Genomics- The Science and Technology Behind the Human Genome Project. Charles R. Cantor, Cassandra L / genomics1-10 / booktext[1]

use in libraries, 50

use of arrays in mapping, 292 walking in gene finding, 435

Costs of DNA sequencing, 527–530 Counterion screening in electrophoresis, 134 Coverage

of clone libraries, 47 of ordered libraries, 275

Cox, David, 212 CpG

as adjuvant, 7 frequency in DNA, 6

in light and dark bands, 510 in HTF islands, 248

islands, 245

Cre recombinase in cloning, 267 Crkvenjakov, Radomir, 413–415 Cross connections

between libraries, 292 by inter-Alu PCR, 515

Cross hybridization

between human and rodent DNA, 208 in SBH, 413

Crosslinking of DNA by psoralen, 524 Crossovers during recombination, 174 CsCl

use in density gradients, 131 Curvature of DNA, 8

Cy5 use in DNA sequencing, 334 Cycle sequencing, 99, 336

for HIV diagnostics, 463 Cystic fibrosis

alleles detected by MDE, 460 spectrum of mutations in, 449

tissue specific expression, 437 Cytogenetic map as framework, 248 Cytogenetics, 208–215, 218–229

Dangling ends in DNA duplexes, 74

DAPI in in situ hybridization, 220 Databases, 569–573

Davidson, Eric, 506

Davidson, Norman, 134 Deamination mutagenesis, 6 7-Deazaguanine

in DNA sequencing, 341 in SBH, 418

Deep Vent DNA polymerase, 107 Degeneracy

of primers in PCR, 119

of the genetic code, 532, 550 DeGennes, Pierre, 138

Delta restriction cloning, 370

INDEX 579

Denaturing gels

gradients for mutation detection, 460 in DNA sequencing, 327

Dendrimers in DNA detection, 94–96 Density effects of DNA base composition,

131

Density gradient centrifugaton chromosome purification by, 43 separation of DNA by, 131

Dephosphorylation of vector arms, 257 Dervan, Peter, 485

Detection of single molecules, 91, 394 Determination of phase in a family, 172 DGGE, 460–461

Diagnosis

by DNA sequencing, 452–453

of presymptomatic illness, 448 Dichroism, linear, 151

Dideoxy fingerprinting of mutations, 462 Dideoxy nucleoside triphosphates, 329–330 Differences between sequences, 554 Differential

cloning, 493–499 display, 500 sequencing, 394

Diffusion

effects, in DNA sequencing, 330 role in electrophoresis, 139

Digoxigenin structure, 94

use in comparative genome hybridization, 230

use in DNA detection, 93 Dimensionality of pooling, 313–315 Dinucleotide frequencies in DNA, 243 Diploid

samples in heteroduplex analysis, 457 stage in meiosis, 169

Direct repeats in recombination, 509 Direct sequencing, 363–367 Directional cloning, 503

Dispersion in gel electrophoresis, 162 Disposable pipet tips, 295 Distance(s)

ambiguities in a bottom up map, 240 geometry, 560

in genetic maps, 174 Distortion

in genetic map distances, 174

in the radiation hybrid map, 215 of cDNA abundance information by PCR,

500

Divalent ion stabilization of triplexes, 474 Diversity in human sequences, 564

DNA

base stacking in, 5 grooves, 5

symmetry of, 1

580 INDEX

DNA arrays, making and using, 295 DNA bending, 133

DNA chips, synthesis of, 406–411 DNA circles in jumping cloning, 258 DNA concatemers as size standards, 141 DNA content, 64

DNA denaturation in amplification, 99 DNA diagnosis, 450

DNA fishing, 437

DNA helicase in replication, 21 DNA knotting, 160–161

DNA ladders, evenness in, 336–337 DNA ligase

enzymatic properties of, 11 in DNA synthesis, 9

use in amplification, 126 use in DNA cloning, 13

use in PSBH, 426 DNA melting

concentration dependence, 70 equilibria in, 67 hairpin formation in, 80 hysteresis in, 80

kinetics of, 77

DNA methylation in imprinting, 206 DNA polymerase

Klenow fragment of, 22 nick translation by, 19 primer extension by, 19 strand displacement by, 19 use in DNA sequencing, 329

use in proofreading hybridization, 428 DNA polymorphisms in mapping, 262

DNA preparation by PCR, 98 in gels, 160

DNA rearrangements, 433

DNA repair for control of mutagenesis, 6 DNA sequence

as unique identifier, 64 of HTF islands, 247

DNA sequencing

by thermal cycling, 99 costs of, 529–530 rates, 526

use in diagnostics, 452–453 DNA shuffling, 116

DNA stacking, duplex stabilization by, 423 DNA synthesis

chemical methods for, 8–9 during the cell cycle, 37

DNA topology

effect in inverse PCR, 112 effect on hybridization, 87

DNA trapping (in) electrophoresis, 149, 155–157

Domains, 561–564 Dominant, defined, 171

Dominant lethal

genes in cancer, 451

mutations effecting recombination, 166 Doolittle, Russell, 550

DOP-PCR, 119 Dot blot, 86

Dot matrix plot, 555–556 Double crossovers

effect on genetic mapping, 175 in interval mapping, 187

Double digests

use in restriction mapping, 252 Down’s syndrome, 39

aneuploidy in, 51

Dpn I

DNA cutting based on, 253

use in coincidence cloning, 503 Driver DNA

use in RDA, 495

use in subtractive cloning, 493 Drmanac, Radoje, 413–415

Drosophila melanogaster

as model organism, 25 gene density in, 543

polytene chromosomes, 234–235 Druckier, Andy, 355

Drug delivery, 522–523 Drug-resistant mutants, 463

dU use in PCR to prevent contamination, 103 Duchenne muscular dystrophy

DNA deletions in, 436

gene isolation by subtraction, 492 gene size, 451

Dujon, Bernard, 261 Duplexes

stabilization by stacking effects, 71 thermodynamics of formation, 75

Dynamic programming, 557

Eag I use in restriction mapping, 256 Editing of mRNA in protozoa, 531 Edmond degradation, 401

Efficiency of PCR, 102 Efstratiadis, Argiris, 383 Eggers, Mitchell, 415

Eight base cutters, table of, 244 Electrical field orientation of gels, 137 Electron microscopy of DNA, 397 Electrophoresis, 131–163

as detected by blotting, 87

for chromosome purification, 48

sequence specific capture during, 486–488 to find polymorphisms by RLGS, 321 triplex behavior in, 473

two dimensional protein fractionation, 27 use in mutation detection, 459

Electrophoretic mobility, defined, 134 Electrospray MS for DNA sequencing, 354

Gene families

effect on hybridization kinetics, 506 examples of, 38

Gene finding, 190, 435–437

by DNA sequence analysis, 530–535 Gene fusions,

See Fusion proteins

Gene location by linkage disequilibrium, 192 Gene number estimates, 27

Gene sizes in human diseases, 451 Genes coding for RNA products, 541 Genethon megaYAC project, 286

Genetic bit analysis, 424, 428 Genetic code, 531–532

Genetic lethality of fragile X, 442 Genetic map(s)

as framework for physical mapping, 248 compared with physical map, 173

distribution of repeats in, 510 in chromosomes, 39

use in in situ hybridization, 221–222 Gilbert, Walter, 155, 328, 376

Glass plates for oligonucleotide arrays, 409 Globin gene chromosomal organization, 38 Gorilla, as target for sequencing, 526

Goss, Stephen, 212 G-quartet in telomeres, 34 GRAIL, 537-540

Gravitational instability in centrifugation, 131 in electrophoresis, 135

Green, Phil, 345, 362

Gridded filter arrays of libraries, 50 G-U mismatch repair, 6

analysis of complete DNA sequence, 541 cost of DNA sequencing, 529

DNA sequence of, 27 Hairpin(s)

effect on DNA renaturation, 84 effect on DNA sequencing, 344 effects on SBH, 419

formation in intramolecular triplexes, 472

formed in DNA melting, 80 found in aptamers, 518 in PCR primers, 116

in telomeric DNA, 265 structure of, 4

half YACs as telomere cloning vectors, 265 Half-jumping clones, 259 Half-linking clones

in analysis of partial digests, 261 use in restriction mapping, 255

Haploidy in meiosis, 169 Haplotype

defined, 171

determined by single-sperm PCR, 217 use in gene finding, 190, 436

use in linkage disequilibrium, 191 Harris, Henry, 212

Harrison, Rhonda, 556

HAT medium for radiation hybrids, 212 Head to head inter-Alu PCR, 511

Helène, Claude, 523–524 Helix-turn-helix motifs, 561–562 Hemi-methylation sites in cloning, 503 Hemi-nested PCR, 105

Hemoglobin gene arrangement, 325 Hemoglobinopathies, 449 Hemophilia B mutations, 453–454 Henikoff, Stephen, 371 Heterochromatin, 37

difficulty in sequencing, 390 Heteroduplexes

in coincidence cloning, 501 use in diagnostics, 455–462

Heterogeneity

in HIV infection, 463 in tumor tissue, 454

of the human genome, 544–545 Heterozygosity, defined, 170

Hexamer libraries in DNA sequencing, 366 Hidden layer in a neural net, 536

High resolution zone in PFG, 147 High throughput PCR, 299

Hinc II use in SDA, 123 Histones, 36

HIV

DNA diagnosis in, 463

detected by QB replication, 128 hncDNA preparation, 388

584 INDEX

hnRNA

as a source of libraries, 303 synthesis of, 23

Holliday structure, 14

in recombination, 166, 176 Homeobox gene arrangement, 547 Homologous chromosomes, 52

in meiosis, 166

in single sperm PCR, 217 Homology

determination by sequence analysis, 551–560

searching in recombination, 176 use in finding DNA seqeunce errors, 546

Homopurine stretches

in S1 hypersensitive sites, 471 Homozygosity

defined, 170

mapping panel for, 205 methods for detection, 204–205 of genes in tumors, 451

Hood, Leroy, 334

Hopping of transposons, 369 Horizontal sequencing studies, 420–421 Hot spots

for mutations in colon cancer, 452 for recombination, 193, 549 for restriction nuclease cleavage, 260

Hot start PCR, 105

Hpa II cleavage of mammalian DNA, 245 HPCE in DNA sequencing, 349

HPRT DNA sequence, 540 HTF island(s), 245

as restriction nuclease hotspots, 260 distribution on human chromosome 21,

277

DNA sequences in, 246–247 in fragile X disease, 447

in the Huntington’s disease region, 543 Human cell DNA content, 64

Human chromosome 4

comparisons of maps for, 229 Human chromosome 11

locations of cosmid clones on, 223 inner product mapping of, 318

Human chromosome 19 cosmid array, 293

Human chromosome 21

compared with chimp chromosomes, 229 inter-Alu PCR products from, 514 mapping panel for, 211

Not I restriction map, 278–279 radiation hybrid map of, 215 restriction fragments detected by Alu, 251 YAC contig in, 280

Human chromosomes banding in, 44–45

genetic size of, 195

number of, 42

physical size of, 195 radiation hybrid map of, 216 rodent cell lines containing, 208–218

Human developmental gene expression, 547 Human disease genes, 439

Human DNA

distribution of Alu in, 250 sequence diversity in, 564

Human gene number, 544

Human genetic map, 195–197 Human Genome Project progress, 527 Human Genome Sciences, Inc., 384 Human telomere cloning, 268

Humster use in in situ hybridization, 224 Huntington’s disease

closing a map gap by FISH, 228 gene search for, 447

genome region as sequencing target, 378 linkage disequilibirum in, 191 sequence analysis in its vicinity, 543 triplet repeats in, 440

Hybrid cell lines

as a mapping panel, 211

as a source for coincidence cloning, 505 as targets for inter-Alu PCR, 511

as targets for sequencing, 527 sources for single chromosome hncDNAs,

388

use in chromosome assignment, 208 use in restriction mapping, 249

Hybridization, 64–96

as a method for DNA sequencing, 403–425 definition, 66

driven by probe concentration, 89 driven by target concentration, 90 effects of mismatches on, 77 for chromosome assignment, 208

for connecting different libraries, 292 stringency in cross species comparisons,

325

to flow sorted chromosomes, 47

use in multiplex sequencing, 375 use in regional assignment, 210

use in studying repeat distribution, 506–507 using PNAs, 492

with inter-Alu PCR products, 515 Hydrophobic amino acids, 534 Hydroxyapatite

use in cDNA normalization, 383

use in differential cloning, 493 use in hybridization, 66

Hypercholesterolemia, 509 Hypercube pooling schemes, 313

Hyperorientation of DNA in gels, 152 Hypoxanthine ribosyl transferase, 212 Hysteresis in DNA melting, 80 Hytidaform mole cDNAs, 388

Identification by DNA sequence, 64–66 Image Consortium, 388

Imaging plates in DNA sequencing, 331 Immune surveillance and mutagenesis, 434 Immunodominant epitopes, 448 Immunoglobulin genes, 548

rearrangements in, 433 Immuno-PCR, 120–122

Imperfections in helices, 75–76 Imprinting in genetics, 206

In gel preparation of DNA, 160

In situ hybridization, 218–229 Inbreeding

as a cause of genetic disease, 205 of strains for use in genetics, 178

Incyte Phamaceuticals, Inc., 384 Indels

detection by sequence comparison, 546 detection in heteroduplexes, 457

Independent segregation of unlinked loci, 181 Indexing, 500

Infectious disease DNA diagnosis, 462 Informativeness of markers, 167 Infra red dyes in DNA sequencing, 332 Inheritance model testing, 183

Inner product mapping, 318–320 Insert sizes

in megaYACs, 286

of various cloning vectors, 241 Insulin-like growth factor 2 imprinting, 206 Interalleleic recombination mutagenesis, 203 Inter-Alu PCR, 510–515

Interbreeding and chromosome number, 59 Intermolecular triplexes, 472

Internal labeling

in DNA sequencing, 338 possible use in PSBH, 429

Internal loop thermodynamics, 75–76 Internet access of GRAIL, 538

Interphase nuclei in in situ hybridization, 224–226

Interrupted restriction nuclease sites, 273 Interspersed repeat PCR, 511–515

Interval mapping in linkage studies, 185 Intramolecular triplexes, 472

Intron(s), 24

effect on PCR, 302 word useage in, 535

Inverse PCR, 112

Inversion of a sequence database, 559 Inverted repeats

effect on PCR, 104

effect on recombination, 509 use in PCR, 113

Ion cyclotron resonance MS of DNA, 357–358

Ionic strength insensitivity of PNA, 491 IR 770-9-dATP structure, 339

INDEX 585

Iron-EDTA-ethidium bromide, 476

I- Sce I use in rapid restriction mapping, 261 Isochores, 544

separation of DNA into, 132 Isoschizomers of rare cutters, 244 Isothermal amplification, 122–127

Jeffreys, Alec, 203 Jones, Vaughan, 160

Joule heating in electrophoresis, 330 Jukes, Thomas, 554

Jumping

libraries, 257–259

of primers, 373–374 of transposons, 369 probes, 88

Junk DNA, 325

for evolutionary studies, 565 is it worth sequencing?, 378

Karyotype definition, 54

human chromosomes, 44 mouse chromosomes, 60–61

Keller, Richard, 394–397 Kennedy’s disease, 437 Kinetics

of DNA melting, 77 of DNA renaturation, 82

of filter hybridization, 88

of subtractive hybridization, 496–499 of triplex formation, 474

Kinks in DNA during PFG, 150, 154 Kleinfelter’s syndrome, 59

Klenow fragment of DNA polymerase I, 22, 99

use in cDNA normalization, 383 use in YAC cloning, 287

Knots in DNA, 160–161 Kohara, Yuji, 270 Kornberg, Arthur, 21

Kpn repeat, 509 Kringles, 562

L1 repeat, 509

use in in situ hybridization, 221 Labels

for fluorescent DNA sequencing, 332–333 for improved STM of DNA, 399 introduction by PCR, 107

Lac repressor in Achilles’ heel methods, 477 lac Z gene color screens, 482–483

Ladder sequencing, 327–334 Lambda bacteriophage

DNA as PFG size standard, 141

repressor use in Achilles’ heel methods, 477 use in libraries, 50

586 INDEX

Landegren, Ulf, 88, 348

Lander, Eric, 180, 275 Lane straightness in PFG, 162 Large scale sequencing

of cDNAs, 384 models for, 529 results, 540–545

target choices for, 378 Laser(s)

ablation of DNA in chromosomes, 231 in chromosome sorting, 45

use in DNA sequencing, 332

use in mass spectrometry, 351, 354–357 use in STM, 398

Latin squares to rearrange arrays, 316 Latt, Samuel, 52

Lawrence, Jeanne, 228

Lehrach, Hans, 413

Length of human chromosomes, 216

Length standards for partial digests, 261 Lerman, Leonard, 138, 459

Lerner, Richard, 519 Lethal alleles, 52

Lex A protein in Achilles’ heel methods, 477 Li, Chuan, 372

Library(ies)

as an array of samples, 239 of single chromosomes, 47 sizes, 241

Ligase chain reaction, 126–127 Ligation

between vector arms prevented, 287 of padlock probes, 88

of short primers in DNA sequencing, 366 of small DNA circles, 112

preferential DNA circularization by, 257 to add PCR priming sites, 108

use in coincidence cloning, 505

use in proofreading hybridization, 424 used to detect expansion in repeats, 516

Light microscopy of chromosomes, 38 Likelihood

of clone order in S. pombe, 307 of clone overlaps, 272

Linear DNA amplification, 99

Linear birefringence of agarose gels, 152 Linear dichroism of DNA, 150

Linear discriminant method for exons, 538 LINES, 509

Link up of clones by polymorphism, 263 Linkage analysis, 180–190

Linkage, defined, 165, 172

Linkage disequilibrium, 191–193 use in gene finding, 436

Linkage group, defined, 172 Linked loci, defined, 173 Linking clones, 254–256

use in analysis of partial digests, 262

use in end-capture electrophoresis, 487 Lipman, David, 559

Liquid gels in DNA sequencing, 349 Liquid handling robots, 294

Loading of samples in DNA sequencing, 335 Locus, defined, 170

LOD score

estimation of recombination frequency, 188 in linkage, 183

Logical and/or, 536 Long PCR, 106

Long sequencing ladder, 340

Low-density liproprotein receptor, 509 lox P sites in large fragment cloning, 267 Luciferase in stepwise sequencing, 401 Lumpkin, Oscar, 138

Luria-Delbruck effects in PCR, 106 Lyon, Mary, 57

Lysosome, 523

Macrorestriction map compared with FISH, 229

fragments as hybridization probes, 306 made in top down strategies, 237

Magnesium ions and triplexes, 470 Magnetic microbeads

in DNA sequencing, 347 use in DNA handling, 295

use in triplex capture, 481 Major groove

of DNA in triplexes, 473

Major Histocompatibility Complex, 17 recombination hotspot in, 194

MALDI MS

for DNA sequencing, 354–356

use of SBH for sample preparation, 421 Male genetic map of chromosome 1, 194 Mapping

functions in genetics, 199 methods for single molecules, 269

of transposon insertion sites, 369–370 panel of hybrid cell lines, 211 strategies, 291

Markers in genetics, 165

Markov statistics of DNA sequences, 243 Masks in photolithography, 407

Mass spectrometry in DNA sequencing, 349 Maternal inheritance of mitochondria, 56 Mathies, Richard, 333, 350

Matrix method of clone ordering, 311

Matrix multiplication in mapping, 320 Maxam, Allan, 328

Maxam-Gilbert sequencing and 5-mC, 391

estimates of clone overlap, 272 McBride, Lincoln, 481

MegaYACs, 285–290

Meiotic recombination, 166–169, 174–177 frequency of, 173

in telomeric light bands, 510 in yeast chromosome III, 548–549

Melting

measurements on arrays, 418 of satellite DNA, 33

Melting temperature definition, 68

effect of mismatches on, 423 of heteroduplexes in gels, 460 of mismatched duplexes, 77

Mental retardation genetics, 440 Merck, Inc., 388

Metacentric chromosomes, 59

Metal ions as MS labels, 352–353 Metallothionein-streptavidin chimera,

353–354 Metaphase chromosomes

as a target for microcloning, 231 banding of, 44–45

in the cell cycle, 52 purification of, 43–46

viewed by in situ hybridization, 219 Metaphase FISH, 221

Methylation

effect onNot I cleavage pattern, 245

possible role in fragile X disease, 445–447 role in restriction, 6

sensitivity of rare cutters, 263 sites in coincidence cloning, 502 sites in Achilles’ heel methods, 477

use in altering restriction digests, 253 5-Methylcytosine

detection in the DNA sequence, 390

effect on restriction digest pattern, 245 in imprinting, 206

role in restriction, 6

role in X chromosome inactivation, 57 role in Z DNA helix, 6

use in short primers, 367 Metrics to compare map types, 216 Meyers, Richard, 212

Microbeads

use in DNA handling, 295 use in DNA sequencing, 347

Microcloning of metaphase DNA, 231–232 Microdeletion in gene finding, 436 Microdissection

of chromosomes, 231–232 of polytene chromosomes, 234

Microlithograpic array in electrophoresis, 137 Microscopy for DNA sequencing, 397–400 Microtitre plate(s), 294–296

containers for ordered libraries, 239 sample container for DNA sequencing, 347 use in pooling, 300

Minimum tiling path and clone size, 288

INDEX 587

Minimum tiling set, 239 as sequencing target, 379

Minisatellite polymorphism, 203 Mirzabekov, Andrei, 408–411, 418, 421 Misincorporation

by DNA polymerases, 101 by Taq polymerase, 106

Mismatches

effect on melting temperature, 421 in heteroduplexes, 455–462

in SBH, 403

thermodynamics of, 75–76 Mispaternity

in genetics, 180 Mispriming

in PCR, 104

source of errors in DNA sequencing, 345 suppression by the use of ssb, 367

Mitochondrial DNA, 54–57

D loop as a mutation hot spot, 466 resequencing by SBH, 421–422

use in the study of human evolution, 57 Mitosis, 37

mechanism of, 52–53

Mitotic nondisjunction in cancer, 451 Mobile elements, 510

Mobility defined, 134

shifts cause by mismatches, 459 Molecular

anthropology, 565 beacons in PCR, 116 indexing, 500 rulers using DNA, 18

sieve chromatography, 135 Monocistronic messages in eukaryotes, 532 Monoclonal antibodies

against carbodiimide-base adducts, 459 in nanoengineering, 16

use in DNA detection, 93–95 Monozygotic twin DNA, 65

Monte Carlo methods for DNAs in gels, 154 Morgan, Thomas Hunt, 173

Mosaicism

caused by X chomosome inactivation, 58 effect on restriction digest pattern, 243 in metaphase chromosome structure, 52

Motifs, 561–564 Motion of DNA in gels, 149

Mouse chromosome banding, 60–63 Mouse DNA invisible to Alu, 250 Mouse genetics, 178–179 Moyzis, Robert, 506

mRNA

editing, 531 instability in cells, 380 quantitation, 382 synthesis of, 23

588 INDEX

Multiphoton detection, 355 Multiple alignments, 560–561 Multiple color labeling in SBH, 425

Multiple crossovers in mapping functions, 199 Multiple-headed pipetors, 294

Multiplex genomic walking, 376–377 Multiplex PCR, 114

applied to antigens, 122 Multiplex sequencing, 375–376 Multipoint mapping, 189

Mung bean nuclease in RDA, 495 Muntjak chromosome numbers, 59 Mural, Richard, 537

Mus musculus

as model organism, 25 genetics, 178

temperature sensitive, 58 Mutation detection

electrophoresis, 459–460 in heteroduplexes, 455–462

Mutation hot spots, 466 examples of, 194

in minisatellites, 203 Mutation rate

in fragile X disease, 443 in humans, 464

mut S protein heteroduplex detection, 459

Nanoengineering using DNA, 15

Nearest neighbor base frequencies, 243

Nearest neighbor interaction equilibria, 73 Negative results in SBH, 404

Neighboring DNA fragment identification, 254

Nested deletions

for making PSBH samples, 429

in clones for DNA sequencing, 371 Nested PCR, 105

in hncDNA preparation, 388 Network formation in renaturation, 84 Neural nets, 535–540 Neurofibromatosis, 450

New mutation detection, 463–467

NFAT protein in Achilles’ heel methods, 477 Nick translation

activity of DNA polymerase, 19 role in replication, 21

use in CGH, 230

Node in a neural net, 536 Noise

in DNA sequence comparisons, 550 in PCR, 103

in single molecule detection, 395 Nomenclature for chromosome bands, 44 Noncoding sequence interpretation, 563 Nondisjunction

as a cause of cancer, 451 in the cell cycle, 52

Non-histone chromosomal proteins, 36 Non-transmitting fragile X males, 442 Noolandi, Jan, 138, 157 Normalization of cDNA libraries, 382 Northern blot, 499

use in gene finding, 437

Not I

fragments of E. coli , 238

map of human chromosome 21, 278–279 recognition site, 242

restriction map ofE. coli , 277 sites in transposons, 368

use in RLGS, 321

Nuclear magnetic resonance, 550 Nucleation

as function of DNA length, 85 energetics of, 73 equilibirum constant for, 72 of DNA duplex formation, 71 rate limiting in renaturation, 81

Nucleic Acid Database, 8 Nucleosome structure, 36

Number of genes in organisms, 541

Obsolescence of cloning vectors, 290 Odds ratio in linkage, 182 Off-set printing

for making a cosmid array, 293–296 use in array manufacture, 411

Oishi, Michio, 88, 385 Oligo-dG tailing of hncDNAs, 388 Oligo-dT

as primer for cDNA production, 380 in differential display, 500

Oligonucleotides

in pooling strategies, 304 synthesis of arrays, 406–411

thermodynamics of duplex formation, 75 Oncogenes, 451–455

effects of homozygosity on, 203 One color sequencing, 337

One letter code for amino acids, 561 Open reading frames

defined, 531

GRAIL analysis of, 537–540 numbers in various genomes, 541 prediction of, 534–535

Optical mapping of DNA fragments, 269