| Contributors |
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xiii | |
| Preface |
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xix | |
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1 Enzyme- or light-triggered cyclopropenes for bioorthogonal ligation |
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1 | (34) |
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1 Bioorthogonal chemistry |
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2 | (1) |
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2 Modern bioorthogonal reactions and their limitations |
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3 | (9) |
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3 An activatable cyclopropene for bioorthogonal tetrazine ligations |
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12 | (16) |
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28 | (1) |
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29 | (6) |
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2 Analysis of metabolically labeled inositol phosphate messengers by NMR |
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35 | (18) |
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36 | (3) |
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2 Chemoenzymatic synthesis of [ 3CfJmyo-inositol |
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39 | (5) |
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44 | (6) |
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50 | (1) |
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50 | (1) |
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50 | (3) |
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3 Photo-releasable derivatives of inositol pyrophosphates |
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53 | (22) |
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54 | (8) |
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62 | (5) |
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67 | (1) |
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68 | (1) |
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69 | (1) |
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69 | (6) |
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4 IMPACT: Imaging phospholipase D activity with clickable alcohols via transphosphatidylation |
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75 | (20) |
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76 | (3) |
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2 IMPACT for bulk and single-cell measurement of PLD activity |
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79 | (4) |
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3 Real-time (RT)-IMPACT for visualization of subcellular localization of PLD activity |
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83 | (6) |
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4 Guidance for selecting which variant of IMPACT to use |
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89 | (3) |
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92 | (1) |
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93 | (2) |
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5 Fluorescent bioorthogonal labeling of class B GPCRs in live cells |
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95 | (18) |
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1 Introduction to fluorescent labeling of GPCR |
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96 | (1) |
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2 Site-specific incorporation of alkene reporters into the class B GPCR |
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97 | (5) |
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3 Bioorthogonal labeling of GCGR in live cells using tetrazine ligation |
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102 | (3) |
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4 Bioorthogonal labeling of GCGR in live cells using photo-click chemistry |
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105 | (2) |
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107 | (1) |
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6 Discussions and critical parameters |
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107 | (1) |
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7 Summary and future directions |
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108 | (1) |
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109 | (1) |
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109 | (4) |
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6 Near-infrared photoactivatable nitric oxide donors with photoacoustic readout |
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113 | (36) |
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114 | (1) |
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2 Selection of photoactivatable nitric oxide releasing molecules |
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115 | (2) |
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117 | (1) |
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4 Synthesis of photoNOD-1 |
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118 | (5) |
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5 In vitro characterization of photoNOD-1 and rNOD-1 |
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123 | (17) |
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6 Characterization of photoNOD-1 in vivo |
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140 | (6) |
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146 | (1) |
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146 | (3) |
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7 H2S donors with optical responses |
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149 | (16) |
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150 | (1) |
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2 Preparation and properties of fluorescent H2S donors |
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151 | (7) |
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3 Probe usage and application in cell models |
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158 | (3) |
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161 | (1) |
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162 | (1) |
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162 | (3) |
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8 Visualization of oxidative stress-induced carbonylation in live mammalian cells |
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165 | (18) |
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166 | (4) |
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170 | (1) |
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170 | (1) |
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171 | (5) |
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5 Representative illustrations |
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176 | (2) |
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6 Preserving TFCH-labeled cells |
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178 | (1) |
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178 | (1) |
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179 | (1) |
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179 | (4) |
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9 Receptor-based fluorescent sensors constructed from ribonucleopeptide |
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183 | (42) |
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184 | (2) |
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2 Construction of receptor-based fluorescent sensors by using a ribonucleopeptide (RNP) complex |
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186 | (7) |
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193 | (26) |
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219 | (1) |
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220 | (5) |
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10 Conformationally restrained pentamethine cyanines and use in reductive single molecule localization microscopy |
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225 | (20) |
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226 | (1) |
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2 Synthetic considerations |
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227 | (2) |
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3 Cyanine reactivity in SMLM |
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229 | (2) |
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4 Properties and applications of constrained pentamethine cyanines |
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231 | (1) |
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232 | (2) |
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234 | (5) |
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7 SMLM microscopy--Sample preparation |
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239 | (2) |
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241 | (1) |
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241 | (1) |
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242 | (3) |
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11 A near-infrared light-mediated cleavable linker strategy using the heptamethine cyanine chromophore |
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245 | (32) |
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1 Introduction--Long wavelength photocages |
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246 | (2) |
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2 Cyanine-based photocages |
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248 | (2) |
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3 Application of cyanines photocages to antibody-targeted drug delivery |
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250 | (1) |
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251 | (2) |
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253 | (10) |
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6 In vitro uncaging and in vivo drug delivery |
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263 | (6) |
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269 | (1) |
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269 | (2) |
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271 | (1) |
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271 | (6) |
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12 Quantitative measurement of cytosolic penetration using the chloroalkane penetration assay |
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277 | (34) |
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278 | (3) |
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2 Chloroalkane penetration assay (CAPA) |
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281 | (2) |
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283 | (8) |
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291 | (4) |
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295 | (3) |
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298 | (1) |
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7 Applications and limitations |
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299 | (6) |
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305 | (6) |
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13 Cell-penetrating and mitochondrion-targeting molecules |
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311 | (18) |
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312 | (1) |
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2 Synthesis of CPM-cargo conjugates |
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313 | (3) |
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3 Mitochondrion-specific cargo delivery by CPMs |
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316 | (5) |
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321 | (6) |
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327 | (1) |
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327 | (1) |
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327 | (2) |
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14 A photocaged DNA nanocapsule for delivery and manipulation in cells |
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329 | (14) |
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330 | (1) |
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2 Incorporation and manipulation of caged-NCs in cells |
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331 | (5) |
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336 | (1) |
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337 | (4) |
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341 | (1) |
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341 | (1) |
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342 | (1) |
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15 A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells |
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343 | (30) |
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344 | (2) |
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2 Overview of the Riboglow RNA tagging platform |
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346 | (4) |
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3 Comparison of Riboglow with related techniques |
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350 | (1) |
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4 Considerations for tagging RNA with Riboglow |
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351 | (4) |
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5 Materials, equipment and reagents |
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355 | (5) |
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6 Step by step protocol 1: mRNA localization to stress granules in U-2 OS cells |
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360 | (3) |
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7 Step by step protocol 2: U1 snRNA localization to U-bodies in HeLa cells |
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363 | (3) |
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8 Precursor technique: Bead loading |
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366 | (3) |
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9 Troubleshooting and Optimization |
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369 | (1) |
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369 | (1) |
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370 | (1) |
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370 | (3) |
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16 Enzymatic covalent labeling of RNA with RNA transglycosylation at guanosine (RNA-TAG) |
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373 | (28) |
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374 | (10) |
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384 | (11) |
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395 | (1) |
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396 | (1) |
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396 | (5) |
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17 Assaying RNA solvent accessibility in living cells with LASER |
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401 | (12) |
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401 | (3) |
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404 | (1) |
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405 | (4) |
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409 | (1) |
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410 | (1) |
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410 | (3) |
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18 Split T7 RNA polymerase biosensors to study multiprotein interaction dynamics |
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413 | (20) |
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414 | (2) |
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2 Evolution of the split T7 RNA polymerase biosensor |
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416 | (4) |
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3 RNAP analysis of Bcl-2 family PPIs |
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420 | (9) |
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429 | (1) |
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430 | (1) |
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430 | (3) |
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19 Cross-linking cellular nucleic acids via a target-directing double click reagent |
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433 | (26) |
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434 | (4) |
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2 Materials and measurement instruments |
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438 | (1) |
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3 Methods for chemical synthesis |
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439 | (2) |
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4 Methods for biological experiments |
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441 | (13) |
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5 Discussion and conclusion |
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454 | (1) |
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455 | (1) |
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455 | (4) |
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20 Click chemistry-based amplification and detection of endogenous RNA and DNA molecules in situ using clamp FISH probes |
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459 | (18) |
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460 | (3) |
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2 Design and synthesis of oligonucleotide probe sets |
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463 | (1) |
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3 Preparation of samples for clampFISH |
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464 | (2) |
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4 ClampFISH hybridization procedure for imaging |
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466 | (5) |
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5 ClampFISH hybridization procedure for tissue sections |
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471 | (1) |
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472 | (1) |
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7 ClampFISH hybridization procedure for flow cytometry or sorting |
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472 | (2) |
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474 | (1) |
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474 | (3) |
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21 Quantification of protein delivery in live cells using fluorescence correlation spectroscopy |
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477 | |
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479 | (4) |
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2 Equipment and materials |
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483 | (4) |
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487 | (7) |
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494 | (1) |
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494 | (5) |
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6 Summary and conclusions |
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499 | (1) |
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500 | (1) |
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500 | (1) |
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500 | |
Lisainfo e-raamatute kohta