ライフサイエンスコーパス: primer extension

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

2 on key features of the sequences accessed by primer extension.

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

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

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

6 weak base pairing interactions to facilitate primer extension.

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

8 a fluorescence image after template-directed primer extension.

9 f hydrogen bonds between base pairs prevents primer extension.

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

11 cleophilic amine generally results in faster primer extension.

12 ranscription initiation sites were mapped by primer extension.

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

14 ations for both nucleotide incorporation and primer extension.

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

16 oncentrations was shown to be preferred over primer extension.

17 ers in combination promote successful 4-base primer extension.

18 on efficiency but promotes limited rounds of primer extension.

19 DNA synthesis in a minimal reconstitution of primer extension.

20 cleotide located downstream from the site of primer extension.

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

22 deep-sequencing methodology for studying RNA primer extension.

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

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

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

26 ribonucleotide 1,N (6)-erA but has poor RNA primer extension activities.

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

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

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

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

31 Does the recently illuminated mechanism of primer extension affect the distribution of sequences th

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

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

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

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

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

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

38 ts using single nucleotide incorporation and primer extension analyses.

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

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

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

42 Primer extension analysis determined that the transcript

43 Primer extension analysis identified a promoter upstream

44 Primer extension analysis identified two rpoS transcript

45 Primer extension analysis located the transcription star

46 Primer extension analysis of RNA isolated from growing,

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

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

55 Primer extension analysis was performed with synthetic n

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

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

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

59 ranscription initiation were established via primer extension analysis.

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

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

62 nd viral replication inhibition, RT-specific primer extension and incorporation kinetics in vitro, an

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

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

65 selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), u

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

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

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

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

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

71 Primer extension and RNase protection assays mapped the

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

73 Primer extension and S1 nuclease protection assays were

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

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

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

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

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

79 2'-hydroxyl acylation with lithium ion-based primer extension, and identifies characteristic structur

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

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

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

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

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

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

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

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

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

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

90 Primer extension assay results demonstrated that both di

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

92 To do this, we developed a high-throughput primer extension assay that allows monitoring of the kin

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

94 o an agarose bead support enables repetitive primer extension assays for specific genomic DNA targets

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

96 Primer extension assays performed in the presence of tra

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

98 Interestingly, primer extension assays using human immunodeficiency vir

99 Primer extension assays were used to determine the trans

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

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

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

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

104 Using dot-blot and primer extension assays, we measured the susceptibility

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

106 Using in vitro primer extension assays, we show that both G4s and stabl

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

141 Primer extension demonstrated that the site of methylati

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

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

144 The sequence space accessed by primer extension dictates potential pathways to self-rep

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

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

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

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

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

150 Primer extension experiments revealed that the 5' ends o

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

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

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

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

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

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

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

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

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

160 Primer extension, in vitro transcription and in vivo exp

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

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

163 Non-enzymatic template-directed RNA primer extension is a model of the copying step in this

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

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

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

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

168 arabinonucleotide is incorporated, continued primer extension is strongly inhibited.

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

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

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

172 Primer extension mapping and ectopic expression in delet

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

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

175 We suggest that primer extension of 3'-phosphate-terminated RNA followed

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

177 migration mechanism, allowing non-enzymatic primer extension on a template that was previously occup

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

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

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

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

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

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

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

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

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

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

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

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

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

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

192 nonenzymatic template-directed generation of primer extension products long enough to encode active r

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

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

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

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

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

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

199 on assays using modified oligonucleotides or primer extension products.

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

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

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

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

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

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

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

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

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

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

210 Primer extension reactions were employed to label select

211 ly acts as a combination of dATP and dTTP in primer extension reactions, and the dGp5dC dimer as a co

212 es are also less efficiently incorporated in primer extension reactions, but the difference is more m

213 ucleotides in nonenzymatic template-directed primer extension reactions.

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

215 Single-nucleotide primer extensions result in successive displacements of

216 Primer extension results in loss of information at both

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

218 Here we present multiplexed primer extension sequencing (MPE-seq), an approach for t

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

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

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

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

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

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

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

226 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) and base-specific chemical prob

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

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

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

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

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

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

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

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

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

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

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

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

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

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

241 selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts compared

242 2'-Hydroxyl acylation analyzed by primer extension (SHAPE) probing revealed that the MTE i

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

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

245 selective 2'-hydroxyl acylation analysed by primer extension (SHAPE) to investigate intramolecular b

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

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

248 Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) we investigated miR-122 interac

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

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

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

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

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

254 5' rapid amplification of cDNA ends and primer extension show that different N-terminal protein

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

256 ic analysis of reverse transcription and RNA primer extension showed that hpol eta favors the additio

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

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

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

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

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

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

263 (selective 2'-hydroxyl acylation analyzed by primer extension) structure probing to viral RNA genomes

264 Primer extension studies confirmed the temperature-depen

265 Primer extension studies have shown that poliota is also

266 Additional primer extension studies identified a fifth csrA promote

267 Primer extension studies identified flhDC decay intermed

268 Primer extension studies using E. coli Pol IV, a transle

269 Primer extension studies using the Klenow fragment (exo(

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

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

272 Primer extension studies with purified pol eta have show

273 good substrate for KOD XL DNA polymerase in primer extension synthesis of modified DNA which exerted

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

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

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

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

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

279 phosphate, is shown to be less inhibitory to primer extension than pyrophosphate, the canonical bypro

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

281 Following primer extension, the reaction temperature is lowered su

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

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

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

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

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

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

288 s, while also illuminating the mechanisms of primer extension utilised by closely related Prim-Pols.

289 Primer extension was used for the synthesis of ONs with

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

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

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

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

294 We show that nonenzymatic primer extension with activated arabinonucleotides is mu

295 Primer extension with RNA from an RNase III null mutant

296 Finally, we demonstrate continued primer extension with strand displacement by employing a

297 This mechanism enables Prim-PolC to couple primer extension with template base dislocation, ensurin

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