ライフサイエンスコーパス: duplex

1 ion of other secondary structures (hairpin-->duplex).

2 total) on eleven RNA sequences (hairpins and duplexes).

3 s inhibited by the stability of the template duplex.

4 petition with the corresponding Watson-Crick duplex.

5 en sRNAs and recycles Hfq from the sRNA-mRNA duplex.

6 of an apparent role in the formation of the duplex.

7 s additionally destabilizing the protospacer duplex.

8 when an internal P*U replaces A-U in an RNA duplex.

9 e lower than that of the corresponding AA.DD duplex.

10 e (>300 nt) within a longer (545 bp or 3 kb) duplex.

11 ntarity, between all sequence positions in a duplex.

12 ine-dependent binding of two CodY dimers per duplex.

13 ncreased numbers of 2-5-linkages in the same duplex.

14 true whether the DNA was single-stranded or duplex.

15 residue embedded within the resulting nicked duplex.

16 emove damaged bases that are embedded in the duplex.

17 and dynamics of a UB incorporated into a DNA duplex.

18 (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex.

19 in multiple registers to extend the helical duplex.

20 of the dynamics of the most prototypical DNA duplex.

21 red, with a focus on contrasting CAG and GAC duplexes.

22 rmation of Im-Ag(I) -Im complexes within the duplexes.

23 able than some of the sequence-complementary duplexes.

24 in the overall structure of the RNA and DNA duplexes.

25 permits hiCLIP to unambiguously identify the duplexes.

26 ith stringent specificity for RNA:DNA hybrid duplexes.

27 stimulates its helicase activity on DNA fork duplexes.

28 y form more stable complexes than mismatched duplexes.

29 mimethylated (HM) and nonmethylated (NM) DNA duplexes.

30 sent the first crystal structures of RNA-PNA duplexes.

31 f unusual, long-range mammalian-specific RNA duplexes.

32 the structural and dynamic properties of two duplexes.

33 intermolecular and long-range intramolecular duplexes.

34 icient RNA helicase, and does not unwind DNA duplexes.

35 nscriptome identifies the exact locations of duplexes.

36 ow that ADARs also react with DNA/RNA hybrid duplexes.

37 ic acid analogue, as a modification of siRNA duplexes.

38 dazoles showed varied stabilization of B-DNA duplex (1.2-23.4 degrees C), and cytotoxicity studies sh

39 ces in the viral genome predicted to contain duplexes, a property that may facilitate both virion inc

40 with the most stable sequence-complementary duplex, AAA.DDD, so in mixtures that contain all eight s

41 one distortions, with a sharp bending of the duplex accompanied by conformational changes in the Ni(I

42 ng two and six 2-5-linkages, showing how RNA duplexes adjust the structures to accommodate these non-

43 he preference for 3'-first pore entry of the duplex and accelerating duplex unzipping, all manifestat

44 systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double

45 T in complex with an RNA template-DNA primer duplex and incoming deoxynucleotide triphosphate (dNTP)

46 tes marginally affected the structure of the duplex and its affinity for SRA at positions where they

47 ction is compatible with a 6-TG-modified DNA duplex and provides a straightforward method by which to

48 ocessivity, determine how they contribute to duplex and single-stranded DNA handling, and test the ce

49 he effective cross-sectional diameter of DNA duplex and the thickness of DNA shell.

50 h that specific receptor forces denature the duplex and thus expose a blocked primer.

51 he corresponding mesophases of the canonical duplex and triplex DNA analogues.

52 trate proof-of-principle applications of the duplex and triplex tags for quantitative proteomics usin

53 at APOBEC3H forms a dimer around a short RNA duplex and, despite the bound RNA, has potent cytidine d

54 ng a commercial antibody specific to RNA/DNA duplexes and a bacterial protein conjugated with a horse

55 ly used to reproduce global structure of DNA duplexes and fine sequence-dependent details.

56 containing duplex, three T-HgII-T containing duplexes and one native duplex containing T-T pair witho

57 topoisomerase I inhibition, binding to B-DNA duplex, and antibacterial activity has been evaluated.

58 rs at high salt concentration, and the inter-duplex angle (IDA) between arms.

59 d "helicases," their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent

60 As a result, some of the mismatch duplexes are more stable than some of the sequence-compl

61 scent dyes that intercalate into the growing duplex as the template strand is copied into XNA.

62 o WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic sign

63 ably, the label is positioned within the DNA duplex, as opposed to outside the helical perimeter, for

64 her than as a hole trap when inserted into a duplex, as previously postulated.

65 and 3 GalNAc conjugated single stranded and duplexed ASOs were studied.

66 of DNA as the remodeler ATPase perturbs the duplex at SHL2.

67 tes is quantified by counting individual DNA duplexes at low target concentrations, and those results

68 imental observation on crystal rotation in a duplex (austenite + ferrite) steel induced by the electr

69 laminin-alpha5 (found in both layers of the duplex BM) and perlecan were lost entirely, with no rest

70 toring these interactions by identifying RNA duplexes bound by a specific RBP.

71 data can directly identify all types of RNA duplexes bound by RBPs, including those that are challen

72 point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (

73 sponding hetero-sequence AD 2-mers also form duplexes, but the observed self-association constants ar

74 Here we demonstrate that in vivo sRNA-mRNA duplexes can be recovered using UV-crosslinking, ligatio

75 tacking interactions between the ends of DNA duplexes, cholesterol-mediated DNA anchoring, and electr

76 d lower stability of the trans-T(p) template duplex, compared to trans-T(m).

77 ile ZF8 and ZF9 span the backbone of the DNA duplex, conferring no sequence specificity but adding to

78 molecular conductance was also measured for duplexes connected to the electrode through two differen

79 st kinetics of SRA binding and sliding to NM duplexes, consistent with its reader role.

80 However, the most stable mismatch duplexes contain DDD and compete with the most stable se

81 nce increase in the presence of a 27-mer DNA duplex containing a central CC mismatch.

82 However, an RNA duplex containing a central I*U pair or central Psi*A pa

83 stable, respectively, than the corresponding duplex containing an A-U pair.

84 esolution crystal structures of the same RNA duplex containing four and eight 2-5-linkages at differe

85 Van't Hoff plots on a duplex containing one modification (10:15) displayed a c

86 T-HgII-T containing duplexes and one native duplex containing T-T pair without HgII.

87 Fluorescence titrations with the 27-mer duplex containing the CC mismatch reveal a DNA binding a

88 rted two crystal structures of a decamer RNA duplex containing two and six 2-5-linkages, showing how

89 -hemolysin is used to capture individual DNA duplexes containing a single cytosine-cytosine mismatch.

90 III and DinG, to bind preferentially to DNA duplexes containing a single site of DNA damage (here a

91 hermodynamic parameters were compared to RNA duplexes containing A-U pairs in order to determine the

92 cleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been e

93 Thermodynamic studies with RNA duplexes containing non-standard nucleotides, whether in

94 ical melting studies were performed with RNA duplexes containing P*U pairs adjacent to different near

95 dulating current signatures are observed for duplexes containing the CC and CA mismatches when the mi

96 and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation

97 d DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq).

98 The duplex destabilization is mediated, in part, by Cas9/gui

99 As the temperature is increased, duplexes dissociate through a path in which the terminal

100 emplated reaction turnover is limited by the duplex dissociation kinetics beyond probes longer than a

101 al perimeter, for an accurate measurement of duplex distance.

102 We find that duplex distortion induced by a crosslink plays a crucial

103 (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of protein

104 a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation an

105 eukaryotic CMG helicase partially encircles duplex DNA at a forked junction and is stopped by a bloc

106 uggest that the interactions unfavorable for duplex DNA binding promote DNA bending in the PAM-proxim

107 ve hexameric helicases are thought to unwind duplex DNA by steric exclusion (SE) where one DNA strand

108 ine-catalyzed strand cleavage at Ap sites in duplex DNA can react with adenine residues on the opposi

109 Duplex DNA cannot access the Mre11 active site in the AT

110 ntisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and

111 ent cryoEM structure of yeast CMG shows that duplex DNA enters the helicase and unwinding occurs in t

112 requirements for the replication of the AAV2 duplex DNA genome and the production of progeny virions

113 Transfection of HEK293 cells with the duplex DNA genome of HBoV1 induces hallmarks of DDR, inc

114 h the Watson and Crick strands, constraining duplex DNA in a bent configuration.

115 G4s can coexist with canonical duplex DNA in the human genome and have been suggested t

116 To unwind duplex DNA in vitro, UvrD needs to be activated either b

117 The opposite strand polarity of duplex DNA necessitates that the leading strand is repli

118 ative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric

119 plementary ssDNA to generate highly branched duplex DNA structures.

120 s, triplex binding inhibits the formation of duplex DNA templating.

121 nature of the 3'-tail and the length of the duplex DNA to be unwound, this activity is sufficiently

122 and hydrolysis to separating the strands of duplex DNA, creating flaps.

123 lly to the minor groove of (CCG)n repeats in duplex DNA, with unique fluorescence features that may s

124 eobase pairs on the structural parameters of duplex DNA.

125 is an inactive double hexamer that encircles duplex DNA.

126 in tracts of four or more ribonucleotides in duplex DNA.

127 We assembled a G4DNA structure flanked by duplex DNA.

128 ur methyl groups symmetrically positioned in duplex DNA.

129 DNA (ssDNA) and facilitates its annealing to duplex DNA.

130 charged concave surface perfectly shaped for duplex DNA.

131 nd catalyzes strand invasion with homologous duplex DNA.

132 s DpnI to cleave methylated adenine sites in duplex DNA.

133 irtually unquenched fluorescence emission in duplex DNA.

134 -alkylthymine adducts in single-stranded and duplex DNAs.

135 all eight sequences, sequence-complementary duplexes dominate.

136 e-stranded (ss) 5'-flaps one nucleotide into duplex (ds) DNA.

137 th respect to symmetrical 1 M KCl, while the duplex dwell time in the nanopore remained acceptable fo

138 rotein that can bind and sequester short RNA duplex effectively and selectively, was modified success

139 t progressively favor tile-tile packing over duplex-end pi-stacking.

140 g, they can interact by pi-stacking of their duplex ends.

141 In these simulations, the -containing DNA duplex exhibits a significantly wider major groove and g

142 DDX3X separates longer RNA duplexes faster than Ded1p and is less potent than Ded1p

143 Incorporation of the duplex fluorescent output [green and red fluorescence pr

144 e-specific Cu(2+) binding motif within a DNA duplex for distance measurements by ESR spectroscopy is

145 chroism, we find that the tC(O)-modified RNA duplexes form regular A-form helices and in UV-melting e

146 The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes in

147 one showed using spectroscopic methods that duplex formation at pH 4.5 largely starts with rA7 and b

148 For all seven architectures, duplex formation is observed for homo-sequence 2-mers (A

149 This turn-on response to duplex formation is the greatest of any reported nucleos

150 hylamino-tC (8-DEA-tC), that responds to DNA duplex formation with up to a 20-fold increase in fluore

151 estigate the sequence dependence of D in DNA duplex formation, we measured individual transition path

152 ation molecules that show sequence-selective duplex formation.

153 at markedly increase their fluorescence upon duplex formation.

154 observed, and folding does not compete with duplex formation.

155 A duplexed, functional multiaddition high throughput scree

156 ed to facilitate the replication of the AAV2 duplex genome and for AAV2 infection.

157 ed that fully support the replication of the duplex genome of this virus and allow the production of

158 ficient for viral DNA replication of an AAV2 duplex genome.

159 scent sense strand PNA probe binding to RNAi duplex guide strands was coupled with anion exchange hig

160 sensors that involve diverse DNA structures (duplex, hairpin, G-quadruplex and single-stranded), liga

161 and functional impact on RNA:RNA and RNA:DNA duplexes, hairpins and pseudoknots.

162 yeast XPA (Rad14) with lesion-containing DNA duplexes have provided valuable insights, but the DNA su

163 c kidney HEK293 cells, the transfection of a duplex HBoV1 genome initiates viral DNA replication and

164 The duplex HBoV1 genome replicates in HEK293 cells and produ

165 t the local conformational dynamics of a DNA duplex in a confined environment.

166 This system forms a highly stable molecular duplex in a nonpolar solvent (Kdim > 1.9 x 10(7) M(-1) i

167 NA probes, with the unzipping of a miRNA-DNA duplex in the nanopore recorded as a resistive current p

168 e were able to recover base-paired sRNA-mRNA duplexes in association with RNase E, allowing proximity

169 abeled DNA in the presence of competitor DNA duplexes, including Egr-1 decoys.

170 d sequences each of the two strands of a DNA duplex independently and only scores mutations that are

171 A mismatch in a d(GAC)6.d(GAC)6 duplex induces negative supercoiling, leading to a local

172 hotophysical properties that is dependent on duplex integrity and the electronic structure of the ana

173 ecules at opposite ends of a seven-base-pair duplex interact extensively with both RNA strands, but f

174 artial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunop

175 osed to form kissing hairpin and/or extended duplex intermolecular contacts.

176 nome maturation) and 2) translocation of the duplex into a procapsid (genome packaging).

177 Here, we transfected uracil-containing DNA duplexes into human cells and measured the probability t

178 As in longer DNA duplexes, intrastrand electron transfer induced by UV ex

179 duplex formation and lowers the stability of duplexes involving these sequences.

180 or these systems, the stability of the AD.AD duplex is 1-2 orders of magnitude lower than that of the

181 -mRNA and the U1 snRNP, in which a short RNA duplex is established between the 5' splice site of a pr

182 ybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript.

183 Venous duplex is recommended for the diagnosis of CRT.

184 CA mismatches when the mismatch site in the duplex is situated in proximity to the latch constrictio

185 The average fluorescence lifetime in RNA duplexes is 4.3 ns and generally two lifetimes are requi

186 tions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugate

187 UV-melting experiments the stability of the duplexes is only slightly higher than that of the corres

188 g proteins at replication forks and other ss duplex junctions.

189 cRNAs act as rheostats within lncRNA-TF gene duplex loci that buffer TF expression, thereby maintaini

190 DNA, we find a high quantum yield inside RNA duplexes (<PhiF> = 0.22) that is virtually unaffected by

191 The duplex mdDiLeu reagents were custom-synthesized with a m

192 sing of low alloy medium-carbon steel with a duplex microstructure composed of nanoscale spheroidized

193 Finally, these conjugate duplexes modified with GNA were capable of maintaining i

194 l denaturation, prevents renaturation of the duplex nucleic acids (dsDNA/RNA).

195 determination of the relative proportion of duplex nucleic acids in mixed ds/ss nucleic acid solutio

196 NA ligase (DraRnl) seals 3-OH/5-PO4 nicks in duplex nucleic acids in which the 3-OH nick terminus con

197 uggest that spermine binds externally to the duplex, offering opportunities for intermolecular intera

198 interact via intermolecular H-bonds to form duplexes or fold via intramolecular H-bonds.

199 r substrates with unpaired regions 3' to the duplex over those with 5' unpaired regions.

200 n adaptor that links the two arms of the RNA duplex permits hiCLIP to unambiguously identify the dupl

201 Mechanically labile DNA duplexes presenting ligands are surface immobilized such

202 directly for experimental NMR observables on duplexes previously not solved, and also to assess the r

203 m the use of deuterated buffer show that the duplex protects 8-DEA-tC against quenching by excited st

204 Integration required at least partially duplex protospacers with free 3'-OH groups, and leader-p

205 is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography

206 , and endogenous reference genes in a single duplexed reaction containing thousands of droplets.

207 lb NPs, thus enabling the probe:target miRNA duplex recognition and binding.

208 targets critical residues essential for PAM duplex recognition, as well as blocks target DNA access

209 bases to link the quadruplex motif with the duplex region.

210 oss the genome, but how these lncRNA-TF gene duplexes regulate tissue development and homeostasis is

211 By using the duplex replicative form of the HBoV1 genome in human emb

212 This disruption in the NANCI-Nkx2.1 gene duplex results in a defective perinatal innate immune re

213 et DNA, formation of the anionic DNA-acpcPNA duplex results in dispersion of the AgNPs as a result of

214 several questions regarding the evolution of duplex retina and supports the hypothesis that, in mamma

215 The duplex retina evolved in jawless vertebrates with the ad

216 mation of rod-specific proteins produced the duplex retina, which has remained remarkably constant in

217 ution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A*T H

218 tudy the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predic

219 ive recycling, we show that all-3',5'-linked duplex RNA can emerge from a backbone heterogeneous mixt

220 Although DDX43 was active on duplex RNA regardless of the orientation of the single-s

221 of the human ADAR2 deaminase domain bound to duplex RNA revealing a protein loop that binds the RNA o

222 Duplex RNA segments have A-form C3' endo sugar puckers b

223 iting reactions with a known requirement for duplex RNA.

224 We demonstrate that introducing anti-GAA duplex RNAs or single-stranded locked nucleic acids into

225 ruplex (G4) structures but little binding to duplex RNAs.

226 ody and permitted NF-kappaB binding to a DNA duplex sequence corresponding to its binding site in the

227 Our aim was to determine whether duplex sequencing could detect extremely rare cancer cel

228 We used duplex sequencing to analyze TP53 mutations in 17 perito

229 dicting disease development, highly accurate duplex sequencing was used to monitor acquisition of hig

230 anges were associated with mC flipping in HM duplexes, showing the outstanding sensitivity of both nu

231 own by SNAs composed of MGMT-targeting siRNA duplexes (siMGMT-SNAs).

232 more stable in complete medium than standard duplex siRNA.

233 NAs was associated with sequestration of the duplex siRNAs by the 2b protein but not with changes in

234 In the presence of an enzyme called duplex specific nuclease (DSN), however, a fraction of t

235 nanomaterials, redox mediators, p19 protein, duplex specific nucleases (DSN) and redox cycling.

236 resolution optical tweezers to probe how DNA-duplex stability affects replication by bacteriophage T7

237 adorned with valuable features such as high duplex stability and a built-in fluorophore, which would

238 e, we examined the effects of hm(5)rC on RNA duplex stability and its impact on structure formation u

239 es on photochemistry of the switches and DNA duplex stability, and is moving towards applications in

240 eriments revealed that hm(5)rC increases RNA duplex stability.

241 w stability of the fully-paired oligo-target duplex, stable probe self-folding, G-rich content, inclu

242 The duplex stem penetrates into the central channel of the N

243 require local dissociation (melting) of the duplex strands.

244 - or (R)-GNA nucleotide incorporation on RNA duplex structure by determining three individual crystal

245 I407M, and V408A, are located within the RNA duplex structure required for RNA editing.

246 lized dye environment upon the free probe to duplex structure transition.

247 mation that has little impact on the overall duplex structure, while the (R)-nucleotide disrupts the

248 tegrity in human islets, which have a unique duplex structure.

249 re compared with those for the corresponding duplex structures having G-C base pairs in place of the

250 wer but more efficient for the quadruplex vs duplex structures.

251 C flipping was found to be much slower in HM duplexes, substantially increasing the lifetime of CpG-b

252 in translesion synthesis, and length of the duplex surrounding an unhooked ICL critically affects po

253 The duplex SVM model enables the prediction of non-canonical

254 parted mass defect to up to 90.6 mDa for the duplex tags and effectively reducing the resolving power

255 and passenger strands of a GalNAc conjugate duplex targeting mouse transthyretin (TTR) indicated tha

256 ciated noncoding intergenic RNA)-Nkx2.1 gene duplex that is essential for buffering Nkx2.1 expression

257 ot require long 3' overhangs, and it unwinds duplexes that are flanked by only a few nucleotides, as

258 not discriminate between nonspecific DNA and duplexes that contain the packaging initiation sequence,

259 Mismatched duplexes that have an excess of H-bond donors are stabil

260 in the overall conductance for a particular duplex, the differences in the electrical conductance wi

261 Although cohesin functions to tether DNA duplexes, the contribution of its individual domains to

262 red interactions with the PAM-containing DNA duplexes, thereby achieving the relaxed PAM recognition.

263 one first-time reported C-HgII-T containing duplex, three T-HgII-T containing duplexes and one nativ

264 iRNA molecules end to end, forming a DNA-RNA duplex through a complementary interaction with high aff

265 The AP enables melting of the duplex to unmask the PQS, adopting a G-quadruplex fold i

266 that SF3b1 functions to stabilize weak U2/BS duplexes to drive spliceosome assembly and splicing.

267 le dG.dT and rG.rU mismatches in DNA and RNA duplexes transiently form tautomeric and anionic species

268 d flow (CBF) was measured using colour-coded duplex ultrasonography at the internal carotid (ICA) and

269 Of 826 (80.9%) subjects who underwent both duplex ultrasound and x-ray, 822 (99.5%) were interpreta

270 tients underwent a screening lower-extremity duplex ultrasound approximately 1 month after arthroplas

271 Duplex ultrasound patency was 84.6% for DA+DCB, 81.3% fo

272 t vasculature compared to 2-dimensional (2D) Duplex ultrasound.

273 hese enzyme complexes are highly processive, duplex unwinding and degrading machines that require tig

274 ing to eIF4G strongly stimulates the rate of duplex unwinding by eIF4A on the IRES.

275 quently, DnaA filaments assemble and promote duplex unwinding by engaging and stretching a single DNA

276 ng truncation of eIF4G that stimulates eIF4A duplex unwinding independently of eIF4E.

277 e recombination in vivo, whereas unregulated duplex unwinding is detrimental for recombination precis

278 hich both strands enter the helicase and the duplex unwinding point is internal, followed by exclusio

279 Using biochemical assays for RNA binding and duplex unwinding, we show that JFH-1 NS3 binds RNA much

280 e ring-shaped hexamers that encircle DNA for duplex unwinding.

281 st pore entry of the duplex and accelerating duplex unzipping, all manifestations of an enhanced elec

282 ecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA libra

283 e of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recogn

284 rized association and only releases annealed duplex when bound strands are fully complementary.

285 lting analysis of GNA-C and GNA-G containing duplexes where it was demonstrated that a higher thermal

286 to the synthesis of double spin-labeled DNA duplexes, where 2'-alkynylnucleosides are incorporated a

287 ncharacterized conformational states of this duplex which can explain biologically relevant conformat

288 a single base mismatch in the growing primer duplex, which attenuates DNA charge transport, inhibits

289 an ATP-dependent unwinding of the U4/U6 RNA duplex, which is a critical step for spliceosomal activa

290 ility chimera that contains a functional RNA duplex with paired silencing and carrier sequences stabi

291 ript that have the ability to form a perfect duplex with position 2-6 (seed sequence) of each microRN

292 from experiments using AGO2-loaded miRNAs in duplex with target mRNAs indicate that UPF1 can dissocia

293 ance value, 0.06G0, was measured for aeg-PNA duplexes with a base stack linker.

294 d DNA substrate to generate two unhooked DNA duplexes with a nick, NEIL3 targets both DNA strands in

295 s able to bind DNA/DNA, RNA/DNA, and DNA/RNA duplexes with similar affinities.

296 Incubation of 135-mer duplexes with single Sp or Gh lesions in human cell extr

297 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bul

298 ' on the target strand are looped-out of the duplex, with the resulting conformational transitions sh

299 a rotationally unconstrained downstream DNA duplex within the open RNAP active site cleft.

300 that is capable of immediately unwinding RNA duplexes without undergoing rate-limiting conformational