Gene Cloning and DNA Analysis: An Introduction, Sixth Edition ...

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Index 317 Mendel, G., 3 messenger RNA, 131–133, 305g methanol, 238 methionine-rich protein, 273t methotrexate, 106, 198t microarray, 215–217, 305g microinjection, 85, 305g microprojectiles, 85, 117, 118, 119, 268, 271 microsatellites, 181, 257, 284–285, 286–287, 305g microscopy, 182 minimal medium, 106, 111, 130, 305g mitochondrial DNA, 173, 292–296, 305g mitochondrial Eve, 292, 305g modification interference assay, 194–197, 305g molecular clock, 292, 305g monellin, 273t Monod, J., 4 Morgan, T.H., 3, 121 mRNA, see Messenger RNA Mullis, K., 4 multicopy plasmid, 39, 305g multigene family, 142, 305g multigene shuffling, 272, 305g multiplex PCR, 285, 305g multiregional evolution, 291–292, 305g muscular dystrophy, 255t Mycoplasma genitalium, 173t Neanderthals, 173, 293–294 neo, 198t neomycin phosphotransferase, 198t, 277 Neurospora crassa, 112, 141 nick 60, 136, 305g nick translation, 136, 306g Nicotiana tabacum, 273t nitrilase, 273t nitrocellulose membrane, 143 Nocardia otitidis–caviarum, 53t non-radioactive labelling, 137, 144 northern transfer and hybridization, 144, 186–187, 275, 306g NotI, 53t nptII, 277 nuclear transfer, 241, 243, 306g nucleases, 46–47 nucleic acid hybridization, 133, 306g nucleotidase, 171 nylon membrane, 143 Ochrobactrum anthropi, 273t OD, see optical density OFAGE, 62–63, 306g oleic acid, 277t oligonucleotides, 306g directed mutagenesis, 202–204, 306g gene synthesis, 247, 249 insertion mutagenesis, 202 primer design for PCR, 149–152, 156 probes, 138–140 synthesis, 139, 140f ompA, 233 oocyte, 241 open reading frame, see ORF open–circular DNA, 36, 306g optical density, 27, 27f ORF, 208, 306g ORF scanning, 208–210, 306g organic extraction, 29–30, 33 origin of replication, 13, 306g ornithine carbamoyltransferase, 273t orotodine-5′-phosphate decarboxylase, 109 orphan, 208, 306g orthogonal field alternation gel electrophoresis, 62–63, 306g Ostrinia nubilialis, 266 Out of Africa hypothesis, 292–293, 306g P elements, 121–122, 306g P1-derived artificial chromosome, 104, 306g PAC, 104, 306g packaging constraints, 84, 97, 98, 120, 123 papillomaviruses, 123–124, 306g partial digestion, 60, 102, 306g pBIN19, 116–117, 274–275 pBR322 DNA sequence, 173 nomenclature, 89 pedigree, 90 recombinant insulin, 247 selectable markers, 75 selection of recombinants, 77–79, 128 selection of transformants, 75 shuttle vector, 106 useful properties, 89–90 pBR327, 90–91 PCR, see Polymerase chain reaction pedigree analysis, 180, 257, 306g PEG, 42, 43, 119, 307g pEMBL8, 96–97 Penicillin, 225, 226t Penicillium, 225, 226t PEP, 271 peptide mass fingerprinting, 218–220 Petunia, 271 pGEM3Z, 93–94 phage, see bacteriophage phage display library, 206, 306g phage display, 220, 306g phagemids, 96–97, 306g pharming, 123, 250–251, 307g animals, 241–242 ethical concerns, 243 plants, 242, 253 Phaseolus vulgaris, 242 phenol extraction, 29, 32, 43, 56 phenotypic expression, 76 phenylketonuria, 255t dX174, 173 PHO5 promoter, 237 phosphinithricin acetyl transferase, 273t phosphoenol pyruvate, 271 Photinus pyralis, 198t physical mapping, 181–182, 307g Pichia pastoris, 112, 238 pilus, 16f, 23, 307g plants cloning vectors, 112–120 DNA preparation, 32–33 gene addition, 264, 265–274 gene subtraction, 264, 274–277 genetic engineering, 264–281 problems, 117, 277–280 recombinant protein, 242 that make their own insecticides, 265–270 transformation, 85, 115–116 plaque, 81–82, 307g plaque hybridization probing, 133–137 plasma supplement, 251t plasmids amplification, 39, 90, 92, 307g basic features, 13–14 classification, 16–17 cloning vectors, 89–94, 106–110, 113–117 compatibility, 16 conformation, 34 conjugation, 16 copy number, 15–16, 39 definition, 11, 307g DNA preparation, 33–39 non–bacterial, 17 size, 15, 35 types, 16–17 Plasmodium falciparum, 63, 255t pMB1, 90 polyacrylamide gel electrophoresis, 57, 166, 167, 194
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GENE CLONING AND DNA ANALYSIS
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This edition first published 2010,
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Contents CONTENTS Preface to the Si
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Contents ix 4.3 Ligation—joining
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Contents xi 8 How to Obtain a Clone
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Contents xiii 11.3 Identifying and
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Contents xv 15.1.2 Herbicide resist
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PART I The Basic Principles of Gene
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4 Part I The Basic Principles of Ge
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6 1.4 What is PCR? Figure 1.2 The b
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8 Figure 1.3 Cloning allows individ
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10 Figure 1.5 Gene isolation by PCR
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12 Further reading FURTHER READING
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14 Figure 2.1 Plasmids: independent
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16 Figure 2.4 Plasmid transfer by c
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18 Figure 2.6 Capsid components Pha
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20 Figure 2.7 λ phage particle att
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22 (a) The linear form of the λ DN
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24 Part I The Basic Principles of G
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26 Bacterial culture Table 3.1 Cent
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28 Bacterial culture Figure 3.3 Har
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30 Figure 3.6 Removal of protein co
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32 Figure 3.8 Collecting DNA by eth
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34 Figure 3.10 DNA purification by
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36 Figure 3.12 Two conformations of
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38 Figure 3.15 Partial unwinding of
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40 Figure 3.18 Preparation of a pha
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42 Figure 3.21 Collection of phage
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44 Further reading FURTHER READING
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48 Figure 4.3 The reactions catalyz
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50 Figure 4.6 (a) Alkaline phosphat
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52 Figure 4.8 (a) Restriction of ph
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54 Figure 4.9 (a) Production of blu
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56 Table 4.2 A 10 × buffer suitabl
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58 Figure 4.13 Visualizing DNA band
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60 Figure 4.15 Using a restriction
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62 Figure 4.17 The influence of DNA
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64 Figure 4.20 (a) Ligating blunt e
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66 Figure 4.23 Adaptors and the pot
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68 Figure 4.25 The use of adaptors:
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70 Figure 4.28 (a) The ends of the
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72 Chapter 5 Introduction of DNA in
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76 Figure 5.4 Normal E. coli cell (
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78 Figure 5.8 (b) Replica plating W
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80 Figure 5.10 (a) The role of the
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82 Figure 5.11 (a) A single-strain
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84 Figure 5.13 Strategies for the s
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86 Figure 5.14 Figure 5.15 (a) Prec
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88 Chapter 6 Cloning Vectors for E.
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90 during purification. pBR322 is 4
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92 (a) pUC8 (b) Restriction sites i
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94 Figure 6.5 The M13 genome, showi
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96 not totally disrupt the lacZ′
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98 Figure 6.10 The λ genetic map,
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100 (a) Cloning with a λ replaceme
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102 Figure 6.15 (a) A typical cosmi
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104 capsid structure. Cosmid-type v
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106 Figure 7.1 The yeast 2 µm plas
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108 Figure 7.4 Cloning with an E. c
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110 Figure 7.7 Chromosome structure
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112 for instance to examine the seg
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114 Figure 7.10 The Ti plasmid and
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116 (a) Wound infection by recombin
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118 Figure 7.15 Direct gene transfe
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120 Caulimovirus vectors Although o
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122 Figure 7.18 Cloning in Drosophi
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124 cause the death of the mouse ce
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126 Chapter 8 How to Obtain a Clone
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128 Figure 8.2 The basic strategies
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130 Figure 8.4 (a) Construction of
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132 Figure 8.5 Preparation of a gen
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134 Figure 8.7 One possible scheme
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136 Figure 8.10 The structure of α
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138 Figure 8.12 Two methods for the
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140 Figure 8.15 A simplified scheme
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142 Figure 8.17 Heterologous probin
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144 skills (Figure 8.19b). The same
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146 The problem of gene expression
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148 Figure 9.1 Hybridization of the
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150 Figure 9.3 Figure 9.4 5’ 3’
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152 Figure 9.7 A typical temperatur
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154 Figure 9.9 Calculating the T m
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156 Figure 9.13 5’ 3’ A G A C T
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158 Figure 9.16 Double-stranded PCR
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160 Figure 9.18 Hybridization of a
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PART II The Applications of Gene Cl
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166 termination sequencing has gain
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168 Figure 10.3 Reading the sequenc
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170 Figure 10.5 The basis to therma
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172 Figure 10.7 Pyrosequencing. Fig
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174 Figure 10.9 Part II The Applica
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176 Figure 10.11 Using oligonucleot
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178 Figure 10.13 Chromosome walking
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180 Figure 10.16 Part II The Applic
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182 Figure 10.20 Fluorescent in sit
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184 s Part II The Applications of G
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186 Figure 11.1 Some fundamentals o
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188 Figure 11.3 The 5′ end of an
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190 Figure 11.6 5' 3' RNA transcrip
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192 Figure 11.8 Possible positions
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194 Figure 11.11 A bound protein pr
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196 Figure 11.14 A modification int
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198 Table 11.1 Figure 11.16 A repor
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200 Pure mRNA Labelled translation
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202 Figure 11.22 (a) Restriction fr
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204 Part II The Applications of Gen
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208 as molecular biology in silico,
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210 Figure 12.4 Part II The Applica
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212 Figure 12.7 Using comparisons b
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214 Figure 12.10 The use of a yeast
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216 Figure 12.11 Serial analysis of
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218 Load the protein sample Figure
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220 Figure 12.16 Analyzing two prot
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Chapter 13 Production of Protein fr
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Chapter 14 Gene Cloning and DNA Ana
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Page 616: Chapter 16 Gene Cloning and DNA Ana
Page 632: Glossary 299 Bacteriophage or phage
Page 636: Glossary 301 CpG island A GC-rich D
Page 640: Glossary 303 Genetic map A genome m
Page 644: Glossary 305 Liposome A lipid vesic
Page 648: Glossary 307 Pharming Genetic modif
Page 652: Glossary 309 Restriction analysis D
Page 656: Glossary 311 Transgenic Referring t
Page 660: Index 313 linear and circular forms
Page 664: Index 315 bacteriophages, 19-23 clo
Page 670: 318 polyethylene glycol, see PEG po
Page 674: 320 T m , 153, 305g tobacco, 269 TO
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