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

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314 cloning vectors (continued) expression vectors, 146, 227–234, 302g insects, 121–122 mammals, 122–124 phagemids, 96–97 plants, 112–120 plant viruses, 119–120 plasmid, 89–94, 106–110, 113–117 retrovirus, 259 role in gene cloning, 5 Saccharomyces cerevisiae, 105–112 Ti plasmid, 113–117 T-tailed, 156 yeast artificial chromosome, 110–112, 311g Clostridium spp., 226t CMV, 240 codon bias, 209, 235, 238, 300g cohesive end, see sticky end cointegration strategy, 114 Col plasmids, 17 ColE1 basic features, 15t, 17 part of pBR322, 90 colicin, 17 colony hybridization probing, 133–137 combinatorial screening, 154, 155f, 300g comparative genomics, 211–212 compatibility, 16, 300g competent cells, 75, 300g complementary DNA, 19, 133, 300g conformation definition, 34, 300g topoisomerase function, 69 types, 36 use in plasmid DNA preparation, 36–39 conjugation, 16, 300g consensus sequence, 210, 229, 300g contig, 174, 300g continuous culture, 225, 300g contour clamped homogeneous electric fields, 63, 300g control sequence, 193–199 copper, 106, 237 copy number, 15–16, 109, 300g corn borer, 266 cos sites definition, 300g in vitro packaging, 81 role in cosmid, 102 role in e replication, 20–21 cosmids, 101–102, 300g cotton bollworm, 269 covalently closed–circular DNA, 36, 300g cowpeas, 273 CpG island, 210, 301g Cre, 278, 279 Crick, F., 4 criminal suspect identification, 283–285 crown gall, 113, 115 Cry proteins, 266t CTAB, 33 CUP1 promoter, 237 cyanogen bromide, 233, 247 cystic fibrosis, 112, 251t, 255t, 256, 259, 262 cytochrome c, 139–140 cytomegalovirus, 240 defined medium, 26, 301g degradative plasmids, 17 Delbrück, M., 4 deletion analysis, 198–199, 301g deletion cassette, 213 delta-12 desaturase, 273t, 277t c–endotoxins, 265–270, 273t denaturation of DNA, 7, 36, 301g density gradient centrifugation, 36–39, 42–43, 301g deoxyribonuclease, 301g deoxyribonuclease I, see DNase I deuterium, 219 dextran, 226t dhfr, 198t diabetes, 246, 251t dialysis, 39, 43 dideoxynucleotide, 167, 301g dihydrofolate reductase, 198t direct gene transfer, 301g chloroplast, 119, 268–269, 271 nucleus, 118 direct selection, 128–131 directed evolution, 272, 301g directed shotgun approach, 183, 301g disarmed plasmid, 116, 301g dithiothreitol, 56, 56t DNA adenine methylase, 273t DNA chip, 217, 301g DNA concentration increasing the concentration, 30–31 measuring, 31–32 DNA labeling, 136–137, 304g DNA ligase, see Ligase DNA manipulation, 45–71 DNA markers, 180–181, 301g Index DNA modifying enzymes, 46, 49–50 DNA polymerase I, 48, 71, 166 DNA preparation animal DNA, 32–33 bacterial DNA, 25–33 bacteriophage DNA, 39–43 ion exchange chromatography, 30, 31, 33, 304g organic extraction, 29–30, 33 plant DNA, 32–33 plasmid DNA, 33–39 total cell DNA, 25–33 DNA profiling, 154, 283–285, 301g DNA purification from a cell extract, 29–33 from bacteriophage e, 39–43 from bacteriophage M13, 43 DNA sequencing, 301g achievements of, 173 chain termination method, 165–171 DNA polymerases, 168–169 genome projects, 173 thermal cycle sequencing, 169 DNA size estimation, 58–59 DNase I, 46, 194 Dolly the sheep, 243 double digestion, 60, 301g Drosophila melanogaster, 3, 103t, 121–122, 173t, 192 Duchenne muscular dystrophy, 255t dwarfism, 247 EcoRI, 53t EDTA, 28–29, 35, 56 electrophoresis, 57, 301g electroporation, 85, 301g elution, 30, 301g embryonic stem cell, 124, 214, 301g emphysema, 251t emulsion, 173 end-filling, 136, 301g end-labelling, 194 endonuclease, lambda, 21 endonucleases, 46–47, 301g enolpyruvlshikimate-3-phosphate synthase, 271, 273t epidermal growth factor, 251t episome, 14, 106–107, 301g EPSPS, 271, 273t erythropoietin, 251t ES cell, 124, 214, 301g Escherichia coli bacteriophage DNA preparation, 39–43
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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 612: 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 666: 316 herpes simplex virus glycoprote
Page 670: 318 polyethylene glycol, see PEG po
Page 674: 320 T m , 153, 305g tobacco, 269 TO
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