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

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312 INDEX Index (g = glossary, f = figure, t = table) 1-aminocyclopropane-1-carboxylic acid, 276 2′–5′ oligoadenylate synthetase, 273t 2 fm plasmid basic features 17, 105–106, 298g cloning vectors, 106–107, 253 selectable markers, 106 3-b-indoleacrylic acid, 231 3′-terminus, 49t, 66, 66f, 298g 5-bromo-4-chloro-3-indolyl-b-Dgalactopyranoside, see X-gal 5′-terminus, 49t, 66, 66f, 298g 32P, 136 35S, 200 A 260 , 32 A 260 /A 280 , 32 AAV, 124, 298g abundancy probing, 137–138 ACC, 276 ACC synthase, 276 acetic acid bacteria, 226t acetolactate synthase, 273t acetone, 226t acyl carrier protein thioesterase, 273t adaptors, 65–66, 171, 298g adeno-associated virus, 124, 298g adenovirus, 24, 123, 298g affinity chromatography, 233, 298g Ag promoter, 250 agarose gel electrophoresis, 57–58, 154, 193–194 agriculture, 264–281, 294–296 Agrobacterium CP4, 271 Agrobacterium rhizogenes, 117 Agrobacterium tumefaciens, 15t, 17, 113–117, 275, 298g agromegaly, 247 AIDS, 250, 251t, 260 alcohol, 226t alcohol oxidase, 238 alfalfa, 273t alkaline denaturation method, 36 alkaline phosphatase, 50 a–peptide, 79 Alteromonas espejiana, 46 AluI, 52, 53t Alzheimer’s, 256 amelogenin, 290 aminocyclopropane carboxylic acid deaminase, 273t, 277t ampicillin resistance, 75–76, 77–80, 90, 92, 101 amylases, 226t anaemia, 251t, 251t ancient DNA, 289, 293, 298g animal cells culture systems, 239–240 DNA preparation, 32–33 recombinant protein, 239–240, 250–251 transformation, 85 viruses as cloning vectors, 123–124 annealing, 7, 298g antibiotics coded by R plasmids, 17, 90 use as reporter genes, 198t use in selection of recombinants, 77–80, 90, 115–116, 128 use in selection of transformants, 75–76, 77–80, 90, 92, 101, 115–116 antibodies, 144–146, 242, 252–253, 254, 256 antisense RNA, 260–261, 274–276, 298g antisense technology, 260–261, 274–276, 298g antitrypsin, 251t AOX promoter, 238 aphIV, 198t Arabidopsis thaliana, 173, 173t, 177 archaeogenetics, 291–296, 298g Arthrobacter luteus, 52, 53t artificial gene synthesis, 204, 298g Aspergillus nidulans, 112, 238–239 Aspergillus oryzae, 46 Aspergillus spp., 226t autoradiography, 137, 298g auxotroph, 106, 129, 298g Avery, O., 3 avidin, 137, 298g BAC, 103, 298g Bacillus amyloliquefaciens, 53t, 273t Bacillus globigii, 53t Bacillus licheniformis, 272 Bacillus spp, 74, 104, 226t Bacillus thuringiensis, 265–266, 273t BacMam vector, 240 bacteria batch and continuous culture, 225 cloning vectors, 88–104 DNA preparation, 25–33 bacterial artificial chromosome, 103, 298g bacteriophage e, 304g arms, 100–101 cI gene, 40, 83, 99, 231–232 cloning experiment with, 100–101 cloning vectors, 97–102 collection of phage from a culture, 42 cosmids, 101–102 culture growth, 40–42 DNA preparation, 39–43 DNA sequencing, 173 DNA yield, 40 frequency of restriction sites, 54, 59–60, 97, 98 gene organization, 19, 98 in vitro packaging, 81, 98, 101 induction, 40, 98 infection cycle, 19–21 eP L promoter, 231–232
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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 608: 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 662: 314 cloning vectors (continued) exp
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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