, 14, 193, 206 contamination, 164 denaturation, 19, 207 double helix, 11 footprinting, 324

major groove, 16 minor groove, 16 probe, 208 purification, 103 sequence, 163

depth of coverage, 306

hierarchical shotgun sequencing, 305 whole genome shotgun sequencing,

304 supercoiling, 22 structure, 11 – 16 synthesizer, 167 topoisomerase, 24 Z-form, 11

DNA binding domain (DBD), 218, 244 DNA gyrase, 34

DNA helicases, 34

462 INDEX

DNA libraries, 183

DNA ligase, 35, 39, 76, 80, 188, 235 DNA methylase, 188

DNA methyltransferases, 69

DNA microarray, 317, 318, 324, 335 DNA polymerase, 31, 32, 83, 234, 297

bacteriophage T7, 298 pol I, 32

pol II, 32 pol III, 32

proof-reading activity, 32 DNA replication, 33, 159

conservative, 29 – 30 dispersive, 30 semi-conservative, 29

DnaA, B, 34 dnaY, 264 Dolly, 392 – 395 Domain, 172

Doped cassette mutagenesis, 251 Doped oligonucleotides, 169, 251 Down’s syndrome, 289 dRhodamine, 300

Drosophila melanogaster, 58, 113, 172, 291

dut, 239

dut−ung− mutagenesis, 238 dUTPase, 239

E. coli (Escherichia coli), 5, 30, 66, 109, 126, 258

genome, 42 EcoRI, 188 EDTA, 278, 286

Electrophoresis, 95, 97 Electroporation, 85, 87, 364

Embryonic stem (ES) cells, 379, 384, 387, 397

Endocytosis, 364, 366 Endoplasmic reticulum (ER), 64

ER retention signal, 64 Enterokinase, 282 Epitope, 214

EPSPSase, 356, 357 Epstein – Barr virus, 362

Error prone DNA replication, 162 Error rate, 253

Error-prone PCR, 253 Erythromycin, 61 Escherich, Theodor, 109 Ethanol, 108

Ethics, 360

Ethidium bromide, 91, 98, 105, 156, 165 Ethyl methane sulphonate (EMS), 232 Euchromatic DNA, 307

Exons, 40, 54

Expressed sequence tags (EST), 308 Expression vector, 111, 246, 258 Exteins, 284

Extra-cellular matrix, 363

F episome, 111 F pilus, 137

F plasmids, 148

origin of replication, 272 Factor Xa, 281, 282

False positives, in two hybrid screening, 225 Field inversion gel electrophoresis, 96 Fields, Stanley, 222

Floxed gene, 390 Fluorescence, 300

fluorescence resonance energy transfer (FRET), 181

fluorescent in situ hybridization (FISH), 289

Formaldehyde, 325 Frame-shift mutation, 60, 233 Franklin, Rosalind, 11

Functional complementation, 216 Fungal resistance, 358

Fusidic acid, 61

G1-phase, 35 G418, 386

Gain of function screening, 217

Galactose metabolizing (GAL) genes, 222, 266

GAL1, 266

GAL1 promoter, 267

GAL4, 165

Gal4p, 165, 219 – 222, 228, 244, 246, 247, 266, 326, 336

Gal80p, 221, 266 Galactokinase, 309, 310

Galactose, 266 Ganciclovir, 386, 387 GC content, 76, 165

GC clamp, 170

Gel filtration chromatography, 275 Gel retardation, 324

Gelsinger, Jesse, 399

Geminiviruses, 350 Gene, 40

assignment, 309 expression factories, 54 gun, 85, 88

knockouts, 42 silencing, 329

Gene therapy, 371, 379, 396, 398, 399, 400 germ-line, 396

General transcription factors (GTF), 51 Genetic markers, 294

Genetic switch, 44 Geneticin (G418), 328 Genome, 40, 183

fully sequenced genomes, 184 genome sequencing projects, 287 genome-wide two-hybrid screens, 333

Genomic DNA, 164, 288 library, 183, 185, 189

Giemsa, 289

Gilbert, Walter, 54, 296 Glutathione, 280, 281

glutathione S-transferase (GST), 279 glutathione agarose, 281

GST-tag, 279 Glyceraldehyde-3-phosphate

dehydrogenase (GPD), 265 Glyphosate, 356, 357

Gonadotropin releasing hormone (GnRH), 393

Griffith, Frederick, 3, 84 Guanine, 7

HAC, see human artificial chromosomes Haeckel, Ernst, 1

Haemophilia B, 400 HeLa cells, 362 Helix – turn – helix, 17 Helper phage, 141

Hemimethylated DNA, 68

Herbicidal Resistance, 356 Hershey, Alfred, 5, 37 Heterochromatic DNA, 307 His-tag, 276, 278, 279

HIS3, 216

HisB, 216

Histone, 25

Histone acetyltransferases (HAT), 49 Histone deacetylases (H-DAC), 49

HIV, 374, 400

HIV protease, 218 Holley, Robert, 295 Holliday junction, 37 Holliday, Robin, 37

Homologous recombination, 37, 129, 310, 327, 329, 333, 384, 385

Homoplasmic, 353 Homopolymer tailing, 195 Horseradish peroxidase, 214 Human α1-antitrypsin, 383

Human artificial chromosomes (HAC), 149 Human Genome Project (HGP), 191, 305 Human T-cell leukemia virus, 373 Hybridization, 203, 206

Hybrid screening, false positives, 225

one hybrid, 228, 229 three hybrid, 228, 229 two hybrid, 218, 224, 227 whole genome, 333

Hydrogen bonds, 18

Hydrophobic interaction chromatography, 275

Hygromycin B, 123 Hyperchromic effect, 19 Hypervariable regions, 211 Hypoxanthine guanine

phosphoribosyltransferase (HPRT), 375

Imidazole, 278

Immobilized metal ion affinity chromatography (IMAC), 276

Immortalized cells, 361 Immunoprecipitation, 325 Immunoscreening, 211, 214 IMPACT system, 285

Inosine, 171

Insecticidal resistance, 355 Insertional inactivation, 117, 118 Insertional vector, 132

Integrase (Int), 39

Integration host factor (IHF), 39

Intein mediated purification with an affinity chitin binding tag (IMPACT), 282, 285

Inteins, 284

VMA1, 284 Introns, 40, 54

Inverted terminal repeats (ITRs), 369, 371 Ion-exchange chromatography, 275 IPTG, 122, 148, 214, 259 – 262, 265, 259 Isopropanol, 108

Isopropyl β-D-thiogalactopyranoside, see IPTG

Isopycnic centrifugation, 105 Isoschizomers, 71

Jacob, Francois,¸ 43

Kanamycin, 123, 376 resistance gene, 345 KanMX cassette, 327

Karyotype, 289

Klenow fragment of E. coli DNA polymerase I, 298

Klinefelter’s Syndrome, 289 Knock-out analysis, 327

conditional knock-out, 388 Kozak sequence, 61

Kunkel strand selection, 238

lac operon, 44, 46, 260 lac promoter, 148, 259 lac repressor, 44

lacI, 259

lacZ, 121, 134, 140, 224, 270, 271 lacZ M15, 121

Lactose, 259, 260 Lactose permease, 44 Lagging strand, 33

Lambda (λ), see Bacteriophage λ Large offspring syndrome (LOS), 394 Leading strand, 33

Leloir pathway, 219, 266 Lentiviruses, 373, 375 Leukaemia, 399

LexA, 227

Lwoff, Andre,´ 126 Library subtraction, 203

Ligation-independent cloning, 335 Linkers, 187

Linking number, 23 Lipofectin , 366 Liposomes, 364

liposome-mediated transfection, 364 Long terminal repeat (LTS), 373, 374, 375 loxP, 125, 126, 146, 148, 352, 359, 388,

390

Lysogenic pathway of λ phage, 129 Lysozyme, 105

Lytic pathway of λ phage, 129

M-phase, 35

M13, 218, 234, 236

origin of replication, 138 phage, 137, 138, 235 plaques, 234

replicative form (RF), 137, 138 vectors, 137

Maize streak virus, 348, 349 Major groove of DNA, 16 Major late promoter (MLP), 369 Malignant melanoma, 323 Maltose, 282

Maltose binding protein (MBP), 282 MBP-tag, 282

Mass spectrometry, 286, 335 Maxam, Allan, 296 Mechanical shearing, 186 Melting temperature, 19 Mendel, Gregor, 1 Meselson, Mathew, 30, 37

Meselson – Stahl experiment, 30, 31 Metabolome, 314

Methionine aminopeptidase, 62 Methotrexate, 377 Microarray, 317, 321, 325 Micrococcal nuclease, 25 Microsatellites, 292

Miescher, Johann Frederick, 2

Minor groove of DNA, 16 Mis-sense mutation, 232 Mismatches, 170

Mitosis, 24 Monocistronic, 47

Monoclonal antibodies, 213, 214 Monocotyledonous plants, 346 Monod, Jacques, 43

Monsanto, 357 Morgan, Thomas, 290 Morula, 380, 393

mRNA, 42, 55, 179, 191, 194, 329 mRNA splicing, 310

Mullis, Kary, 153

Multiple cloning site (MCS), 121 Multipotent stem cells, 397 Mutagenesis, 231 – 255

alanine scanning, 250 cassette, 240, 241, 252 charged-to-alanine, 251 doped cassette, 251 efficiency, 243 PCR-based, 241

primer extension, 233 – 234 Quikchange , 248 – 249

Mutation frequency, 236 Mutation rates, 231 Mutation, 231

frame-shift, 60, 233 mis-sense, 232 nonsense, 233 point, detection, 175 silent, 60, 232 transition, 232, 254

transversion, 232, 254 MutH, 237

MutL, 237

MutS, 237

N-end rule, 264 Nathans, Daniel, 66 Neomycin, 123

Neomycin phosphotransferase, 376 Neomycin resistance, 386

Nick translation, 195 Nicked DNA, 238

Nitriloacetic acid (NTA), 276

INDEX 465

Nitrocellulose, 100, 214 Non-histone proteins, 25 Non-homologous integration, 362 Non-sense mutation, 233 Northern blotting, 103, 314 Nuclear localization signal, 64

Nuclear magnetic resonance (NMR), 336, 339

Nuclear polyhedrosis viruses, 269 Nuclear transfer, 390, 392, 394, 395 Nuclein, 2

Nucleoside, 7 Nucleosomes, 24, 25, 53 Nucleotide, 7

Nucleotide triphosphates (NTP), 297 Nylon membranes, 100

Occlusion bodies, 269 Okazaki fragment, 33, 35

Oligo-dT, 193, 193, 196, 198, 319 Oligonucleotide, 153, 155, 159, 169, 188,

209, 234, 235, 240, 248, 296, 297 primers, 165, 167, 203, 241

Oncogenes, 315

One-hybrid screening, 228, 229 Open reading frame (ORF), 40, 307 Operator, 44

Opines, 342 OriC, 34, 73, 115

Origin of replication, 34, 258 Ornithine transcarbamylase (OTC), 399

p15a, 116 pac site, 146

Packaging site ( ), 375 PAC, 146

Paired box, 174

Partial restriction digests, 186 Parvoviruses, 400 pBluescript, 142

pBR322, 112, 116, 117, 119, 122, 141, 263 PCR, 153, 156, 159, 199, 200, 210, 241,

381 amplification, 333 extension, 155, 161

PCR-based libraries, 199 PCR-based mutagenesis, 241

466 INDEX

PCR (continued)

diagnosis of genetic disease, 173 hot start, 163

Peptide/DNA complexes, 366

Pfu DNA polymerase, 163, 164, 171 Phage, 5

Phage Display, 218 Phagemids, 141 Phenol, 105 Phenotype, 1 Phosphatase, 137

Phosphoglycerate kinase (PGK), 265 Phosphoramidite, 167 Phosphorothioate, 237

Physical mapping, 293

Pichia pastoris, 268 Pilus, 111

pJB8, 136

Plasma membrane, 363

Plasmid, 21, 80, 85, 105, 106, 108, 112, 164, 248

Plasmin, 207 pMB1, 114, 116

Point mutations, detection, 175 PolyA polymerase, 55 Polyacrylamide gel, 89, 103, 287 Polyadenylation, 55, 375, 378

PolyA tail, 193 Polycistronic, 353 Polyclonal antibodies, 213 Polyhedrin, 269 Polynucleotide, 9 Polynucleotide kinase, 209 Polypeptides, 59 Polysome, 61

Positional effects, 347 Post-transcriptional modifications, 191 Post-translational modifications, 259

glycosylation, 259, 269 methylation, 259 phosphorylation, 259

Potato virus X, 350 POU domain, 172

POU homeodomain, 172 POU specific domain, 172

Ppr1p, 244, 246, 247 Prescission protease, 281

Prey, 224 Primary cells, 361

Primary library, 190 Primase, 34 Primers, 153, 158

Primer extension mutagenesis, 233 – 234 Probe, 100

Promoter, 43, 44, 257

Pronuclear injection, 379, 381, 383 disadvantages of, 383

Pronucleus, 380 – 382

Proof-reading activity of DNA polymerases, 32

Propeller twist, 14 Protein A, 286

Protein detection arrays, 335 Protein engineering, 254

Protein production and purification, 257, 275

Protein purification tags, 276 Protein – protein interactions, 222 Proteinase K, 207

Proteolysis, 264

Proteome, 314

Protoplast transformation, 347 pSC101, 117

Pseudogenes, 308 Ptashne, Mark, 127

pUC plasmids 119, 122, 140, 141, 263 pUC18, 119, 304

Pulsed-field gel electrophoresis (PFGE), 95, 145

Pulse time, 96, 97 Purines, 7, 9 Puromycin, 62 Put3p, 244, 246, 247 Pyrimidine, 7, 9

Pyrococcus furiosis, 163

Quiescence, 392

Quikchange mutagenesis, 248 – 249

Radiation hybrid maps, 294, 295 Random-primed library, 198 Real-time PCR, 179

Recognition sites, 287 Recombination, 37, 132

Relaxed plasmids, 113 Repetitive DNA sequences, 145 Replacement vector, 132 Replication, 131

Replicative form (RF) of M13, 137, 138 Replicon, 66

Repressor, 44

Reptation, 94

Restriction enzymes, 66, 148, 186, 237, 271, 287

type I, 70 type II, 71 type III, 71

Restriction fragment length polymorphisms (RFLP), 292

Restriction maps, 294 Retroviruses, 33, 372, 373, 375

Reverse transcriptase, 33, 178, 183, 192, 196, 199, 200, 319, 374, 375

Reverse transcription – polymerase chain reaction, see RT – PCR

Reverse two hybrid screen, 229 Rho termination, 46 Ribonuclease, 5 Ribonucleotides, 7

Ribose, 7, 9

Ribosome binding site (RBS), 258 Ribosome inactivating protein (RIP), 359 Ribosomes, 61

RNA, 53

interference (RNAi), 329, 330, 332, 333 hydrolysis, 195

RNA-induced silencing complex (RISC), 332

RNA polymerase, 34, 47, 51, 55, 124, 257 RNA pol I, 47

RNA pol II, 47, 51, 53, 191 CTD, 51, 53

RNA pol III, 47, 51 RNA primer, 34 RNA silencing, 330 RNA splicing, 55, 310

RNA-dependent RNA polymerase (RdRp), 331

RNA-DNA hybrid, 195, 200 RNAse, 105, 115, 193, 200, 331

RNAse H, 195

INDEX 467

Roberts, Richard, 54

Rolling circle replication, 131 ROP protein, 116

Rosetta, 264 Roundup Ready, 357

Rous sarcoma virus (RSV), 272, 378 rRNA, 43, 61

rrnB, 263

RT – PCR, 177, 179, 199, 314

S-adenosylmethionine, 70 S-phase, 35

S1 nuclease, 195

Saccharomyces cerevisiae, 34, 42, 124, 165, 244, 265

Sanger, Fred, 296

Schistosoma japonicum, 281 Schizosaccharomyces pombe, 265, 269 Screening, 206, 210, 232

by function, 216 by interaction, 217

Secondary cell, 362 Selectable marker, 258

Semi-conservative DNA replication, 29 Senescence, 361

Sequenase , 298 Sequence repeats, 307

Sequence tagged site (STS), 295 Sequencing DNA, 296 – 306 Sf21, 270

Sf9, 270

Sharp, Philip, 54

Shine – Dalgarno sequence, 61 Sickle cell anaemia, 175 Signal sequence, 64

Silent mutation, 60, 232 Similarity searches, 309

Single-gene human genetic disorder, 397 Single-nucleotide polymorphism (SNP), 292 Single-stranded binding protein (SSB), 34 Single-stranded M13 DNA, 240

siRNA, 331

Site-specific recombination, 37, 388, 399 Small inhibiting RNAs, see siRNA

Small nuclear ribonucleoproteins (snRNP), 58

Smith, Hamilton O., 66