ライフサイエンスコーパス: primer extension

1 eotide or DNA probes by polymerase-catalyzed primer extension.

2 g the N3 or O2 contacts that interfered with primer extension.

3 selective 2'-hydroxyl acylation analysed by primer extension.

4 weak base pairing interactions to facilitate primer extension.

5 hat sites of RNA modification be detected by primer extension.

6 a fluorescence image after template-directed primer extension.

7 f hydrogen bonds between base pairs prevents primer extension.

8 on efficiency but promotes limited rounds of primer extension.

9 iphosphates (ddNTPs), dNTP-ONH(2)s terminate primer extension.

10 ranscription initiation sites were mapped by primer extension.

11 -nt RNAs from the PPT region were tested for primer extension.

12 ations for both nucleotide incorporation and primer extension.

13 g change in the protein-induced stops in the primer extension.

14 oncentrations was shown to be preferred over primer extension.

15 containing bulge structures by single round primer extension.

16 ated start of transcription as determined by primer extension.

17 DNA synthesis in a minimal reconstitution of primer extension.

18 cleotide located downstream from the site of primer extension.

19 w that it is a highly reactive substrate for primer extension.

20 abilized and gain function via non-enzymatic primer extension.

21 RNA, DNA, and TNA templates by nonenzymatic primer extension.

22 PolDIP2 can regulate the TLS polymerase and primer extension activities of PrimPol, further enhancin

23 itiation activities but a marked increase in primer extension activities, indicating an ability to fo

24 itro analysis of RdRp de novo initiation and primer extension activities.

25 titution in vivo and direct telomeric-repeat primer extension activity assays to compare the ribonucl

26 accumulation, RNP affinity purification, and primer extension activity assays.

27 cleotide hybridization was used to probe the primer-extension activity of individual telomerase enzym

28 omer addition as well as trimer-assisted RNA primer extension, allowing efficient copying of a variet

29 Reverse transcription-PCR (RT-PCR) and primer extension analyses also revealed a complex transc

30 DNase I footprinting and primer extension analyses have further defined the DNA-b

31 Pulse-chase, Northern blotting, and primer extension analyses in the L40-depleted strain cle

32 In the absence of functional SpPrp18, primer extension analyses on a tfIId(+) intron 1-contain

33 selective 2'-hydroxyl acylation analyzed by primer extension analyses revealed adaptation of the S(M

34 characterized by bgaB fusion expression and primer extension analyses uncovered evidence for a secon

35 hich we mapped by S1 nuclease protection and primer extension analyses.

36 ts using single nucleotide incorporation and primer extension analyses.

37 The 5' end of exon 1 was defined by primer extension analyses; deletion of an inhibitor sequ

38 Using primer extension analysis and reporter assays, we show t

39 Primer extension analysis determined that the transcript

40 Primer extension analysis identified a promoter upstream

41 Primer extension analysis identified two rpoS transcript

42 Nuclease protection analysis and primer extension analysis indicate no aberrant transcrip

43 anomalous assignment for the start site when primer extension analysis is used.

44 Primer extension analysis located the transcription star

45 Primer extension analysis of RNA isolated from growing,

46 Using primer extension analysis of several test mRNAs, we show

47 Primer extension analysis of spx RNA shows the same addi

48 Primer extension analysis of the mRNA from genes associa

49 Primer extension analysis of the rot promoter revealed a

50 Selective 2'-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of

51 Primer extension analysis revealed four putative transcr

52 Primer extension analysis revealed that MazF-cd cleaved

53 Reverse transcription primer extension analysis reveals that rRNA extracted fr

54 Quantitative primer extension analysis showed that the promoter from

55 Primer extension analysis uncovered a second intergenic

56 Selective 2'-hydroxyl acylation analyzed by primer extension analysis was consistent with a 13-base

57 Primer extension analysis was performed with synthetic n

58 Using primer extension analysis, the promoter of the nag opero

59 ratio of P2 to P1 transcripts, determined by primer extension analysis, was high for the strong rrnO

60 Using primer extension analysis, we identified two potential t

61 or mntH in B. abortus 2308 was determined by primer extension analysis.

62 ranscription initiation were established via primer extension analysis.

63 cription start sites for each gene mapped by primer extension analysis.

64 (selective 2'-hydroxyl acylation analyzed by primer extension) analysis, and toeprinting, we found th

65 nscription initiation site was identified by primer extension and a putative sigma70-like promoter wa

66 cluding selective 2'OH acylation analyzed by primer extension and circular dichroism spectroscopy are

67 Primer extension and DNase I footprinting identified mul

68 selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) th

69 selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to

70 ance of hydrogen bonding interactions during primer extension and pyrophosphorolysis.

71 nown lesions imidazolone and oxazolone using primer extension and pyrosequencing experiments.

72 Primer extension and quantitative real-time reverse tran

73 hich is more efficient than simple templated primer extension and relies on a 5'-phosphate group on t

74 such as RNA ligation, reverse transcription, primer extension and reverse transcriptase-polymerase ch

75 uding short RNAs not amenable to analysis by primer extension and RNAs with functionally important st

76 Primer extension and RNase protection assays mapped the

77 rt- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of

78 Primer extension and S1 nuclease protection assays were

79 er template DNA, triggering another round of primer extension and strand displacement.

80 A with apurinic endonuclease IV, followed by primer extension and/or PCR amplification to detect the

81 rporation of a limiting dNTP is required for primer-extension and Taq polymerase-mediated 5-3' exonuc

82 nucleotides act as catalysts that accelerate primer extension, and allow for the one-pot copying of m

83 lectrophoretic mobility shift assay, RT-PCR, primer extension, and beta-galactosidase assay results,

84 n of PV genomic RNA, PV polymerase-catalyzed primer extension, and cell-free PV synthesis that a pyri

85 2'-hydroxyl acylation with lithium ion-based primer extension, and identifies characteristic structur

86 A combination of macroarray data, primer extension, and in vitro transcription analyses al

87 ing decreased processivity, a slower rate of primer extension, and increased strand transfer activity

88 hpd, hmgA, and dhcA promoters were mapped by primer extension, and purified His(6)-PhhR was shown to

89 he position of those sites was determined by primer extension, and they were shown to be situated in

90 In this study, we used a comprehensive primer extension approach to map the frequency and codon

91 SHAPE (selective 2'OH acylation analysed by primer extension) approach, where a mixed structural pop

92 We established a new automated primer extension assay and successfully validated it for

93 e structure and function of mt-tRNA(Asp) The primer extension assay demonstrated that the m.7551A > G

94 chromatography (RP-HPLC) and quantified in a primer extension assay from cord blood.

95 ition, promoter consensus binding search and primer extension assay helped us to identify a new sigma

96 cipitated with HBV core antibody; and (iv) a primer extension assay maps the 5' end of the minus stra

97 Primer extension assay results demonstrated that both di

98 Moreover, primer extension assay revealed that N(4)-CMdC was a str

99 We used an in vitro primer extension assay to examine the progression of DNA

100 Using an in vitro primer extension assay, we observed sequence-specific sy

101 Using primer extension assays in vitro, we found that a single

102 Ribonuclease protection and primer extension assays show that each promoter is activ

103 ata from mRNA decay studies and quantitative primer extension assays support a model in which bound C

104 Primer extension assays were used to determine the trans

105 eir interactions using primase, helicase and primer extension assays, and a 'stripped down' reconstit

106 te that the purified O-ribosomes are pure by primer extension assays, and structurally homogenous by

107 In primer extension assays, pol eta and pol kappa replicate

108 omatin immunoprecipitation-single-nucleotide primer extension assays, we measured the chromatin compo

109 Using transcriptional fusions and primer extension assays, we show here that tolC has two

110 sults were compared with those of individual primer extension assays.

111 Biochemical, reporter-based and primer-extension assays indicate that BCX4430 inhibits v

112 Polymerase-mediated primer-extension assays reveal that tCfTP is efficiently

113 native substrate and RNA-chain terminator in primer-extension assays using a surrogate respiratory sy

114 (selective 2'-hydroxyl acylation analysed by primer extension) assays show that part of the regulated

115 PFV RT displayed a drastic reduction in primer extension at low dNTP concentrations where HIV-1

116 XP PTE modifications impaired DNA polymerase primer extension at the lower temperatures that exist pr

117 bstrates compete at equal concentrations for primer extension at the same site in the polymerase-prim

118 resent study, we developed a new multiplexed primer extension-based spoligotyping assay using automat

119 he observed reduction in k(pol) in mispaired primer extension being due to the position of the enzyme

120 n of the 3'-terminal nucleotide residue, and primer extension beyond a mispair differed not only betw

121 bdomain, required for processivity, impaired primer extension beyond the abasic site.

122 ct base pair synthesis, as well as continued primer extension beyond the unnatural base pair, is sens

123 Primer extension by DNA polymerase delta (pol delta) dis

124 In the presence of phosphatase, primer extension by DNA polymerase using nonfluorescent

125 en fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstratin

126 cesses including DNA strand displacement and primer extension by DNA polymerases that resulted in pre

127 ovo RNA primer synthesis by DnaG and initial primer extension by DnaEBs are carried out by a lagging

128 nd that most mismatches decrease the rate of primer extension by more than 2 orders of magnitude rela

129 WRN excises 3'-terminal mismatches to enable primer extension by Pol delta.

130 In addition, PriL, but not PriX, facilitates primer extension by PriS.

131 ein and its DNA-binding domain (DBD) inhibit primer extension by telomerase.

132 single-nucleotide incorporation followed by primer extension by Vent(exo-) polymerase.

133 The combination of primer extension, bypass, and bioorthogonal modification

134 Unlike ddNTPs, however, primer extension can be resumed by cleaving an O-N bond

135 d to template strands, and template-directed primer extension can still occur, all within a phase-sep

136 selective 2'-hydroxyl acylation analyzed by primer extension chemical probing with mutagenesis to pr

137 SHAPE (selective 2'-hydroxyl acylation and primer extension) chemical footprinting showed that the

138 (selective 2'-hydroxyl acylation analyzed by primer extension) chemical probing analysis further reve

139 (selective 2'-hydroxyl acylation analyzed by primer extension) chemical probing experiments showed th

140 (selective 2'-hydroxyl acylation analyzed by primer extension) chemical probing methodology together

141 (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry measures local nucleotide fl

142 omatin immunoprecipitation-single nucleotide primer extension (ChIP-SNuPE) assays, we measured the al

143 thumb of the polymerase also stabilizes this primer extension complex.

144 A working model of nonenzymatic RNA primer extension could illuminate how prebiotic chemistr

145 Primer extension demonstrated that the site of methylati

146 ever, we have found that the initial rate of primer extension depends on the pH and concentration at

147 logy is limited, sometimes severely, because primer extension detection obscures structural informati

148 We observed that HIV-1 RT performs fast primer extension DNA synthesis on single-stranded region

149 for Taq DNA polymerase, they do not support primer extension/elongation at low stringency conditions

150 As a result, the primer extension/elongation proceeds only at an elevated

151 (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing informat

152 RNAs was also unchanged as judged by in vivo primer extension experiments and by Northern blotting an

153 Primer extension experiments revealed that the 5' ends o

154 In vivo and in vitro primer extension experiments showed that MqsR is an mRNA

155 In in vivo primer extension experiments using two different mRNAs,

156 In vitro primer extension experiments with bacterial and mammalia

157 In in vivo primer extension experiments with two different mRNAs, t

158 eared 30 min after YafO induction in in vivo primer extension experiments, consistent with Northern b

159 nce for ScoC repression in vivo was shown by primer extension for P(A4) and P(A3) from the wild-type

160 Primer extension from a 3'-terminal CEdG was observed on

161 lected with deoxyinosine triphosphate during primer extension, gave a modest improvement (FNR = 12%,

162 selective 2'-hydroxyl acylation analyzed by primer extension (hSHAPE) of rRNAs within bound ribosome

163 Primer extension identified one transcriptional start po

164 s 3'-end, we examined de novo initiation and primer extension in a system devoid of self-priming and

165 Primer extension, in vitro transcription and in vivo exp

166 st efficient at stalling ribosomes, based on primer extension inhibition (toeprint) assays and report

167 Primer extension inhibition assays provided further evid

168 Moreover, primer extension inhibition assays showed that the TE in

169 ocess resembles replication repair, in which primer extension is blocked by a lesion in the template;

170 that the polymerase activity of HSV-1 Pol on primer extension is influenced by sequence context and t

171 Thus, continued primer extension is limited by deintercalation and rearr

172 Moreover, detection by primer extension is more complex than the actual structu

173 Chemical primer extension is the enzyme-free incorporation of nuc

174 dynamic NMR results, combined with previous primer extension kinetic data by Miller & Grollman, supp

175 Primer extension located the transcriptional start site

176 modates RNA as one of the two strands during primer extension, mainly by inserting dNMPs opposite unm

177 Primer extension mapping and ectopic expression in delet

178 By modifying classical primer extension methods, we localized specific internuc

179 fied methylation-sensitive single-nucleotide primer extension (MS-SNuPE) assay, we observed stage-spe

180 Methylation-sensitive single-nucleotide primer extension (Ms-SNuPE) is a technique that can be u

181 Primer extension of wild-type B. burgdorferi grown in vi

182 he kinetics and the fidelity of nonenzymatic primer extension on mixed-sequence RNA templates.

183 prominent cleavage products observed during primer extension on this template correlated with pause

184 out a detailed kinetic analysis of in vitro primer extension opposite DFT-containing templates by th

185 substrates for DNA polymerases applicable in primer extension or PCR synthesis of modified oligonucle

186 (selective 2'-hydroxyl acylation analyzed by primer extension, or SHAPE).

187 ctions is Selective 2' Hydroxyl Acylation by Primer Extension, or SHAPE.

188 e growing primer strand, and it explains why primer extension past the lesion is prohibited even thou

189 lacing the insertion polymerase to carry out primer extension past the lesion.

190 sites were mapped by alkaline digestion and primer extension pausing.

191 Using a quantitative primer-extension PCR assay we identified miRNAs, includi

192 ication through these artificial linkages by primer extension, PCR, and deep sequencing reveals that

193 PFOR); and low transcript levels of porGDAB (primer extension), phenotypes consistent with an involve

194 tents of modification are then determined by primer extension, polyacrylamide gel electrophoresis and

195 er daughter strand as an undamaged template, primer extension, primer switching back to its cognate t

196 e most efficient at synthesizing full-length primer extension product, with all of the dUTP derivativ

197 HPLC-ESI-MS/MS analysis of primer extension products confirmed the ability of bypas

198 ermophilic DNA polymerases and the resulting primer extension products hybridize with good specificit

199 spectrometry analysis of all of the pol eta primer extension products indicated multiple components,

200 for sequence determination, the 3'-OH of the primer extension products is regenerated through differe

201 In addition, the mean lengths of primer extension products obtained with s(2)U is greater

202 The fidelity of the primer extension products resulting from the sequential

203 at no 8-nitroG.G base pairing is seen in the primer extension products suggests that the polymerases

204 Fluorescent labeling of the primer extension products was achieved by fluorophores w

205 promoters were identified for each of these primer extension products.

206 th multiplexed paired-end deep sequencing of primer extension products.

207 on assays using modified oligonucleotides or primer extension products.

208 Deep Vent, but also bypassed for full length primer extension products.

209 Furthermore, the primer-extension pulse-chase analysis affirmed that the

210 More importantly, during processive primer extension, pyrophosphate (PPi) release was rate-l

211 Here we show that a primer extension reaction can be used to monitor directl

212 Here we show that a primer extension reaction can be used to monitor oxidati

213 the second signal transduction step based on primer extension reaction coupled with TaqMan probe.

214 Subsequently, a primer extension reaction is carried out, and the extens

215 ior reaction kinetics and improved yields of primer extension reaction products.

216 sites are detected as stops in an optimized primer extension reaction, followed by electrophoretic f

217 activated monomer is maintained prior to the primer extension reaction.

218 iation by the genotype 1b and 2a RdRps while primer extension reactions are not affected or inhibited

219 oxynucleotides and used them as templates in primer extension reactions catalyzed by pol eta, kappa a

220 In contrast, primer extension reactions of random templates, as well

221 Primer extension reactions were employed to label select

222 Primer extension reactions with selected transcription u

223 bility to perform templated and nontemplated primer extension reactions, and its preference for addin

224 templates in template-directed nonenzymatic primer-extension reactions.

225 Single-nucleotide primer extensions result in successive displacements of

226 Primer extension results in loss of information at both

227 se was designed and incorporated into DNA by primer extension, reverse transcription and polymerase c

228 l selective 2-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneousl

229 selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation s

230 selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), that can be use

231 selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

232 Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis revealed that this seq

233 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to examine the seconda

234 Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis was performed on a 365

235 Selective 2'OH acylation analyzed by primer extension (SHAPE) applied to free and HDAg-bound

236 hown that selective 2'-hydroxyl acylation by primer extension (SHAPE) can give near-zero error rates

237 ranscript selective 2'-hydroxyl acylation by primer extension (SHAPE) chemical probing, we show that

238 Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistries exploit small elect

239 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry coupled with analysis

240 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry exploits the discover

241 Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry is a powerful approac

242 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry with multiplexed pair

243 Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry yields quantitative R

244 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry, we determined the se

245 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments greatly improves th

246 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) indicates specificity in bindin

247 Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) interrogates local backbone fle

248 Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a powerful approach for char

249 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) mapping.

250 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) RNA structure probing.

251 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to examine the structure of Tet

252 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to obtain nucleotide-resolution

253 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to structural analysis of authe

254 selective 2' hydroxyl acylation analysed by primer extension (SHAPE), a technique that allows struct

255 mpute the selective 2' hydroxyl acylation by primer extension (SHAPE)-directed ensemble for the RNA f

256 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE).

257 Selective 2'-Hydroxyl Acylation Analyzed by Primer Extension (SHAPE).

258 5' rapid amplification of cDNA ends and primer extension show that different N-terminal protein

259 We map the primary dksA promoter by primer extension, show that its activity increases in a

260 Selective 2'-hydroxyl acylation and primer extension, small-angle X-ray scattering, and Mont

261 y genes, a custom designed Single Nucleotide Primer Extension (SNPE) multiplexing mutation assay was

262 ture methods as well as PCR-based and single-primer extension (SPEX) approaches to reexamine the same

263 Polepsilon is not required for the initial primer extension step of BIR but is required to complete

264 Reflex workflow needs only a small number of primer extension steps to rapidly enable uniform sequenc

265 the mitochondria leads to protein-dependent primer extension stops spaced every approximately 20 bas

266 (selective 2'-hydroxyl acylation analyzed by primer extension) structure probing indicated that these

267 Primer extension studies confirmed the temperature-depen

268 Primer extension studies have shown that poliota is also

269 Primer extension studies have shown that the Y-family DN

270 Additional primer extension studies identified a fifth csrA promote

271 Primer extension studies identified flhDC decay intermed

272 Primer extension studies using the Klenow fragment (exo(

273 in a DNA template strand, and standing start primer extension studies were conducted with Klenow frag

274 ity of the modified DNA has been verified by primer extension studies with DNA polymerases I and IV f

275 Primer extension studies with purified pol eta have show

276 exogenous AC diribonucleotides into an ACCC primer (extension synthesis).

277 ion of strand displacement and single strand primer extension synthesis rates.

278 We describe the use of the primer extension technique in conjunction with specifica

279 Using a fluorescent primer extension technique, we mapped the modified nucle

280 (Selective 2'-hydroxyl acylation analysed by primer extension) technology has emerged as one of the l

281 luorescence situ in hybridization (FISH) and primer extension telomere repeat amplification (PETRA).

282 tronger blockade to Klenow fragment-mediated primer extension than N(6)-CMdA.

283 We determined by primer extension that the salKR promoter is located with

284 Following primer extension, the reaction temperature is lowered su

285 Selective 2'-Hydroxyl Acylation analyzed by Primer Extension to confirm the formation and functional

286 yme-assisted specificity step, a solid-phase primer extension to distinguish between members of miRNA

287 selective 2'-hydroxyl acylation analyzed by primer extension to resolve the HCV 5'-UTR's RNA seconda

288 vious characterizations of template-directed primer extension using 5'-phosphoryl-2-methylimidazole-a

289 fied nucleic acid is a suitable template for primer extension using deep vent (exo-) DNA polymerase,

290 ormation are subsequently scored as stops to primer extension using reverse transcriptase.

291 Primer extension was used for the synthesis of ONs with

292 By using UV cross-linking and primer extension, we have obtained direct evidence for t

293 Here, using UV cross-linking followed by primer extension, we show that the protein substrates an

294 P and MeP did not support robust primer extension whereas sG and NitroC did.

295 ymatic synthesis of acrylate-modified DNA by primer extension, whereas dG(BA)TP was an inhibitor of p

296 and the -1 deletion is produced upon further primer extension which is more facile than nucleotide in

297 Primer extension with RNA from an RNase III null mutant

298 e DNA polymerase-catalyzed single-nucleotide primer extensions with high sensitivity and spatial reso

299 rimental reconstructions of nonenzymatic RNA primer extension yield a mixture of 2'-5' and 3'-5' inte

300 (selective 2'-hydroxyl acylation analyzed by primer extension) yields an experimental measurement of