ライフサイエンスコーパス: template strand

1 promoter opening and trapping of the DNA non-template strand.

2 ese pyrimidine analogues when present in the template strand.

3 y incorporated opposite 5-nitroindole in the template strand.

4 h in the absence and the presence of the non-template strand.

5 unit caused by steric repulsion with the DNA template strand.

6 ly around the extrahelical nucleotide on the template strand.

7 ize dGTP and dATP when tC and tCo are in the template strand.

8 NA through the complex and/or around the DNA template strand.

9 elted promoter through interactions with the template strand.

10 and while maintaining association with their template strand.

11 se H, which removes mRNA hybridized with the template strand.

12 cated in proximity to the 5' overhang of the template strand.

13 otides are incorporated in register with the template strand.

14 5' end and to lesions located in the intact template strand.

15 A that form opposite from DNA lesions on the template strand.

16 quences binding to 10 +/- 2 locations on the template strand.

17 hanism that involves misalignment of the DNA template strand.

18 base pair in which 7-deazaguanine was in the template strand.

19 t attributable to the presence of MeG on the template strand.

20 imer termini lack complementary bases in the template strand.

21 interact with phosphates 7 and 8 of the DNA template strand.

22 erted opposite the complementary base in the template strand.

23 lication forks encountering obstacles on the template strand.

24 se is more sensitive to substitutions in the template strand.

25 ives cross-linking to the +1 position on the template strand.

26 r strand than the equivalent position in the template strand.

27 hich RT disrupts the RNA helix to access the template strand.

28 initiation that provides RNAP access to the template strand.

29 rastrand d(GpTpG) cross-links located on the template strand.

30 e RNA transcript and re-anneals with the non-template strand.

31 -1 RT contains key contacts for the incoming template strand.

32 ymerase to isomerize and engage with the DNA template strand.

33 sponse to the presence or absence of the non-template strand.

34 owed full-length replication of the adducted template strand.

35 trand (<4%) with variable methylation on the template strand.

36 rpin may also help displace the RNA from the template strand.

37 n a bidirectional stripping of RecA from the template strand.

38 by a single enzyme moving along a stretched template strand.

39 dless of the corresponding nucleotide on the template strand.

40 P to clamp down on the downstream end of the template strand.

41 both photoproducts occurs exclusively on the template strand.

42 led by sequence-specific elements in the non-template strand.

43 ed with transcription, specifically with the template strand.

44 articular, where and when TLS occurs on each template strand.

45 cap guanine with an opposing cytosine in the template strand.

46 cceptor probe with high efficiency on an RNA template strand.

47 est at damaged sites to permit repair of the template strand.

48 one by the latter enzyme as it traverses the template strand.

49 er: when the G-rich strand serves as the non-template strand.

50 licase within TFIIH to generate the unpaired template strand.

51 forks that have encountered obstacles on the template strands.

52 might affect interactions with primer and/or template strands.

53 replication forks stalled at lesions in the template strands.

54 s inhibited by the presence of uracil in DNA template strands.

55 are brought together by hybridization to DNA template strands.

56 n DNA gaps with unrepaired UV lesions in the template strand act both as substrates for translesion p

57 A single-strand break in the non-template strand adjacent to the G-rich stretch dramatica

58 ase advances one nucleotide space on the DNA template strand after a correct nucleotide is incorporat

59 nature of the protein-DNA contacts with the template strand ahead of the primer terminus.

60 ynucleotide opposite an abasic lesion in the template strand, albeit slowly.

61 piral of ATPase domains that tracks only the template strand, allowing recognition of both RNA and DN

62 scription complex because removal of the non-template strand also disrupts transcription bubble reann

63 netics of polymerization with 8-oxodG in the template strand also revealed relatively low fidelity in

64 tite substrate containing a quencher-labeled template strand, an unlabeled primer and a fluorophore-l

65 mechanism in which APOBEC3G binds the viral template strand and blocks reverse transcriptase-catalys

66 polymerase) can efficiently bypass tC on the template strand and incorporate deoxyribose-triphosphate

67 n; the primer is elongated to the end of the template strand and is then further extended with a non-

68 This DNA is already methylated by Dam on the template strand and later becomes fully methylated; aber

69 Abasic substitutions in the non-template strand and promoter sequence changes were made

70 The assay uses a 5' end-labeled template strand and relies on an increase in the polariz

71 DNA polymerases predict contacts between the template strand and S769, F771, and R841, and our DNA bi

72 pposite nucleoside analogues inserted into a template strand and subsequent extension of the newly sy

73 that the distance between the 5' end of the template strand and the 5' end of the primer decreases b

74 DNA substrates labeled at the 5' end of the template strand and the 5' end of the primer with the fl

75 tions suggest that in the absence of the non-template strand and the lid, a new channel opens within

76 by controlling dNTP-induced movements of the template strand and the primer-terminal 3'-OH as the enz

77 d, where the RNA gets separated from the DNA template-strand and double-stranded upstream DNA is form

78 rather than (CAG)(43), comprised the leading template strand, and complete rather than partial deleti

79 interacts with the incoming nucleotide, the template strand, and key active-site residues from other

80 ynthesized DNA across discontinuities in the template strand, and nuclease activity removed a limited

81 og and other substitutions at -11 in the non-template strand, and sigma70 variants bearing amino acid

82 tly, a dGh/dIa site was synthesized in a DNA template strand, and standing start primer extension stu

83 outinely stall at lesions encountered on the template strand, and translesion DNA synthesis (TLS) is

84 ers and activated monomers can still bind to template strands, and template-directed primer extension

85 Although a template strand AP site impedes DNA synthesis, translesi

86 In this initial unstable "open" complex the template strand appears correctly positioned in the acti

87 G and benzo[c]phenanthrene-dA adducts in the template strand are durable roadblocks to POL elongation

88 ation sequencing technologies is that single template strands are amplified clonally onto a solid sur

89 n all sigma(70) family factors, with the non-template strand around position -4 relative to the trans

90 by incorporating three deoxycytidines in the template strand as the first 3 bases to be copied by the

91 o NAD+ does not depend on the -1 base of the template strand, as was suggested earlier.

92 ich is located in close proximity to the non-template strand at promoter position -18.

93 engage with the flipped out base of the non-template strand at the +1 site.

94 lowing the shortened primer to rebind to the template strand at the pol site and incorporate the corr

95 Pol lambda makes limited contacts with the template strand at the polymerase active site, and super

96 teraction of the RNAP sigma subunit with non-template strand bases of a conserved -10 element (consen

97 has been assumed that RecA binds to the DNA template strand being copied.

98 s that concern the regulated transfer of the template strand between a preinsertion site and an inser

99 Force exerted on the template strand biases the complexes toward the pre-tran

100 UV lesions in the template strand block the DNA replication machinery.

101 Unrepaired DNA lesions in the template strand block the replication fork.

102 are asymmetrically distributed: transcribed (template) strand breaks downstream of bp-14 (relative to

103 ype TFIIIB generated by certain transcribed (template) strand breaks near the transcriptional start s

104 Our data suggest that the non-template strand bulge is extruded into solvent in comple

105 omplexes containing a 5-mer RNA, whereas the template strand bulge remains within the template strand

106 not require new DNA synthesis on the unwound template strand but did require RNA primer synthesis by

107 e targeting vector can be displaced from the template strand by an active T7 phage RNA polymerase.

108 ere, we report a method for folding a custom template strand by binding individual staple sequences t

109 A gap in the non-template strand cannot be bypassed.

110 A nick on the template strand cannot be bypassed.

111 Promoter activity is greatest when the 'non-template' strand carries T and G at positions -15 and -1

112 f synthetic promoters in which the preferred template strand 'CC' initiation sequence was moved away

113 repairing mispairs comprised of loops on the template strand compared to loops on the primer strand.

114 transcription templates with RNA in the non-template strand confirm that the source of the ssDNA cof

115 The template strand contained a nine-nucleotide overhang and

116 If the template strand contains a short sequence of G residues,

117 critical event in directing and placing the template strand correctly in the T7 RNA polymerase activ

118 data suggest that the following base on the template strand dictates the addition of the mutated bas

119 ization and processivity on both DNA and RNA templates, strand displacement, ribonucleotide misincorp

120 ir of nucleotide on the non-transcribed (non-template) strand displayed a 5-10-fold higher level of a

121 ingle-stranded DNA-binding protein (SSB) for template strand DNA in the presence of DNA polymerase th

122 ilar to what was observed previously for the template strand downstream from the primer terminus.

123 tly blocked by bulky chemical lesions on the template strand during DNA replication.

124 to the newly synthesized strand and not the template strand during DNA synthesis.

125 of Loop1 and to juxtapose the discontinuous template strand during NHEJ of incompatible ends.

126 spectroscopy reveals a reorganization of the template strand during this process, and molecular model

127 ed to initiate DNA synthesis on the parental template strands during DNA replication.

128 elements are capable of targeting one of the template strands during DNA replication.

129 bind to and unbind from transiently exposed template strands during DNA synthesis.

130 rescent reporter 2-aminopurine (2-AP) on the template strand, either at the templating position oppos

131 We report that circularizing a DNA template strand encoding a pre-microRNA hairpin mimic ca

132 However, the DNase I footprint on the non-template strand extends from the +1 to the +9 position f

133 Although the single-stranded template strand extends in opposite directions from 3' a

134 tes DNA polymerase I to successfully inhibit template strand extension.

135 erall, the data are most consistent with the template strand following a path over the fingers subdom

136 his protocol does not require synthesis of a template strand for adenylation.

137 cerevisiae, sgRNA/dCas9 targeting to the non-template strand for antisense transcription results in a

138 evealed a preference for a purine in the non-template strand for tsp in both promoters.

139 ascent RNA intermittent reannealing with the template strand, for prolonged access of AID.

140 The ORNs bind to the DNA template strand, forming an antiparallel heteroduplex in

141 network of Pol II interactions with the non-template strand forms a rigid domain with the trigger lo

142 stall replication on encountering uracil in template strands, four bases ahead of the primer-templat

143 into the center of the clamp and exit of the template strand from the complex.

144 of an adenine (A) opposite the 8-oxoG on the template strand, generating an A:8-oxoG mispair.

145 )-EtdT or O(4)-EtdT at a defined site in the template strand, herein we examined the effects of these

146 Methylation on the template strand, however, does not increase RFX1 complex

147 own that Afu Pol-D activity is slowed by the template strand hypoxanthine, extending previous results

148 e61 residue, which is thought to contact the template strand immediately ahead of the dNTP-binding si

149 ow DNA polymerases to overcome breaks in the template strand in an error-prone manner.

150 The critical role of the template strand in approximating the reactive 3'-OH and

151 wever, whereas I-HmuI and I-HmuII cleave the template strand in exon 2, I-TwoI cleaves the coding str

152 ster" role of the adenine base at -11 of the template strand in overall base unpairing.

153 e center-proximal contacts stabilize the DNA template strand in the active center cleft and/or positi

154 helix-hairpin-helix motif interacts with the template strand in the downstream duplex eight base-pair

155 be double-stranded (ds) to function, the non-template strand in the initiation region is dispensable,

156 e-230 in limiting the internalization of the template strand in the polymerization active site is dis

157 that interact with the ssDNA overhang of the template strand in the pre-polymerase ternary complex, w

158 on', whereby transferring information from a template strand in the presence of its complementary str

159 we found that removal of nucleosides on the template strand in the region from -13 to at least +8 re

160 for NPH I is the upstream portion of the non-template strand in the transcription bubble.

161 facilitates DNA melting by trapping the non-template strand in the unwound conformation.

162 ) or the 5th/6th nucleotide (Arg(47)) of the template strand in the upstream duplex portion counting

163 leotide and closed protein conformation, the template strand in the vicinity of the active site has s

164 left and then separating the nontemplate and template strands in the region surrounding the start sit

165 Complementarity between the template and non-template strands in this region is also required for NPH

166 Probes placed at positions +1 and +2 of the template strand indicate that the 5' end of the RNA rema

167 anganate footprinting on the nontemplate and template strands indicates that when polymerase is in a

168 alls upon encountering an abasic site in the template strand, indicating that, like many replicative

169 downstream template base, on a "looped out" template strand instead of mispairing opposite a next av

170 Loss of the template strand interaction, Q849A, resulted in the inab

171 Our results indicate that the primer and template strand interactions of the Klenow polymerase wi

172 rand interactions, while variant Q849A lacks template strand interactions.

173 and play a role in directing the melted DNA template strand into the RNA polymerase active site.

174 protein/DNA interactions that direct the DNA template strand into the RNAP active site.

175 To convert template strands into a compatible state for attachment

176 The entire template strand is at the bend angle Theta(TP) = 85 +/-

177 t intercalate into the growing duplex as the template strand is copied into XNA.

178 ities: it acts as a pseudo-template when the template strand is discontinuous or unavailable, whilst

179 ith DNA reveal that the 5'-trajectory of the template strand is dramatically altered as it exits the

180 ires that the promoter DNA is melted and the template strand is loaded into the active site of the RN

181 NAP has been displaced until a lesion in the template strand is located.

182 This extent of protection on the non-template strand is similar to what was observed previous

183 se enzymes catalyze DNA replication when the template strand is subjected to a stretching force.

184 e level of gene repair is higher than if the template strand is targeted.

185 ncement of gene repair observed when the non-template strand is targeted.

186 We find that the coding base on the template strand is unperturbed by the binding of incorre

187 stable duplex formation between product and template strands is not required for template-dependent

188 ed G residue is present at the 3'-end of the template strand, it is copied regiospecifically in the p

189 loop formation by the nascent transcript and template strand, leading to suppression of transcription

190 In the first cycle, misalignment of the template strand leads to incorporation of a nucleotide t

191 nd Y-family DNA polymerases in response to a template strand lesion.

192 polymerases can extend primer strands across template strand lesions that stall replicative polymeras

193 oops, while maintaining efficient repair of "template strand" loops.

194 specifically discriminates against tC in the template strand may suggest that DinB discriminates agai

195 predominantly deletion errors as a result of template-strand misalignment.

196 acts the DNA primer strand and positions the template strand near the RNase H active site, influencin

197 stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription

198 interactions with individual -10 element non-template strand nucleotides and indicate that recognitio

199 RecA filaments assembled in cis on a damaged template strand obstructing translesion DNA synthesis de

200 nopurine (2AP) as a fluorescent probe in the template strand of a 13/20mer primer/template (D) to det

201 pdC substitution within the template strand of a DNA duplex does not appear to signi

202 The cleavage of Gh in the template strand of a replication or transcription bubble

203 es the removal of noncoding lesions from the template strand of active genes, and hence contributes t

204 stranded DNA; it binds preferentially to the template strand of active mtDNA ori sequences in vitro;

205 l (NGN) domain of Spt5 that contacts the non-template strand of DNA both upstream of RNAPII and in th

206 d that residue rtV173 is located beneath the template strand of HBV nucleic acid near the active site

207 nd various degrees of similarity for the non-template strand of introns in the human genome.

208 Uniquely, the nvRNAP recognizes the template strand of its promoters and is capable of speci

209 e polymerization either by repositioning the template strand of nucleic acid or by affecting other re

210 is the highly conserved -11A base in the non-template strand of the -10 promoter region.

211 at interaction of final sigma70 with the non-template strand of the anti-ITS is required for function

212 he transcript to slip back and pair with the template strand of the DNA at a new register before tran

213 n the nascent RNA remains base-paired to the template strand of the DNA before it is displaced and th

214 strand template but not appreciably with the template strand of the DNA stem greater than two nucleot

215 1 of pol beta lies in close proximity to the template strand of the DNA.

216 ntially photocross-linked to the 5' extended template strand of the dsDNA template-primer substrate.

217 detected CSR-associated ssDNA breaks in the template strand of the H chain alpha switch region, the

218 r, interaction of final sigma70 with the non-template strand of the initial transcribed sequence (ITS

219 mouse brain and is transcribed from the non-template strand of the Nos1 locus.

220 0) RNA polymerase (RNAP) holoenzyme with non-template strand of the open promoter complex transcripti

221 at resolution of G4 structures on the G-rich template strand of the telomere requires some overlappin

222 ohomology pairing between the primer and the template strands of DNA.

223 Surprisingly, the template and non-template strands of the DNA at the upstream edge of the

224 ion was defined for both the nontemplate and template strands of the promoter.

225 r separation of the nascent RNA from the DNA template strand or transcription termination.

226 excision of G(O) might misdirect MMR to the template strand, our findings suggest that OGG1 activity

227 s, together with a molecular modeling of the template strand overhang in Klenow fragment, indicated i

228 promoter, Fe(2+) cleavage assays to monitor template strand positions near the active-site, and Bpa

229 L may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting m

230 While the template strand promotes destabilization via a weak olig

231 The mechanism of this unique "template-strand proof-reading" has been studied using eq

232 lts obtained with a force applied to the DNA template strand provide insights into the effect of the

233 tion via a weak oligo(rU:dA) hybrid, the non-template strand provides distinct sequence-specific dest

234 dividual positions during one pass along the template strand ranged from 10% to 24.5% without optimiz

235 We report that a G-rich sequence in the non-template strand reduces the yield of T7 RNA polymerase t

236 her than the PCR, enriches for fully ligated template strands, reducing the incidence of duplicate se

237 ly down to 88%, whereas crRNAs targeting the template strand repress expression down to 8%.

238 luding likely specific interactions with the template-strand residues of the -10 element.

239 Breaks in the non-template strand result in much weaker blockage signals e

240 he RNAP binding affinity to template and non-template strand segments of the transcription bubble dow

241 am edge of the RNA-DNA hybrid, where the DNA template strand separates from the RNA transcript and re

242 ements show that Y261 plays a role in primer-template strand separation.

243 We have previously developed a novel DNA template strand sequencing technique, called Strand-seq,

244 s new probe at specific positions in the non-template strand shows clearly that the elongation bubble

245 C37 is required for this function of the non-template strand signal.

246 trand break and displace the downstream non- template strand simultaneously with extension of the pri

247 her show that interactions between sigma and template-strand single-stranded DNA (ssDNA) preorganize

248 bda) generates single-base deletions through template-strand slippage within short repetitive DNA reg

249 as frameshift mutations) resulting from DNA template-strand slippage.

250 ling suggested that N265D leads to a loss of template strand-specific hydrogen bonding, indicating th

251 rand single-stranded DNA (ssDNA) preorganize template-strand ssDNA to engage the RNAP active center.

252 g associated frameshift error rates based on template-strand stability, the close connection between

253 mote DNA lesion bypass in vitro through the 'template-strand switch' mechanism.

254 Detection of template strand switching in the middle of an inverted r

255 ster strands, possibly by means of transient template strand switching or copy choice.

256 26 viruses recovered, 16 showed evidence of template strand switching, from minus-strand genome DNA

257 is not known but could perhaps result from a template-strand-switching, or copy choice, process.

258 At promoters in which the template strand (T strand) is intact, initiation is dire

259 stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register a

260 AG, which occurs much more frequently on the template strand than on the putatively displaced nontemp

261 single-strand loops on either the primer or template strand that are subsequently processed by the M

262 preferentially removes DNA lesions from the template strand that block translocation of RNA polymera

263 is imputed to stack on the nucleobase of the template strand that includes the 1st bp of the downstre

264 hates, for example, at the start site of the template strand that, when ethylated, perturb the bindin

265 On the template strand, the DNase I downstream boundary of this

266 ite either 5- or 6-nitrobenzimidazole in the template strand, the enzymes did incorporate the analogu

267 dentified during translocation of single DNA template strands through a modified Mycobacterium smegma

268 s from the displaced RNA re-annealing to the template strand thus forcing the primer terminus to beco

269 ructure, and (b) Arg(841) interacts with the template strand to achieve the optimal strand separation

270 ring DNA synthesis, and bypasses them on the template strand to cause deletion.

271 beit at reduced efficiency of 7%, on the non-template strand to continue rolling circle DNA synthesis

272 DNA polymerases use an uninterrupted template strand to direct synthesis of DNA.

273 , and 3) insert extra bases in the primer or template strands to mimic frameshift intermediates.

274 imer terminus or in the coding region of the template strand, to monitor and interpret conformational

275 The polymerase tracking along the template strand traps the C(6) to prevent lock formation

276 the template strand bulge remains within the template strand tunnel, exerting stress on interactions

277 trate here that altering the topology of the template strand two nucleotides ahead of the catalytic c

278 ubble (-11 to +2), but unusual reactivity of template strand upstream cytosines (-12, -14, and -15) o

279 Pol D appears to interact with template strand uracil irrespective of its distance ahea

280 eal family B DNA polymerases bind tightly to template-strand uracil and stall replication on encounte

281 n a specialised pocket that binds tightly to template-strand uracil, causing the stalling of DNA repl

282 ase stalled at a noncoding lesion in the DNA template strand, uses the energy from ATP hydrolysis to

283 ectly to repeat sequences; targeting the non-template strand was more effective.

284 of incorporation of 8-oxo-dG with dA in the template strand was reduced 500-fold.

285 The promoter and exon 1 regions of the template strand were completely demethylated, whereas re

286 Five different types of template strands were used: homogeneous (1) RNA or (2) D

287 atoms from the n-2 and n-3 positions of the template strand, where n is the template base that would

288 vailable purine 2-3 bp downstream on the non-template strand whereas deleting a single bp at position

289 also forms a crystal contact with the ssDNA template strand, which binds into the protein-binding po

290 It may interact with the template strand, which sets the location of the transcri

291 A induced the formation of a CAG loop in the template strand, which was skipped over by DNA polymeras

292 resence or absence of discontinuities in the template strand, which will in turn determine the final

293 adduct is oriented toward the 5'-end of the template strand while the (-)-trans adduct lies toward t

294 rate any dNMP or rNMP opposite oxo-dG in the template strand with manganese as cofactor, with a kinet

295 This binding occurs via the non-template strand with the identity of the two conserved j

296 of the melted dsDNA promoter also align the template strand within the active site for efficient RNA

297 o TFIIF was dependent on the sequence of the template strand within the single-stranded bubble.

298 n on templates that lack portions of the non-template strand within the transcription bubble showed t

299 A cofactor is obtained from the unpaired non-template strand within the transcription bubble.

300 placement of the 3' end of the transcribed (template) strand within the confines of the transcriptio