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Ligase Chain Reaction 149 24. Stary, A. (1999) Correct samples for diagnostic tests in sexually transmitted diseases: which sample for which test? FEMS Immunol Med Microbiol 24, 455– 459. 25. Stary, A., Najim, B., and Lee, H. H. (1997) Vulval swabs as alternative specimens for ligase chain reaction detection of genital chlamydial infection in women. J. Clin. Microbiol. 35, 836–838. 26. Schepetiuk, S., Kok, T., Martin, L., Waddell, R., and Higgins, G. (1997) Detection of Chlamydia trachomatis in urine samples by nucleic acid tests: comparison with culture and enzyme immunoassay of genital swab specimens. J. Clin. Microbiol. 35, 3355–3357. 27. Dubuis, O., Gorgievski-Hrisoho, M., Germann, D., and Matter, L. (1997) Evaluation of 2-SP transport medium for detection of Chlamydia trachomatis and Neisseria gonorrhoeae by two automated amplification systems and culture for chlamydia. J. Clin. Pathol. 50, 947–950. 28. Hook, E. W., III, Smith, K., Mullen, C., Stephens, J., Rinehardt, L., Pate, M. S., and Lee, H. H. (1997) Diagnosis of genitourinary Chlamydia trachomatis infections by using the ligase chain reaction on patient-obtained vaginal swabs. J. Clin. Microbiol. 35, 2133–2135. 29. Stary, A., Schuh, E., Kerschbaumer, M., Gotz, B., and Lee, H. (1998) Performance of transcription-mediated amplification and ligase chain reaction assays for detection of chlamydial infection in urogenital samples obtained by invasive and noninvasive methods. J. Clin. Microbiol. 36, 2666–2670. 30. Carroll, K. C., Aldeen, W. E., Morrison, M., Anderson, R., Lee, D., and Mottice, S. (1998) Evaluation of the Abbott LCx ligase chain reaction assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine and genital swab specimens from a sexually transmitted disease clinic population. J. Clin. Microbiol. 36, 1630–1633. 31. Garrino, M. G., Glupczynski, Y., Degraux, J., Nizet, H., and Delmee, M. (1999) Evaluation of the Abbott LCx Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis complex in human samples. J. Clin. Microbiol. 37, 229–232. 32. Moore, D. F. and Curry, J. I. (1998) Detection and identification of Mycobacterium tuberculosis directly from sputum sediments by ligase chain reaction. J. Clin. Microbiol. 36, 1028–1031. 33. Ausina, V., Gamboa, F., Gazapo, E., Manterola, J. M., Lonca, J., Matas, L., et al. (1997) Evaluation of the semiautomated Abbott LCx Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis in respiratory specimens. J. Clin. Microbiol. 35, 1996–2002. 34. Lindbrathen, A., Gaustad, P., Hovig, B., and Tonjum, T. (1997) Direct detection of Mycobacterium tuberculosis complex in clinical samples from patients in Norway by ligase chain reaction. J. Clin. Microbiol. 35, 3248–353. 35. Fadda, G., Ardito, F., Sanguinetti, M., Posteraro, B., Ortona, L., Chezzi, C., et al. (1998) Evaluation of the Abbott LCx Mycobacterium tuberculosis assay in comparison with culture methods in selected Italian patients. New Microbiol. 21, 97–103. 36. Birkenmeyer, L. and Armstrong, A. S. (1992) Preliminary evaluation of the ligase chain reaction for specific detection of Neisseria gonorrhoeae. J. Clin. Microbiol. 30, 3089–3094. 37. Wilson, V. L., Wei, Q., Wade, K. R., Chisa, M., Bailey, D., Kanstrup, C. M., et al. (1999) Needle-in-a-haystack detection and identification of base substitution mutations in human tissues. Mutat. Res. 406, 79–100. 38. Abravaya, K., Carrino, J. J., Muldoon, S., and Lee, H. H. (1995) Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucleic Acids Res. 23, 675–682.
150 Benjamin, Smith, and Waites
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TM Methods in Molecular Biology Vol
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Xin Wang and W. Scott Young III 105
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63. Primed In Situ Nucleic Acid Lab
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4 Bartlett and Stirling The thing t
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6 Bartlett and Stirling Fig. 2. Res
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8 Carroll and Casimir of PCR. Such
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10 Carroll and Casimir cost more th
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12 Carroll and Casimir are no longe
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14 Carroll and Casimir Should these
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16 McDonagh Fig. 1. Unidirectional
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18 McDonagh stored. This means that
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20 McDonagh
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22 Stirling which will either not a
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24 Stirling
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28 Bartlett References 1. US Depart
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30 Bartlett and White 11. 5 M sodiu
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32 Bartlett and White
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34 Pearson and Stirling 11. Microfu
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36 Going 3. Methods 3.1. Section Cu
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38 Going pipet filler. Spread the p
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40 Going digitally to record the di
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42 Going
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44 Pearson 7. Add 60 µL of chlorof
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46 Bartlett 3. Methods 3.1. RNA Ext
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48 Pearson 3. Method The method of
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50 Stirling and Bartlett 4. Protein
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52 Stirling and Bartlett
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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
Page 97 and 98: 98 Grunenwald 2. Foord, O. S. and R
Page 99 and 100: 100 Grunenwald
Page 101 and 102: 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
Page 109 and 110: 110 Wang and Young Fig. 3. Expresse
Page 111 and 112: 112 Wang and Young 2. First-strand
Page 113 and 114: 114 Wang and Young 3′-RACE outlin
Page 115 and 116: 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
Page 133 and 134: 134 Iannone et al.
Page 135 and 136: 136 Benjamin, Smith, and Waites amp
Page 137 and 138: 138 Benjamin, Smith, and Waites the
Page 139 and 140: 140 Benjamin, Smith, and Waites 2.2
Page 141 and 142: 142 Benjamin, Smith, and Waites 2.
Page 147: 148 Benjamin, Smith, and Waites 8.
Page 151 and 152: 152 Olmos et al. Fig. 1. RT-hemines
Page 153 and 154: 154 Olmos et al. This nested RT-PCR
Page 155 and 156: 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.
Page 161 and 162: 162 Abe 5. Moloney murine leukemia
Page 163 and 164: 164 Abe Table 2 Detection Rate of H
Page 165 and 166: 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.,
Page 173 and 174: 174 Tellier et al. 13. Thin-wall PC
Page 175 and 176: 176 Tellier et al. 13 min for the l
Page 177 and 178: 178 Tellier et al.
Page 179 and 180: 182 Stirling efficiency of the reac
Page 181 and 182: 184 Stirling
Page 183 and 184: 186 Cremer and Moos Fig. 1. Rearran
Page 185 and 186: 188 Cremer and Moos 4. Count cells
Page 187 and 188: 190 Cremer and Moos Fig. 3. Alignme
Page 189 and 190: 192 Cremer and Moos Fig. 4. Testing
Page 191 and 192: 194 Cremer and Moos 5. Compare the
Page 193 and 194: 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
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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
Page 289 and 290:
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
Page 309 and 310:
316 Aubele and Smida 2.2. Chemicals
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318 Aubele and Smida References 1.
Page 313 and 314:
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.
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348 Kösel et al. Fig. 1. Schematic
Page 341 and 342:
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
Page 369 and 370:
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
Page 459 and 460:
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
Page 477 and 478:
490 Preston Fig. 1. Design of degen
Page 479 and 480:
492 Preston 2. Remove the AmpliTaq
Page 481 and 482:
494 Preston 3.3. Cloning and DNA Se
Page 483 and 484:
496 Preston MgCl 2 concentrations b
Page 485 and 486:
498 Preston 21. Hung, T., Mak, K.,
Page 487 and 488:
500 Ravassard et al. Fig. 1. Constr
Page 489 and 490:
502 Ravassard et al. size dispersio
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504 Ravassard et al. 9. ddH 2 O. 10
Page 493 and 494:
506 Ravassard et al. 3.2.2. RNA Mix
Page 495 and 496:
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
Page 515 and 516:
528 Burke and Barik concentration o
Page 517 and 518:
530 Burke and Barik purified mutant
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532 Burke and Barik
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