John M. S. Bartlett.pdf - Bio-Nica.info

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43. Detection of Microsatellite Instability and Lossof Heterozygosity Using DNA Extracted fromFormalin-Fixed Paraffin-Embedded Tumor Materialby Fluorescence- Based Multiplex Microsatellite PCR 301 Joanne Edwards and John M. S. Bartlett 44. Reduction of Shadow Band Synthesis DuringPCR Amplification of Repetitive Sequencesfrom Modern and Ancient DNA 309 Wera M. Schmerer 45. Degenerate Oligonucleotide-Primed PCR 315 Michaela Aubele and Jan Smida 46. Mutation Detection Using RT-PCR-RFLP Hitoshi Nakashima, Mitsuteru Akahoshi, and Yosuke Tanaka 319 47. Multiplex Amplification RefractoryMutation System for the Detectionof Prothrombotic Polymorphisms 323 David Stirling 48. PCR-SSCP Analysis of Polymorphism 328 --- A Simple and Sensitive Method for Detecting DifferencesBetween Short Segments of DNA Mei Han and Mary Ann Robinson 49. Sequencing---- A Technical Overview 337 David Stirling 50. Preparation and Direct Automated Cycle Sequencingof PCR Products 341 Susan E. Daniels 51. Nonradioactive PCR Sequencing Using Digoxigenin 347 Siegfried Kösel, Christoph B. Lücking, Rupert Egensperger,and Manuel B. Graeber 52. Direct Sequencing by Thermal Asymmetric PCR 355 Georges-Raoul Mazars and Charles Theillet 53. Analysis of Nucleotide Sequence Variationsby Solid-Phase Minisequencing 361 Anu Suomalainen and Ann-Christine Syvänen 54. Direct Sequencing with Highly Degenerateand Inosine-Containing Primers 367 Zhiyuan Shen, Jingmei Liu, Robert L. Wells, and Mortimer M. Elkind 55. Determination of Unknown Genomic SequencesWithout Cloning 373 Jean-Pierre Quivy and Peter B. Becker 56. Cloning PCR Products for Sequencing in M13 Vectors 385 David Walsh 57. DNA Rescue by the Vectorette Method 393 Marcia A. McAleer, Alison J. Coffey, and Ian Dunham 58. Technical Notes for Sequencing Difficult Templates 401 David Stirling 59. PCR-Based Detection of Nucleic Acidsin Chromosomes, Cells, and Tissues 405 Technical Considerations on PRINS and In Situ PCR and Comparison with In Situ Hybridization Ernst J. M. Speel, Frans C. S. Ramaekers, and Anton H. N. Hopman 60. Cycling Primed In Situ Amplification 425 John H. Bull and Lynn Paskins 61. Direct and Indirect In Situ PCR 433 Klaus Hermann Wiedorn and Torsten Goldmann 62. Reverse Transcriptase In Situ PCR----New Methods in Cellular Interrogation 445 Mark Gilchrist and A. Dean Befus iii
63. Primed In Situ Nucleic Acid Labeling Combined with Immunocytochemistry to Simultaneously Localize DNA and Proteins in Cells and Chromosomes 453 Ernst J. M. Speel, Frans C. S. Ramaekers, and Anton H. N. Hopman 64. Cloning and Mutagenesis--- A Technical Overview 467 Helen Pearson and David Stirling 65. Using T4 DNA Polymeraseto Generate Clonable PCR Products 469 Kai Wang 66. A T-Linker Strategy for Modificationand Directional Cloning of PCR Products 475 Robert M. Horton, Raghavanpillai Raju, and Bianca M. Conti-Fine 67. Cloning Gene Family Members Using PCRwith Degenerate Oligonucleotide Primers Gregory M. Preston 485 68. cDNA Libraries from a Low Amount of Cells 499 Philippe Ravassard, Christine Icard-Liepkalns, Jacques Mallet,and Jean Baptiste Dumas Milne Edwards 69. Creation of Chimeric Junctions, Deletions, and Insertions by PCR 511 Genevieve Pont-Kingdon 70. Recombination and Site-Directed MutagenesisUsing Recombination PCR 517 Douglas H. Jones and Stanley C. Winistorfer 71. Megaprimer PCR---- Application in Mutagenesis and Gene Fusion 525 Emily Burke and Sailen Barik iv
Page 1 and 2: TM Methods in Molecular Biology Vol
Page 3: Xin Wang and W. Scott Young III 105
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
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Page 29 and 30: 28 Bartlett References 1. US Depart
Page 31 and 32: 30 Bartlett and White 11. 5 M sodiu
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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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54 Stirling 3. Methods 3.1. Fungal
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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
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82 Hyndman and Mitsuhashi 3.1. Effi
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84 Hyndman and Mitsuhashi Fig. 1. H
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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
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104 Stirling
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106 Wang and Young full-length cDNA
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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
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114 Wang and Young 3′-RACE outlin
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116 Wang and Young
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118 Dassanayake and Samaranayake co
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120 Dassanayake and Samaranayake 5.
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122 Dassanayake and Samaranayake Re
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124 Iannone et al. Fig. 1. Diagram
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Table 1 Oligonucleotides Descriptio
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128 Iannone et al. 5. For microsphe
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130 Iannone et al. 4. To adjust for
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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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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
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154 Olmos et al. This nested RT-PCR
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156 Olmos et al. Table 2 Volume and
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158 Olmos et al. 8. The sensitivity
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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
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168 Tellier et al. of Pfu (and ther
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170 Tellier et al. 2. Cline, J., Br
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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
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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.,
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198 McDonagh the dilution method is
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200 McDonagh 2.2. Basic PCR 1. dNTP
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202 McDonagh Fig. 2. Quantitative P
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204 McDonagh
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206 Bartlett Table 1 Example Assay
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208 Bartlett 3.4. Calculation of Re
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210 Bartlett 11. Cerenkov counting
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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
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224 Bartlett
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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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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
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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
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278 Oien 50-mL conical tubes. Resus
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280 Oien Forward Primer, and then r
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282 Oien 8. PCR. With SAGE, achievi
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284 Oien
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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
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296 Rithidech and Dunn 11. Ethidium
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298 Rithidech and Dunn Fig. 1. PCR
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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
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312 Schmerer References 1. Kunkel,
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314 Schmerer
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316 Aubele and Smida 2.2. Chemicals
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318 Aubele and Smida References 1.
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320 Nakashima, Akahoshi, and Tanaka
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322 Nakashima, Akahoshi, and Tanaka
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324 Stirling 9. TAE (20×): 484 g o
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326 Stirling
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328 Han and Robinson Fig. 1. Basic
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330 Han and Robinson sequence diffe
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332 Han and Robinson 4. Notes 1. PC
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334 Han and Robinson
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338 Stirling of simple and improved
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340 Stirling concentrations interfe
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342 Daniels to sequence a 500-bp PC
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344 Daniels 4. Load all of the samp
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346 Daniels References 1. Orita, M.
Page 339 and 340:
348 Kösel et al. Fig. 1. Schematic
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350 Kösel et al. 3. Methods 3.1. P
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352 Kösel et al. Fig. 2. Sequencin
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354 Kösel et al. 5. Kwok, S. and H
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356 Mazars and Theillet Fig. 1. Sch
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358 Mazars and Theillet of genomic
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360 Mazars and Theillet
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362 Suomalainen and Syvänen Fig. 1
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364 Suomalainen and Syvänen detect
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366 Suomalainen and Syvänen temper
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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
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374 Quivy and Becker Fig. 1. The us
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376 Quivy and Becker that decreases
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378 Quivy and Becker 2. Solution of
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380 Quivy and Becker 7. Precipitate
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382 Quivy and Becker 7. Prepare a p
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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
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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
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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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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
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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
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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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462 Speel, Ramaekers, and Hopman bu
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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
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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
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488 Preston 1. 10× PCR buffer: 100
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490 Preston Fig. 1. Design of degen
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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.,
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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
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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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