Details

Electrophoresis in Practice


Electrophoresis in Practice

A Guide to Methods and Applications of DNA and Protein Separations
5. Aufl.

von: Reiner Westermeier

108,99 €

Verlag: Wiley-VCH
Format: PDF
Veröffentl.: 16.03.2016
ISBN/EAN: 9783527695164
Sprache: englisch
Anzahl Seiten: 458

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Beschreibungen

This fifth edition of the successful, long-selling classic has been completely revised and expanded, omitting some topics on obsolete DNA electrophoresis, but now with a completely new section on electrophoretic micro-methods and on-the-chip electrophoresis.<br />The text is geared towards advanced students and professionals and contains extended background sections, protocols and a trouble-shooting section. It is now also backed by a supplementary website providing all the figures for teaching purposes, as well as a selection of animated figures tested in many workshops to explain the underlying principles of the different electrophoretic methods.
Foreword XIX <p>Abbreviations, Symbols, Units XXI</p> <p>Preface XXV</p> <p><b>Part I Fundamentals 1</b></p> <p>Introduction 1</p> <p>Principle 1</p> <p>Areas of Applications 3</p> <p>The Sample 3</p> <p>The Buffer 4</p> <p>Electroendosmosis 5</p> <p>References 6</p> <p><b>1 Electrophoresis 7</b></p> <p>1.1 General 7</p> <p>1.1.1 Electrophoresis in Free Solution 7</p> <p>1.1.2 Electrophoresis in Supporting Media 12</p> <p>1.1.3 Gel Electrophoresis 13</p> <p>1.1.3.1 Gel Types 13</p> <p>1.1.3.2 Instrumentation for Gel Electrophoresis 17</p> <p>1.1.3.3 Current and Voltage Conditions 17</p> <p>1.1.4 Power Supply 19</p> <p>1.1.5 Separation Chambers 20</p> <p>1.1.5.1 Vertical Systems 20</p> <p>1.1.5.2 Horizontal Systems 21</p> <p>1.2 Electrophoresis in Nonrestrictive Gels 25</p> <p>1.2.1 Agarose Gel Electrophoresis 25</p> <p>1.2.1.1 Zone Electrophoresis 25</p> <p>1.2.1.2 Immunoelectrophoresis 26</p> <p>1.2.1.3 Affinity Electrophoresis 27</p> <p>1.2.2 Polyacrylamide Gel Electrophoresis of Low MolecularWeight Substances 28</p> <p>1.3 Electrophoresis in Restrictive Gels 28</p> <p>1.3.1 The Ferguson Plot 28</p> <p>1.3.2 Agarose Gel Electrophoresis 29</p> <p>1.3.2.1 Proteins 29</p> <p>1.3.2.2 Nucleic Acids 29</p> <p>1.3.3 Pulsed-Field Gel Electrophoresis 30</p> <p>1.3.4 Polyacrylamide Gel Electrophoresis of Nucleic Acids 32</p> <p>1.3.4.1 DNA Sequencing 32</p> <p>1.3.4.2 DNA Typing 34</p> <p>1.3.4.3 Mutation Detection Methods 35</p> <p>1.3.4.4 Denaturing PAGE of Microsatellites 37</p> <p>1.3.4.5 Two-dimensional DNA Electrophoresis 37</p> <p>1.3.5 Polyacrylamide Gel Electrophoresis of Proteins 37</p> <p>1.3.5.1 Disc Electrophoresis 37</p> <p>1.3.5.2 Gradient Gel Electrophoresis 39</p> <p>1.3.5.3 SDS Electrophoresis 40</p> <p>1.3.5.4 Cationic Detergent Electrophoresis 47</p> <p>1.3.5.5 Blue Native Electrophoresis 47</p> <p>1.3.5.6 Rehydrated Polyacrylamide Gels 48</p> <p>1.3.5.7 Two-Dimensional Electrophoresis Techniques 49</p> <p>1.3.5.8 GeLC-MS 50</p> <p>References 51</p> <p><b>2 Isotachophoresis 57</b></p> <p>2.1 Migration with the Same Speed 57</p> <p>2.2 "Ion Train" Separation 59</p> <p>2.3 Zone Sharpening Effect 59</p> <p>2.4 Concentration Regulation Effect 59</p> <p>2.5 Quantitative Analysis 60</p> <p>References 61</p> <p><b>3 Isoelectric Focusing 63</b></p> <p>3.1 Principles 63</p> <p>3.2 Gels for IEF 65</p> <p>3.2.1 Polyacrylamide Gels 65</p> <p>3.2.2 Agarose Gels 67</p> <p>3.3 Temperature 68</p> <p>3.4 Controlling the pH Gradient 68</p> <p>3.5 Kinds of pH Gradients 69</p> <p>3.5.1 Free Carrier Ampholytes 69</p> <p>3.5.1.1 Electrode Solutions 70</p> <p>3.5.1.2 Denaturing IEF: Urea IEF 71</p> <p>3.5.1.3 Separator IEF 72</p> <p>3.5.1.4 Plateau Phenomenon 73</p> <p>3.5.1.5 TheWorkflow of a Carrier Ampholyte IEF Run 73</p> <p>3.5.2 Immobilized pH Gradients (IPG) 73</p> <p>3.5.2.1 Preparation of Immobilized pH Gradients 75</p> <p>3.5.2.2 Applications of Immobilized pH Gradients 76</p> <p>3.6 Protein Detection in IEF Gels 77</p> <p>3.7 Preparative Isoelectric Focusing 77</p> <p>3.7.1 Carrier Ampholyte IEF in Gel 77</p> <p>3.7.2 Carrier Ampholyte IEF in Free Solution 78</p> <p>3.7.3 Immobilized pH Gradients 78</p> <p>3.7.3.1 Isoelectric Membranes 78</p> <p>3.7.3.2 Off-Gel IEF 79</p> <p>3.8 Titration Curve Analysis 80</p> <p>References 82</p> <p><b>4 High-Resolution Two-Dimensional Electrophoresis 85</b></p> <p>4.1 IEF in Immobilized pH Gradient Strips 85</p> <p>4.1.1 Strip Lengths 86</p> <p>4.1.2 pH Gradient Types 86</p> <p>4.1.3 The Influence of Salts and Buffer Ions on the Separation 87</p> <p>4.1.4 Basic IPG Gradients 88</p> <p>4.1.5 Advantages of Immobilized pH Gradient Strips in 2D Electrophoresis 89</p> <p>4.1.6 Rehydration of IPG Strips 90</p> <p>4.1.6.1 Basic pH Gradients 90</p> <p>4.1.6.2 Reswelling Tray 91</p> <p>4.1.6.3 Cover Fluid 91</p> <p>4.1.6.4 Rehydration Time 92</p> <p>4.1.7 Sample Application on IPG Strips 92</p> <p>4.1.8 IEF Conditions 95</p> <p>4.1.8.1 Electrode Pads 95</p> <p>4.1.8.2 Temperature 95</p> <p>4.1.8.3 Electric Conditions 95</p> <p>4.1.8.4 Time 96</p> <p>4.1.9 Instrumentation 96</p> <p>4.1.9.1 The Strip Tray Accessory 97</p> <p>4.1.9.2 Dedicated Instruments for IPG Strips 97</p> <p>4.1.9.3 Running IEF in IPG Strips 97</p> <p>4.2 SDS-PAGE 98</p> <p>4.2.1 Equilibration of the IPG Strips 98</p> <p>4.2.2 Technical Concepts for the Second Dimension (SDS-PAGE) 99</p> <p>4.2.2.1 Vertical Set-ups 99</p> <p>4.2.2.2 Horizontal Set-ups 99</p> <p>4.2.3 Gel Types 101</p> <p>4.2.3.1 Gel Sizes 101</p> <p>4.2.3.2 Vertical Gels 101</p> <p>4.2.3.3 Horizontal Gels 102</p> <p>4.2.4 Gel Casting 102</p> <p>4.2.4.1 Gels for Multiple Vertical Systems 102</p> <p>4.2.4.2 Gels for Horizontal Systems 104</p> <p>4.2.5 Running the SDS Gels 105</p> <p>4.2.5.1 Vertical Systems 105</p> <p>4.2.5.2 Horizontal Systems 106</p> <p>4.3 Proteomics 106</p> <p>References 108</p> <p><b>5 Protein Sample Preparation 111</b></p> <p>5.1 Protein Quantification Methods 111</p> <p>5.2 Preparation of Native Samples 112</p> <p>5.3 Samples for SDS Electrophoresis 113</p> <p>5.3.1 SDS Treatment 113</p> <p>5.3.1.1 Nonreducing SDS Treatment 114</p> <p>5.3.1.2 Reducing SDS Treatment 115</p> <p>5.3.1.3 Reducing SDS Treatment with Subsequent Alkylation 116</p> <p>5.3.2 Clean-up and Protein Enrichment 117</p> <p>5.3.2.1 Precipitation 117</p> <p>5.3.2.2 Protein Enrichment by Affinity Beads 118</p> <p>5.4 Samples for High-Resolution 2D PAGE 118</p> <p>5.4.1 CellWashing 119</p> <p>5.4.2 Cell Disruption 119</p> <p>5.4.3 Sample Acquisition and Storage 119</p> <p>5.4.4 Protease Inactivation 122</p> <p>5.4.5 Phosphatase Inactivation 122</p> <p>5.4.6 Alkaline Conditions 123</p> <p>5.4.7 Removal of Contaminants 123</p> <p>5.4.7.1 Precipitation Methods 123</p> <p>5.4.7.2 Affinity Beads 125</p> <p>5.4.8 Prefractionation 125</p> <p>5.4.8.1 Depletion of Highly Abundant Proteins 125</p> <p>5.4.8.2 Equalizer Technology 125</p> <p>5.4.8.3 Preseparation of Cell Organelles 126</p> <p>5.4.8.4 Prefractionation according to Isoelectric Points 126</p> <p>5.4.9 Special Case: Plant Proteins 127</p> <p>References 127</p> <p><b>6 Protein Detection 131</b></p> <p>6.1 Fixation 131</p> <p>6.1.1 IEF Gels 132</p> <p>6.1.2 Agarose Gels 132</p> <p>6.1.3 SDS Polyacrylamide Gels 132</p> <p>6.2 Poststaining Methods 133</p> <p>6.2.1 Organic Dyes 133</p> <p>6.2.1.1 Monodisperse Coomassie Brilliant Blue Staining 133</p> <p>6.2.1.2 Colloidal Coomassie Brilliant Blue Staining 133</p> <p>6.2.1.3 Acid Violet 17 Staining for IEF Gels 134</p> <p>6.2.2 Silver Staining 134</p> <p>6.2.2.1 Colloidal Silver Staining 134</p> <p>6.2.2.2 Silver Nitrate Staining 134</p> <p>6.2.2.3 Ammoniacal Silver Staining 135</p> <p>6.2.3 Negative Staining 136</p> <p>6.2.3.1 Copper Staining 136</p> <p>6.2.3.2 Imidazole Zinc Staining 136</p> <p>6.2.4 Fluorescent Staining 136</p> <p>6.2.5 Specific Detection 138</p> <p>6.2.5.1 Proteins with Posttranslational Modifications 138</p> <p>6.2.5.2 Isoenzymes 139</p> <p>6.2.6 Stain-Free Technology 140</p> <p>6.3 Prelabeling 140</p> <p>6.3.1 Prelabeling with Fluorescent Tags 140</p> <p>6.3.2 Radioactive Labeling of Living Cells 141</p> <p>6.3.3 Labeling with Stable Isotopes 141</p> <p>6.4 Difference Gel Electrophoresis (DIGE) 143</p> <p>6.4.1 Minimum Lysine Labeling 143</p> <p>6.4.2 SaturationCysteine Labeling 144</p> <p>6.4.3 The Internal Standard 146</p> <p>6.4.4 Experimental Design 147</p> <p>6.4.5 Major Benefits of 2D DIGE 147</p> <p>6.4.6 Specific Labeling of Cell-Surface Proteins 148</p> <p>6.4.7 Comparative Fluorescence Gel Electrophoresis 148</p> <p>6.5 Imaging, Image Analysis, Spot Picking 149</p> <p>6.5.1 Quantitative Evaluation 149</p> <p>6.5.1.1 Quantification Prerequisites 149</p> <p>6.5.1.2 Critical Issues in Quantification 150</p> <p>6.5.2 Imaging Systems 151</p> <p>6.5.2.1 Optical Density 152</p> <p>6.5.2.2 Densitometry 152</p> <p>6.5.2.3 CCD Cameras 153</p> <p>6.5.3 Image Analysis 154</p> <p>6.5.3.1 One-Dimensional Gel Software 155</p> <p>6.5.3.2 Two-Dimensional Gel Software 156</p> <p>6.5.4 Protein Identification and Characterization 158</p> <p>6.5.4.1 Spot-Picking 159</p> <p>References 160</p> <p><b>7 Blotting 165</b></p> <p>7.1 Transfer Methods 165</p> <p>7.1.1 Diffusion Blotting 165</p> <p>7.1.2 Capillary Blotting 165</p> <p>7.1.3 Pressure Blotting 166</p> <p>7.1.4 Vacuum Blotting 167</p> <p>7.1.5 Electrophoretic Blotting 168</p> <p>7.1.5.1 Tank Blotting 168</p> <p>7.1.5.2 Semidry Blotting 169</p> <p>7.1.5.3 Electrophoretic Blotting of Film-Backed Gels 171</p> <p>7.2 Blotting Membranes 171</p> <p>7.3 Buffers for Electrophoretic Transfers 172</p> <p>7.3.1 Proteins 172</p> <p>7.3.1.1 Tank Blotting 172</p> <p>7.3.1.2 Semidry Blotting 173</p> <p>7.3.2 Nucleic Acids 174</p> <p>7.3.2.1 Tank Blotting 174</p> <p>7.3.2.2 Semidry Blotting 174</p> <p>7.4 General Staining 174</p> <p>7.5 Blocking 175</p> <p>7.6 Specific Detection 175</p> <p>7.6.1 Hybridization 175</p> <p>7.6.2 Enzyme Blotting 176</p> <p>7.6.3 Immunoblotting 176</p> <p>7.6.4 Lectin Blotting 179</p> <p>7.6.5 Stripping, Reprobing 179</p> <p>7.6.6 Double Blotting 180</p> <p>7.7 Protein Sequencing 180</p> <p>7.8 Transfer Issues 180</p> <p>7.9 Electro-Elution of Proteins from Gels 181</p> <p>References 183</p> <p><b>Part II Equipment and Methods 187</b></p> <p>Equipment 187</p> <p>Methods 187</p> <p>Small Molecules 187</p> <p>Proteins 187</p> <p>DNA 188</p> <p>Instrumentation 188</p> <p>Accessories 189</p> <p>Consumables 190</p> <p><b>8 Special Laboratory Equipment 191</b></p> <p><b>9 Consumables 193</b></p> <p><b>10 Chemicals 195</b></p> <p>10.1 Reagents 195</p> <p>Method 1 PAGE of Dyes 197</p> <p>M1.1 Sample Preparation 197</p> <p>M1.2 Stock Solutions 197</p> <p>M1.3 Preparing the Casting Cassette 198</p> <p>M1.3.1 Gasket 198</p> <p>M1.3.2 Slot-Former 198</p> <p>M1.3.3 Assembling the Gel Cassette 199</p> <p>M1.4 Casting Ultra-Thin-Layer Gels 200</p> <p>M1.5 Electrophoretic Separation 201</p> <p>M1.5.1 Removing the Gel from the Cassette 201</p> <p>Method 2 Agarose and Immunoelectrophoresis 205</p> <p>M2.1 Sample Preparation 205</p> <p>M2.2 Stock Solutions 206</p> <p>M2.3 Preparing the Gels 206</p> <p>M2.3.1 Agarose Gel Electrophoresis 206</p> <p>M2.3.1.1 Preparing the Slot-Former 207</p> <p>M2.3.1.2 Assembling the Gel Cassette 207</p> <p>M2.3.2 Immunoelectrophoresis Gels 209</p> <p>M2.3.2.1 Punching Out the SampleWells and Troughs 210</p> <p>M2.4 Electrophoresis 211</p> <p>M2.4.1 Grabar–Williams Technique 212</p> <p>M2.4.2 Laurell Technique 212</p> <p>M2.5 Protein Detection 214</p> <p>M2.5.1 Coomassie Staining (Agarose Electrophoresis) 214</p> <p>M2.5.2 Immunofixing of Agarose Electrophoresis 214</p> <p>M2.5.3 Coomassie Staining (Immunoelectrophoresis) 215</p> <p>M2.5.4 Silver Staining 215</p> <p>References 216</p> <p>Method 3 Titration Curve Analysis 217</p> <p>M3.1 Sample Preparation 217</p> <p>M3.2 Stock Solutions 217</p> <p>M3.3 Preparing the Blank Gels 218</p> <p>M3.3.1 Preparing the Casting Cassette 218</p> <p>M3.3.2 Assembling the Gel Cassette 219</p> <p>M3.3.3 Filling the Gel Cassette 220</p> <p>M3.3.4 Removing the Gel from the Cassette 221</p> <p>M3.3.5 Washing the Gel 221</p> <p>M3.4 Titration Curve Analysis 222</p> <p>M3.4.1 Reswelling the Rehydratable Gel 222</p> <p>M3.4.2 Formation of the pH Gradient 222</p> <p>M3.4.3 Native Electrophoresis in the pH Spectrum 223</p> <p>M3.5 Coomassie and Silver Staining 224</p> <p>M3.5.1 Colloidal Coomassie Staining 224</p> <p>M3.5.2 Acid Violet 17 Staining 224</p> <p>M3.5.3 Five-Minute Silver Staining of Dried Gels 225</p> <p>M3.6 Interpreting the Curves 225</p> <p>References 227</p> <p>Method 4 Native PAGE in Amphoteric-Buffers 229</p> <p>M4.1 Sample Preparation 230</p> <p>M4.2 Stock Solutions 230</p> <p>M4.3 Preparing the Empty Gels 231</p> <p>M4.3.1 Slot-Former 231</p> <p>M4.3.2 Assembling the Casting Cassette 232</p> <p>M4.3.3 Polymerization Solutions 233</p> <p>M4.3.4 Filling the Cooled Gel Cassette 234</p> <p>M4.3.5 Removing the Gel from the Casting Cassette 234</p> <p>M4.3.6 Washing the Gel 234</p> <p>M4.4 Electrophoresis 235</p> <p>M4.4.1 Rehydration in Amphoteric Buffers 235</p> <p>M4.5 Coomassie and Silver Staining 240</p> <p>M4.5.1 Colloidal Coomassie Staining 240</p> <p>M4.5.2 Acid Violet 17 Staining 240</p> <p>M4.5.3 Five-Minute Silver Staining of Dried Gels 241</p> <p>References 242</p> <p>Method 5 Agarose IEF 243</p> <p>M5.1 Sample Preparation 243</p> <p>M5.2 Preparing the Agarose Gel 244</p> <p>M5.2.1 Making the Spacer Plate Hydrophobic 244</p> <p>M5.2.2 Assembling the Casting Cassette 244</p> <p>M5.2.3 Preparation of Electrode Solutions 246</p> <p>M5.3 Isoelectric Focusing 247</p> <p>M5.4 Protein Detection 249</p> <p>M5.4.1 Coomassie Blue Staining 249</p> <p>M5.4.2 Immunofixation 249</p> <p>M5.4.3 Silver Staining 250</p> <p>References 251</p> <p>Method 6 PAGIEF in Rehydrated Gels 253</p> <p>M6.1 Sample Preparation 253</p> <p>M6.2 Stock Solutions 254</p> <p>M6.3 Preparing the Blank Gels 254</p> <p>M6.3.1 Making the Spacer Plate Hydrophobic 254</p> <p>M6.3.2 Assembling the Casting Cassette 255</p> <p>M6.3.3 Filling the Gel Cassette 256</p> <p>M6.3.4 Removing the Gel from the Casting Cassette 257</p> <p>M6.3.5 Washing the Gel 257</p> <p>M6.4 Isoelectric Focusing 257</p> <p>M6.4.1 Rehydration Solution with Carrier Ampholytes (SERVALYT™, Pharmalyte™) 257</p> <p>M6.4.2 Reswelling the Gel 257</p> <p>M6.4.3 Separation of Proteins 259</p> <p>M6.4.4 Sample Application 259</p> <p>M6.5 Coomassie and Silver Staining 260</p> <p>M6.5.1 Colloidal Coomassie Staining 260</p> <p>M6.5.2 Acid Violet 17 Staining 261</p> <p>M6.5.3 Five-Minute Silver Staining of Dried Gels 261</p> <p>M6.5.4 The Most Sensitive Silver Staining Procedure for IEF 262</p> <p>M6.6 Perspectives 264</p> <p>References 266</p> <p>Method 7 Horizontal SDS-PAGE 267</p> <p>M7.1 Sample Preparation 267</p> <p>M7.1.1 Nonreducing SDS Treatment 267</p> <p>M7.1.2 Reducing SDS Treatment 268</p> <p>M7.1.3 Reducing SDS Treatment with Alkylation 268</p> <p>M7.2 Prelabeling with Fluorescent Dye 269</p> <p>M7.2.1 Labeling 269</p> <p>M7.2.2 Detection 269</p> <p>M7.3 Stock Solutions for Gel Preparation 270</p> <p>M7.4 Preparing the Casting Cassette 271</p> <p>M7.4.1 Preparing the Slot-Former 271</p> <p>M7.4.2 Assembling the Casting Cassette 272</p> <p>M7.5 Gradient Gel 273</p> <p>M7.5.1 Pouring the Gradient 273</p> <p>M7.6 Electrophoresis 277</p> <p>M7.6.1 Preparing the Separation Chamber 277</p> <p>M7.6.2 Placing the Gel on the Cooling Plate 277</p> <p>M7.6.3 Electrophoresis 278</p> <p>M7.7 Protein Detection 279</p> <p>M7.7.1 Hot Coomassie Staining 279</p> <p>M7.7.2 Colloidal Staining 280</p> <p>M7.7.2.1 Stock Solutions 280</p> <p>M7.7.2.2 Fixation Solution 280</p> <p>M7.7.2.3 Staining Solution 280</p> <p>M7.7.2.4 Staining Procedure 281</p> <p>M7.7.3 Reversible Imidazole–Zinc Negative Staining 281</p> <p>M7.7.4 Silver Staining 281</p> <p>M7.7.4.1 Blue Toning 282</p> <p>M7.7.5 Fluorescent Staining with SERVA Purple 283</p> <p>M7.7.5.1 Stock Solutions 283</p> <p>M7.7.5.2 Staining Protocol 283</p> <p>M7.7.5.3 Detection 284</p> <p>M7.8 Blotting 284</p> <p>M7.9 Perspectives 285</p> <p>M7.9.1 Gel Characteristics 285</p> <p>M7.9.2 SDS Electrophoresis inWashed and Rehydrated Gels 285</p> <p>M7.9.3 SDS Disc Electrophoresis in a Rehydrated and Selectively Equilibrated Gel 285</p> <p>M7.9.4 Peptide Separation 286</p> <p>References 287</p> <p>Method 8 Vertical PAGE 289</p> <p>M8.1 Sample Preparation and Prelabeling 290</p> <p>M8.2 Stock Solutions for SDS- PAGE 290</p> <p>M8.3 Single Gel Casting 291</p> <p>M8.3.1 Discontinuous SDS-Polyacrylamide Gels 292</p> <p>M8.3.2 Porosity Gradient Gels 293</p> <p>M8.4 Multiple Gel Casting 295</p> <p>M8.4.1 Multiple Discontinuous SDS Polyacrylamide Gels 296</p> <p>M8.4.2 Multiple SDS Polyacrylamide Gradient Gels 298</p> <p>M8.5 Electrophoresis 299</p> <p>M8.5.1 Running Conditions 300</p> <p>M8.6 SDS Electrophoresis of Small Peptides 301</p> <p>M8.7 Blue Native PAGE 303</p> <p>M8.8 Two-Dimensional Electrophoresis 306</p> <p>M8.9 DNA Electrophoresis 307</p> <p>M8.10 Long-Shelf-Life Gels 308</p> <p>M8.11 Protein Detection 308</p> <p>M8.12 Preparing Glass Plates with Bind-Silane 308</p> <p>M8.12.1 Coating a Glass Plate with Bind-Silane 309</p> <p>M8.12.2 Removal of Gel and Bind-Silane from a Glass Plate 309</p> <p>References 310</p> <p>Method 9 Semidry Blotting of Proteins 311</p> <p>M9.1 Transfer Buffers 313</p> <p>M9.2 Technical Procedure 314</p> <p>M9.2.1 GelsWithout Support Film 315</p> <p>M9.2.2 Gels on Film Backing 315</p> <p>M9.2.2.1 Using a Nitrocellulose (NC) Blotting Membrane 316</p> <p>M9.2.2.2 Using a PVDF Blotting Membrane 316</p> <p>M9.2.2.3 Transfer from Cut-Off Gels 317</p> <p>M9.3 Staining of Blotting Membranes 318</p> <p>References 320</p> <p>Method 10 IEF in Immobilized pH Gradients 321</p> <p>M10.1 Sample Preparation 322</p> <p>M10.2 Stock Solutions 322</p> <p>M10.3 Immobiline Recipes 323</p> <p>M10.3.1 Custom-Made pH Gradients 323</p> <p>M10.4 Preparing the Casting Cassette 327</p> <p>M10.4.1 Making the Spacer Plate Hydrophobic 327</p> <p>M10.4.2 Assembling the Casting Cassette 327</p> <p>M10.5 Preparing the pH Gradient Gels 328</p> <p>M10.5.1 Pouring the Gradient 328</p> <p>M10.5.1.1 Setting Up the Casting Apparatus 328</p> <p>M10.5.1.2 Filling the Cassette 329</p> <p>M10.5.1.3 Washing the Gel 331</p> <p>M10.5.1.4 Storage 332</p> <p>M10.5.1.5 Rehydration 332</p> <p>M10.6 Isoelectric Focusing 332</p> <p>M10.6.1 Placing the Gel on the Cooling Plate 332</p> <p>M10.6.2 Sample Application 335</p> <p>M10.6.3 Electrode Solutions 335</p> <p>M10.6.4 Focusing Conditions 335</p> <p>M10.6.5 Measuring the pH Gradient 336</p> <p>M10.7 Staining 336</p> <p>M10.7.1 Colloidal Coomassie Staining 336</p> <p>M10.7.2 Acid Violet 17 Staining 337</p> <p>M10.7.3 Staining Procedure 337</p> <p>M10.7.4 Silver Staining 337</p> <p>M10.7.5 Practical Tip 337</p> <p>M10.8 Strategies for IPG Focusing 337</p> <p>References 339</p> <p>Method 11 High-Resolution 2D Electrophoresis 341</p> <p>M11.1 Sample Preparation 342</p> <p>M11.1.1 Sample Clean-Up 343</p> <p>M11.2 Prelabeling of Proteins with Fluorescent Dyes 346</p> <p>M11.2.1 Labeling of One Sample 346</p> <p>M11.2.2 DIGE Labeling 347</p> <p>M11.2.2.1 Experimental Design 347</p> <p>M11.2.2.2 Sample Preparation 347</p> <p>M11.2.2.3 Reconstitution of the CyDyes 348</p> <p>M11.2.2.4 Minimal Labeling of the Lysines 349</p> <p>M11.2.2.5 Saturation Labeling of the Cysteines 350</p> <p>M11.2.2.6 Preparation for Loading the Samples onto the IPG Strips 351</p> <p>M11.2.2.7 Detection of DIGE Spots 352</p> <p>M11.3 Stock Solutions for Gel Preparation 352</p> <p>M11.4 Preparing the Gels 354</p> <p>M11.4.1 IPG Strips 354</p> <p>M11.4.2 SDS Polyacrylamide Gels 358</p> <p>M11.5 Separation Conditions 359</p> <p>M11.5.1 First Dimension (IPG-IEF) 359</p> <p>M11.5.1.1 IPG-IEF with Conventional Equipment 360</p> <p>M11.5.1.2 IPG-IEF with IPG Strip Kit (Figure ) 360</p> <p>M11.5.1.3 IPG-IEF in Individual Ceramic Trays 362</p> <p>M11.5.1.4 Equipment and Trays for Cup Loading 363</p> <p>M11.5.2 Equilibration 366</p> <p>M11.5.3 Second Dimension (SDS Electrophoresis) 366</p> <p>M11.5.3.1 Vertical Gels 366</p> <p>M11.5.3.2 Horizontal Gels 367</p> <p>M11.6 Staining Procedures 370</p> <p>M11.6.1 Staining of Multiple Gels 371</p> <p>M11.6.2 Colloidal Coomassie Staining 371</p> <p>M11.6.2.1 Stock Solutions 371</p> <p>M11.6.2.2 Fixation Solution 372</p> <p>M11.6.2.3 Staining Solution 372</p> <p>M11.6.2.4 Staining Procedure: 372</p> <p>M11.6.3 Reversible Imidazole–Zinc Negative Staining 372</p> <p>M11.6.4 Silver Staining 373</p> <p>M11.6.4.1 Mass Spectrometry Analysis of Silver-Stained Spots 374</p> <p>M11.6.4.2 Blue Toning 374</p> <p>M11.6.5 Fluorescent Staining with SERVA Purple 374</p> <p>M11.6.5.1 Stock Solutions 374</p> <p>M11.6.5.2 Staining Protocol 375</p> <p>M11.6.5.3 Detection 376</p> <p>References 377</p> <p>Method 12 PAGE of DNA Fragments 379</p> <p>M12.1 Stock Solutions 380</p> <p>M12.2 Preparing the Gels 381</p> <p>M12.3 Sample Preparation 385</p> <p>M12.4 Electrophoresis 386</p> <p>M12.5 Silver Staining 391</p> <p>Appendix Troubleshooting 393</p> <p>A1.1 Frequent Mistakes 393</p> <p>A1.1.1 Miscalculation of the Cross-Linking Factor of a Polyacrylamide Gel 393</p> <p>A1.1.2 Polymerization Temperature and Time for a Polyacrylamide Gel 393</p> <p>A1.1.3 Creating Aggregates in SDS Samples 394</p> <p>A1.1.4 Titration of the Running Buffer in SDS Electrophoresis 394</p> <p>A1.1.5 Incomplete Removal of PBS from Cells 395</p> <p>A1.1.6 Over-focusing of IPG Strips in 2D PAGE 395</p> <p>A1.1.6.1 Protein Degradation in Basic pH Gradients 395</p> <p>A1.1.6.2 The "Thiourea Effect" 395</p> <p>A1.2 Isoelectric Focusing 396</p> <p>A1.2.1 PAGIEF with Carrier Ampholytes 396</p> <p>A1.2.2 Agarose IEF with Carrier Ampholytes 402</p> <p>A1.2.3 Immobilized pH Gradients 405</p> <p>A1.3 SDS Electrophoresis 410</p> <p>A1.3.1 Horizontal SDS-PAGE 410</p> <p>A1.3.2 Vertical PAGE 418</p> <p>A1.4 Two-Dimensional Electrophoresis 419</p> <p>A1.5 Semi-Dry Blotting 426</p> <p>A1.6 DNA Electrophoresis 431</p> <p>Index 435</p>
Reiner Westermeier worked after PhD graduation and Post-doc at the Technische Universitat Munchen for 30 years as a specialist for electrophoresis methods for leading bioanalytics and biotechnology companies. His area of responsibility included co-operation in product development, writing of scientic papers and method instructions, trouble shooting in customer laboratories, performing seminars and practical courses on electrophoresis and proteomics, as well as giving scientific talks at congresses on a world-wide basis. He is editor and author of several books, e.g. 'Electrophoresis in Practice' (in German and in English), 'Proteomics in Practice', and 'Difference Gel Electrophoresis'.

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