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Contents 1. A Short History of the Polymerase Chain Reaction 3 John M. S. Bartlett and David Stirling 2. PCR Patent Issues 7 Peter Carroll and David Casimir 3. Equipping and Establishing a PCR Laboratory 15 Susan McDonagh 4. Quality Control in PCR 20 David Stirling 5. Extraction of Nucleic Acid Templates 27 John M. S. Bartlett 6. Extraction of DNA from Whole Blood 29 John M. S. Bartlett and Anne White 7. DNA Extraction from Tissue 33 Helen Pearson and David Stirling 8. Extraction of DNA from Microdissected Archival Tissues 35 James J. Going 9. RNA Extraction from Blood 43 Helen Pearson 10. RNA Extraction from Frozen Tissue 45 John M. S. Bartlett 11. RNA Extraction from Tissue Sections 47 Helen Pearson 12. Dual DNA/RNA Extraction 49 David Stirling and John M. S. Bartlett 13. DNA Extraction from Fungi, Yeast, and Bacteria 53 David Stirling 14. Isolation of RNA Viruses from Biological Materials 55 Susan McDonagh 15. Extraction of Ancient DNA 57 Wera M. Schmerer 16. DNA Extraction from Plasma and Serum 63 David Stirling 17. Technical Notes for the Detection of Nucleic Acids 65 John M. S. Bartlett 18. Technical Notes for the Recovery and Purificationof PCR Products from Acrylamide Gels 77 David Stirling 19. PCR Primer Design 81 David L. Hyndman and Masato Mitsuhashi 20. Optimization of Polymerase Chain Reactions 89 Haiying Grunenwald 21. Subcycling PCR for Long-Distance Amplificationsof Regions with High and Low Guanine–Cystine Content---- Amplification of the Intron 22 Inversion of the FVIII Gene David Stirling 101 22. Rapid Amplification of cDNA Ends i
Xin Wang and W. Scott Young III 105 23. Randomly Amplified Polymorphic DNA Fingerprinting--The Basics 117 Ranil S. Dassanayake and Lakshman P. Samaranayake 24. Microsphere-Based Single NucleotidePolymorphism Genotyping 123 Marie A. Iannone, J. David Taylor, Jingwen Chen, May-Sung Li,Fei Ye, and Michael P. Weiner 25. Ligase Chain Reaction 135 William H. Benjamin, Jr., Kim R. Smith, and Ken B. Waites 26. Nested RT-PCR in a Single Closed Tube 151 Antonio Olmos, Olga Esteban, Edson Bertolini, and Mariano Cambra 27. Direct PCR from Serum 161 kenji Abe 28. Long PCR Amplification of Large Fragmentsof Viral Genomes 167 ---A Technical Overview Raymond Tellier, Jens Bukh, Suzanne U. Emerson, and Robert H. Purcell 29. Long PCR Methodology 173 Raymond Tellier, Jens Bukh, Suzanne U. Emerson, and Robert H. Purcell 30. Qualitative and Quantitative PCR-----A Technical Overview 181 David Stirling 31. Ultrasensitive PCR Detection of Tumor Cells in Myeloma 185 Friedrich W. Cremer and Marion Moos 32. Ultrasensitive Quantitative PCR to Detect RNA Viruses 197 Susan McDonagh 33. Quantitative PCR for cAMP RI Alpha mRNA 205 ---- Use of Site-Directed Mutation and PCR Mimics John M. S. Bartlett 34. Quantitation of Multiple RNA Species 211 Ron Kerr 35. Differential Display----- A Technical Overview 217 John M. S. Bartlett 36. AU-Differential Display, Reproducibilityof a Differential mRNA Display Targeted to AU Motifs 225 Orlando Dominguez, Lidia Sabater, Yaqoub Ashhab,Eva Belloso, and Ricardo Pujol-Borrell 37. PCR Fluorescence Differential Display 237 Kostya Khalturin, Sergej Kuznetsov, and Thomas C. G. Bosch 38. Microarray Analysis Using RNA Arbitrarily Primed PCR 245 Steven Ringquist, Gaelle Rondeau, Rosa-Ana Risques,Takuya Higashiyama, Yi- Peng Wang, Steffen Porwollik,David Boyle, Michael McClelland, and John Welsh 39. Oligonucleotide Arrays for Genotyping 255 --- Enzymatic Methods for Typing Single Nucleotide Polymorphisms and Short Tandem Repeats Stephen Case-Green, Clare Pritchard, and Edwin Southern 40. Serial Analysis of Gene Expression 271 Karin A. Oien 41. Mutation and Polymorphism Detection----- A Technical Overview 287 Joanne Edwards and John M. S. Bartlett 42. Combining Multiplex and Touchdown PCRfor Microsatellite Analysis 295 Kanokporn Rithidech and John J. Dunn ii
Page 1: TM Methods in Molecular Biology Vol
Page 5 and 6: 63. Primed In Situ Nucleic Acid Lab
Page 7 and 8: 4 Bartlett and Stirling The thing t
Page 9 and 10: 6 Bartlett and Stirling Fig. 2. Res
Page 11 and 12: 8 Carroll and Casimir of PCR. Such
Page 13 and 14: 10 Carroll and Casimir cost more th
Page 15 and 16: 12 Carroll and Casimir are no longe
Page 17 and 18: 14 Carroll and Casimir Should these
Page 19 and 20: 16 McDonagh Fig. 1. Unidirectional
Page 21 and 22: 18 McDonagh stored. This means that
Page 23 and 24: 20 McDonagh
Page 25 and 26: 22 Stirling which will either not a
Page 27 and 28: 24 Stirling
Page 29 and 30: 28 Bartlett References 1. US Depart
Page 31 and 32: 30 Bartlett and White 11. 5 M sodiu
Page 33 and 34: 32 Bartlett and White
Page 35 and 36: 34 Pearson and Stirling 11. Microfu
Page 37 and 38: 36 Going 3. Methods 3.1. Section Cu
Page 39 and 40: 38 Going pipet filler. Spread the p
Page 41 and 42: 40 Going digitally to record the di
Page 43 and 44: 42 Going
Page 45 and 46: 44 Pearson 7. Add 60 µL of chlorof
Page 47 and 48: 46 Bartlett 3. Methods 3.1. RNA Ext
Page 49 and 50: 48 Pearson 3. Method The method of
Page 51 and 52: 50 Stirling and Bartlett 4. Protein
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52 Stirling and Bartlett
Page 55 and 56:
54 Stirling 3. Methods 3.1. Fungal
Page 57 and 58:
56 McDonagh 2. Add 0.4 mL of TNE bu
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58 Schmerer 2. Materials To apply t
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60 Schmerer 3. The additional purif
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62 Schmerer
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64 Stirling
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66 Bartlett Table 1 Recommended Aga
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68 Bartlett Table 2 Separation of D
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70 Bartlett 2. 5× TBE: 54 g of Tri
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72 Bartlett 7. Remove upper aqueous
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74 Bartlett 4. Many modern electrop
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76 Bartlett
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78 Stirling 11. Store at -20°C for
Page 81 and 82:
82 Hyndman and Mitsuhashi 3.1. Effi
Page 83 and 84:
84 Hyndman and Mitsuhashi Fig. 1. H
Page 85 and 86:
86 Hyndman and Mitsuhashi Fig. 3. H
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88 Hyndman and Mitsuhashi can be ge
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90 Grunenwald may be affected by ea
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92 Grunenwald 50°C will generally
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94 Grunenwald of template DNA, a su
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96 Grunenwald than absolutely neces
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98 Grunenwald 2. Foord, O. S. and R
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100 Grunenwald
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102 Stirling Table 1 Thermal Cycler
Page 103 and 104:
104 Stirling
Page 105 and 106:
106 Wang and Young full-length cDNA
Page 107 and 108:
108 Wang and Young Fig. 1. (A) Nort
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110 Wang and Young Fig. 3. Expresse
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112 Wang and Young 2. First-strand
Page 113 and 114:
114 Wang and Young 3′-RACE outlin
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116 Wang and Young
Page 117 and 118:
118 Dassanayake and Samaranayake co
Page 119 and 120:
120 Dassanayake and Samaranayake 5.
Page 121 and 122:
122 Dassanayake and Samaranayake Re
Page 123 and 124:
124 Iannone et al. Fig. 1. Diagram
Page 125 and 126:
Table 1 Oligonucleotides Descriptio
Page 127 and 128:
128 Iannone et al. 5. For microsphe
Page 129 and 130:
130 Iannone et al. 4. To adjust for
Page 131 and 132:
132 Iannone et al. 6. Target concen
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134 Iannone et al.
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136 Benjamin, Smith, and Waites amp
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138 Benjamin, Smith, and Waites the
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140 Benjamin, Smith, and Waites 2.2
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142 Benjamin, Smith, and Waites 2.
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Page 147 and 148:
148 Benjamin, Smith, and Waites 8.
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150 Benjamin, Smith, and Waites
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152 Olmos et al. Fig. 1. RT-hemines
Page 153 and 154:
154 Olmos et al. This nested RT-PCR
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156 Olmos et al. Table 2 Volume and
Page 157 and 158:
158 Olmos et al. 8. The sensitivity
Page 159 and 160:
160 Olmos et al.
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162 Abe 5. Moloney murine leukemia
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164 Abe Table 2 Detection Rate of H
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166 Abe 4. For HBV, nested PCR usin
Page 167 and 168:
168 Tellier et al. of Pfu (and ther
Page 169 and 170:
170 Tellier et al. 2. Cline, J., Br
Page 171 and 172:
172 Tellier et al. 38. Tamiya, S.,
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174 Tellier et al. 13. Thin-wall PC
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176 Tellier et al. 13 min for the l
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178 Tellier et al.
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182 Stirling efficiency of the reac
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184 Stirling
Page 183 and 184:
186 Cremer and Moos Fig. 1. Rearran
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188 Cremer and Moos 4. Count cells
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190 Cremer and Moos Fig. 3. Alignme
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192 Cremer and Moos Fig. 4. Testing
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194 Cremer and Moos 5. Compare the
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196 Cremer and Moos 11. Klein, E.,
Page 195 and 196:
198 McDonagh the dilution method is
Page 197 and 198:
200 McDonagh 2.2. Basic PCR 1. dNTP
Page 199 and 200:
202 McDonagh Fig. 2. Quantitative P
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204 McDonagh
Page 203 and 204:
206 Bartlett Table 1 Example Assay
Page 205 and 206:
208 Bartlett 3.4. Calculation of Re
Page 207 and 208:
210 Bartlett 11. Cerenkov counting
Page 209 and 210:
212 Kerr Fig. 1. Fluorescent probes
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214 Kerr after the PCR. This reduce
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218 Bartlett As with any experiment
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220 Bartlett Even once novel regula
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222 Bartlett Notwithstanding these
Page 219 and 220:
224 Bartlett
Page 221 and 222:
226 Dominguez et al. Table 1 Primer
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228 Dominguez et al. 4. Oligonucleo
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230 Dominguez et al. Fig. 2. cDNA n
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232 Dominguez et al. 3.4. Gel Elect
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234 Dominguez et al. 3. If the cont
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236 Dominguez et al. 11. Joshi, C.
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238 Khalturin, Kuznetsov, and Bosch
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Page 237 and 238:
Page 239 and 240:
Page 241 and 242:
246 Ringquist et al. In this chapte
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248 Ringquist et al. 5. Total RNA s
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250 Ringquist et al. 3. Purificatio
Page 247 and 248:
252 Ringquist et al. 2. The present
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254 Ringquist et al.
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256 Case-Green, Pritchard, and Sout
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272 Oien Fig. 1. A schematic diagra
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274 Oien 4. 100% and 70% ethanol. 5
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276 Oien 2. Purify polyA + mRNA fro
Page 273 and 274:
278 Oien 50-mL conical tubes. Resus
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280 Oien Forward Primer, and then r
Page 277 and 278:
282 Oien 8. PCR. With SAGE, achievi
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284 Oien
Page 281 and 282:
288 Edwards and Bartlett technology
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290 Edwards and Bartlett ing less p
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292 Edwards and Bartlett Stepwise m
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294 Edwards and Bartlett
Page 289 and 290:
296 Rithidech and Dunn 11. Ethidium
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298 Rithidech and Dunn Fig. 1. PCR
Page 293 and 294:
300 Rithidech and Dunn
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302 Edwards and Bartlett Studies th
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304 Edwards and Bartlett 11. Hot st
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306 Edwards and Bartlett Fig. 1. Ex
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308 Edwards and Bartlett 3. Sartor,
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310 Schmerer the investigation conc
Page 305 and 306:
312 Schmerer References 1. Kunkel,
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314 Schmerer
Page 309 and 310:
316 Aubele and Smida 2.2. Chemicals
Page 311 and 312:
318 Aubele and Smida References 1.
Page 313 and 314:
320 Nakashima, Akahoshi, and Tanaka
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322 Nakashima, Akahoshi, and Tanaka
Page 317 and 318:
324 Stirling 9. TAE (20×): 484 g o
Page 319 and 320:
326 Stirling
Page 321 and 322:
328 Han and Robinson Fig. 1. Basic
Page 323 and 324:
330 Han and Robinson sequence diffe
Page 325 and 326:
332 Han and Robinson 4. Notes 1. PC
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334 Han and Robinson
Page 329 and 330:
338 Stirling of simple and improved
Page 331 and 332:
340 Stirling concentrations interfe
Page 333 and 334:
342 Daniels to sequence a 500-bp PC
Page 335 and 336:
344 Daniels 4. Load all of the samp
Page 337 and 338:
346 Daniels References 1. Orita, M.
Page 339 and 340:
348 Kösel et al. Fig. 1. Schematic
Page 341 and 342:
350 Kösel et al. 3. Methods 3.1. P
Page 343 and 344:
352 Kösel et al. Fig. 2. Sequencin
Page 345 and 346:
354 Kösel et al. 5. Kwok, S. and H
Page 347 and 348:
356 Mazars and Theillet Fig. 1. Sch
Page 349 and 350:
358 Mazars and Theillet of genomic
Page 351 and 352:
360 Mazars and Theillet
Page 353 and 354:
362 Suomalainen and Syvänen Fig. 1
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364 Suomalainen and Syvänen detect
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366 Suomalainen and Syvänen temper
Page 359 and 360:
368 Shen et al. ladder. Also, direc
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370 Shen et al. 3. Mineral oil. 4.
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372 Shen et al. extended primers, w
Page 365 and 366:
374 Quivy and Becker Fig. 1. The us
Page 367 and 368:
376 Quivy and Becker that decreases
Page 369 and 370:
378 Quivy and Becker 2. Solution of
Page 371 and 372:
380 Quivy and Becker 7. Precipitate
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382 Quivy and Becker 7. Prepare a p
Page 375 and 376:
384 Quivy and Becker
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386 Walsh by most, but not all M13
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388 Walsh PCR products are now flus
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390 Walsh 5. For palindromic restri
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392 Walsh
Page 385 and 386:
394 McAleer, Coffey, and Dunham Fig
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396 McAleer, Coffey, and Dunham Tab
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398 McAleer, Coffey, and Dunham Tab
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400 McAleer, Coffey, and Dunham
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402 Stirling 5. Homopolymer Regions
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406 Speel, Ramaekers, and Hopman Ta
Page 397 and 398:
408 Speel, Ramaekers, and Hopman Fi
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410 Speel, Ramaekers, and Hopman po
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Table 2 Comparison of PRINS, in Sit
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414 Speel, Ramaekers, and Hopman te
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Table 3 Summary of Control Experime
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418 Speel, Ramaekers, and Hopman 3.
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420 Speel, Ramaekers, and Hopman ad
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422 Speel, Ramaekers, and Hopman 25
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Page 415 and 416:
426 Bull and Paskins Fig. 1. Result
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428 Bull and Paskins 2.3. Detection
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430 Bull and Paskins 6. Shake the s
Page 421 and 422:
432 Bull and Paskins
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434 Wiedorn and Goldmann Fig. 1. IS
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436 Wiedorn and Goldmann 41. Protei
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438 Wiedorn and Goldmann 2. Incubat
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440 Wiedorn and Goldmann 3.15. Prim
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442 Wiedorn and Goldmann ficient se
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444 Wiedorn and Goldmann 25. Kommin
Page 435 and 436:
446 Gilchrist and Befus Fig. 1. Sch
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448 Gilchrist and Befus 2. Cells ar
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450 Gilchrist and Befus Fig. 3. RT
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452 Gilchrist and Befus References
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454 Speel, Ramaekers, and Hopman of
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456 Speel, Ramaekers, and Hopman Fi
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Page 449 and 450:
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462 Speel, Ramaekers, and Hopman bu
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Page 455 and 456:
468 Pearson and Stirling into PCR p
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470 Wang 2. Materials 2.1. PCR 1. D
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472 Wang Fig. 1. A brief outline of
Page 461 and 462:
474 Wang
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476 Horton, Raju, and Conti-Fine Fi
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478 Horton, Raju, and Conti-Fine th
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480 Horton, Raju, and Conti-Fine 1.
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482 Horton, Raju, and Conti-Fine ot
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484 Horton, Raju, and Conti-Fine
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486 Preston amplification approach
Page 475 and 476:
488 Preston 1. 10× PCR buffer: 100
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490 Preston Fig. 1. Design of degen
Page 479 and 480:
492 Preston 2. Remove the AmpliTaq
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494 Preston 3.3. Cloning and DNA Se
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496 Preston MgCl 2 concentrations b
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498 Preston 21. Hung, T., Mak, K.,
Page 487 and 488:
500 Ravassard et al. Fig. 1. Constr
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502 Ravassard et al. size dispersio
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504 Ravassard et al. 9. ddH 2 O. 10
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506 Ravassard et al. 3.2.2. RNA Mix
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508 Ravassard et al. 4. Wash twice
Page 497 and 498:
510 Ravassard et al.
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512 Pont-Kingdon Fig. 1. Constructi
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514 Pont-Kingdon 9. Invert tube and
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516 Pont-Kingdon
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518 Jones and Winistorfer Fig. 1. D
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520 Jones and Winistorfer Fig. 2. D
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522 Jones and Winistorfer The yield
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524 Jones and Winistorfer 7. Goulde
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526 Burke and Barik Fig. 1. The bas
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528 Burke and Barik concentration o
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530 Burke and Barik purified mutant
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532 Burke and Barik
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