ライフサイエンスコーパス: strand displacement

1 olymerase enzyme that couples synthesis with strand displacement.

2 gering another round of primer extension and strand displacement.

3 dron) that is based on DNA hydridization and strand displacement.

4 tions using cycles of annealing-digestion or strand displacement.

5 esis through GC-rich sequences, which impede strand displacement.

6 lies exclusively on sequence recognition and strand displacement.

7 ent (exo(-)) pol (D368A) was capable of slow strand displacement.

8 binding plasmid DNA is demonstrated to be by strand displacement.

9 e propelled by DNAzymes, protein enzymes and strand displacement.

10 to compete with the grafted strands through strand displacement.

11 be efficiently reversed via toehold-mediated strand displacement.

12 mismatched base pairs as kinetic barriers to strand displacement.

13 nd-displacement, and the binding-induced DNA strand-displacement.

14 n in response to oligonucleotides that drive strand-displacement (17) reactions.

15 including 1) continuously tuning the rate of strand displacement, 2) dynamic control of strand displa

16 HSV-1 pol modulates its ability to engage in strand displacement, a function that may be important to

17 Toehold-mediated strand displacement, a programmable form of dynamic DNA

18 x DNA termini when a DNA polymerase with the strand-displacement ability is used.

19 lymerase with both reverse-transcriptase and strand displacement activities to obtain sensitivities o

20 tions for its extraordinary processivity and strand displacement activities.

21 our study demonstrates that the kinetics of strand displacement activity can be tuned through dsProb

22 The strand displacement activity is distinguished from the s

23 Such strand displacement activity is highly unusual for a DNA

24 rinic endonuclease activity of APE1, the DNA strand displacement activity of DNA polymerase beta, and

25 The strand displacement activity of DNA polymerase delta is

26 e primer region is raised into a flap by the strand displacement activity of DNA polymerase delta.

27 te, forms a strong non-polar barrier for the strand displacement activity of DNA polymerase delta.

28 1, a 5'-3' helicase, not only stimulates the strand displacement activity of Pol delta but it also al

29 The strand displacement activity of POLN was higher than exo

30 We have investigated the time-dependent strand displacement activity of several targets with dou

31 Compared to the short target, strand displacement activity of the longer targets is sl

32 The scheme proceeds by first using the strand displacement activity of the Vent (exo-) polymera

33 templates, the enzyme possesses an intrinsic strand displacement activity on flapped templates.

34 h translocates on dsDNA but does not display strand displacement activity typical for a helicase.

35 lymerase (pol) was shown to lack significant strand displacement activity with or without its process

36 A lesion bypass properties, including strong strand displacement activity, low fidelity favoring inco

37 Mammalian HELQ is a 3'-5' DNA helicase with strand displacement activity.

38 mechanism utilizing a DNA polymerase with a strand displacement activity.

39 -proficient polymerases correlated with poor strand displacement activity.

40 enzyme that is responsible for modulation of strand displacement activity.

41 onally, tPollambda was found to possess weak strand-displacement activity during polymerization.

42 vity, Polmu was identified to possess a weak strand-displacement activity.

43 of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple ann

44 This study evaluated the performance of strand displacement amplification (SDA) and transcriptio

45 transcription-mediated amplification (TMA), strand displacement amplification (SDA), and PCR amplifi

46 ature rolling circle amplification (RCA) and strand displacement amplification (SDA).

47 and urine specimens by PCR (Roche Cobas) or strand displacement amplification (SDA; Becton Dickinson

48 ) (Gen-Probe Inc., San Diego, CA), ProbeTec (strand displacement amplification [SDA]) (Becton Dickins

49 e and C. trachomatis by the Becton Dickinson strand displacement amplification assay (SDA) with the B

50 n, transcription-mediated amplification, and strand displacement amplification assays, respectively,

51 nt and real-time detection of the isothermal strand displacement amplification reaction that produces

52 (AC2; Aptima Combo 2; Gen-Probe Inc.) and a strand displacement amplification test (SDA; ProbeTec; B

53 imers with 29 DNA polymerase can be used for strand-displacement amplification of different vector co

54 single-stranded DNAs (ssDNAs) for isothermal strand-displacement amplification.

55 d synthesis may serve to regulate sequential strand displacement and flap cleavage at other genomic s

56 ization is signaled through toehold-mediated strand displacement and loss of a competitive FRET pathw

57 mutation detection based on toehold-mediated strand displacement and nuclease-mediated strand digesti

58 ties that obtain additive benefits from both strand displacement and nucleolytic digestion, thus prov

59 h) perturbed dynamic processes including DNA strand displacement and primer extension by DNA polymera

60 , our results allow a unified explanation of strand displacement and single strand primer extension s

61 association of cRNA molecules, can stimulate strand displacement, and can function as an RNA chaperon

62 n through the mechanism of primer extension, strand displacement, and ramification.

63 e been engineered using toehold-mediated DNA strand displacement, and their programmable applications

64 sociative (combinative) toehold-mediated DNA strand-displacement, and the binding-induced DNA strand-

65 ssay (TMA), the BD ProbeTec ET amplified DNA strand displacement assay (SDA), and the Roche Cobas Amp

66 lamydial or gonococcal infection detected by strand displacement assay, were analyzed.

67 A strand-displacement assay is employed to assess the heli

68 Using an RNA strand-displacement assay, we have demonstrated that Mtr

69 Strand displacement assays were conducted by mixing (DMA

70 These findings, combined with strand-displacement assays, indicate that DnaA opens rep

71 tiation sequences, which trigger the toehold strand displacement assembly of two G-quadruplex contain

72 Here, we study strand displacement at multiple levels of detail, using

73 bines discrimination by competition with DNA strand displacement-based catalytic amplification.

74 e the robustness and specificity of one such strand displacement-based catalytic reaction.

75 e properties facilitate the incorporation of strand displacement-based DNA components in synthetic ch

76 Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effe

77 in contrast, prior strand displacement-based probes designed for kinetic di

78 Here, we review DNA strand-displacement-based devices, and look at how this

79 Results obtained from our sequential strand displacement beacon assay are consistent with tho

80 We describe a sequential strand displacement beacon assay that is able to quantif

81 to be fluorescently labeled, the sequential strand displacement beacon method is able to quantify mu

82 oligonucleotides using a single (universal) strand displacement beacon.

83 ed and are often combined to achieve desired strand displacement behaviors and functions.

84 The strand displacement burst synthesis rate for Escherichia

85 fication using nicking endonuclease-mediated strand displacement by a DNA polymerase.

86 We propose a model in which strand displacement by DNA polymerase III holoenzyme dep

87 increased the rate (2/s) and processivity of strand displacement by exo(-) pol, the rate was slower t

88 To investigate RNA annealing and strand displacement by Hfq, we used oligonucleotides tha

89 flaps that arise during OFP due to excessive strand displacement by pol delta and/or by an as yet uni

90 n that allows the flexible regulation of DNA strand displacement by splitting an input strand into an

91 amic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces a

92 ow that the efficiency of marker erasing via strand displacement can be limited by non-toehold mediat

93 We demonstrate that the dynamics of strand displacement can be manipulated by changing stran

94 The kinetics of strand displacement can be modulated by toeholds, short

95 roperties of extremely high processivity and strand displacement capacity, together with its high fid

96 Strand displacement cascades are commonly used to make d

97 demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo using fl

98 Our results suggest that DNA strand displacement cascades could be used to endow auto

99 an artificial neural network model) into DNA strand displacement cascades that function as small neur

100 work paves the way for accurate modeling of strand displacement cascades, which would facilitate the

101 Here, we describe automata based on strand-displacement cascades directed by antibodies that

102 Strand displacement characteristics of the polymerase sh

103 ental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct

104 ontrol is achieved via a rationally designed strand displacement circuit that responds to pH and acti

105 uilding on the richness of DNA computing and strand displacement circuitry, we show how molecular sys

106 uccessfully design and construct complex DNA strand displacement circuits.

107 d frameworks, DNA tile self-assembly and DNA strand-displacement circuits, can be systematically inte

108 d on a shift in the equilibrium of DNA-based strand displacement competition reaction.

109 d DNA (dsDNA) by forming very stable PNA-DNA strand-displacement complexes via double duplex invasion

110 amer structure, thus suggesting that the DNA strand-displacement concept can be extended to functiona

111 ous upstream DNAzymes, can be coupled to DNA strand-displacement devices, and is highly resistant to

112 is completed by DNA polymerase I by means of strand displacement DNA synthesis and 5 '-nuclease activ

113 We demonstrate that WRN stimulates pol beta strand displacement DNA synthesis and that this stimulat

114 gp2.5 enables T7 DNA polymerase to catalyze strand displacement DNA synthesis at a nick in DNA.

115 ngle-stranded DNA, and it does not stimulate strand displacement DNA synthesis at high concentration.

116 DNA polymerase, which is unable to catalyse strand displacement DNA synthesis by itself, can increas

117 nd, in contrast to wild-type gp2.5, promotes strand displacement DNA synthesis by T7 DNA polymerase.

118 The strand displacement DNA synthesis by the DNA polymerase

119 terminus results in a reduced efficiency in strand displacement DNA synthesis catalyzed by gene 4 pr

120 TRF2 also stimulated Pol beta strand displacement DNA synthesis in reconstituted BER r

121 reverse transcriptases (RTs) are capable of strand displacement DNA synthesis in vitro, unassisted b

122 Here, we demonstrate that the strand displacement DNA synthesis is facilitated by the

123 on intermediate by inhibiting a nonspecific, strand displacement DNA synthesis reaction and favoring

124 2- to 11-nucleotide flap created by pol beta strand displacement DNA synthesis.

125 he dL residue through the combined action of strand-displacement DNA synthesis by polbeta and excisio

126 he Pol-beta protein (T79A/K81A/R83A) blocked strand-displacement DNA synthesis in which tetrahydrofur

127 igher helicase activity in DNA unwinding and strand-displacement DNA synthesis than that observed for

128 However, when protein binding was coupled to strand-displacement DNA synthesis, only one of the two b

129 signal amplification strategy by the toehold strand displacement-driven cyclic assembly of G-quadrupl

130 Strand displacement, during which a single strand displa

131 ficient to allow the polymerase to carry out strand displacement even in the absence of PCNA.

132 A nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics.

133 The method is based on fluorescent reporter strand displacement from a tripartite substrate containi

134 We introduce a method to control strand displacement from their less accessible "bottom"

135 Toehold-mediated strand displacement has enabled the construction of soph

136 Toehold-mediated strand displacement has proven extremely powerful in pro

137 biophysics of nucleic acid hybridization and strand displacement have been used for the rational desi

138 uding hybridization, enzymatic cleavage, and strand displacement; however, their overall translocatio

139 Here we show that the kinetics of strand displacement in surface-immobilized nanomachines

140 computational devices implemented using DNA strand displacement, in a convenient web-based graphical

141 he single mismatch was detected by measuring strand displacement-induced resistance (and hence curren

142 The retention of strand displacement inhibition by Y122A, even in the abs

143 ment reactions in this scheme, allowing fast strand displacement initiated by reversible toehold bind

144 DNA strand displacement is a key reaction in DNA homologous

145 Toehold-mediated DNA strand displacement is introduced as a method to purify

146 Excessive strand displacement is normally prevented by the 3.-exon

147 Modest (approximately 7 nt) strand displacement is observed after the gap between mo

148 Toehold-mediated strand displacement is often used in solution to drive s

149 Kinetic control of strand displacement is particularly important in autonom

150 Toehold-mediated DNA strand displacement is the fundamental basis for the con

151 Strand displacement is weak compared with nuclease activ

152 Although the dependence of strand displacement kinetics on toehold length has been

153 Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the

154 Here, we measured toehold-mediated strand displacement kinetics using single-molecule fluor

155 nd they provide a biophysical explanation of strand displacement kinetics.

156 nds, starting at the multiple origins of the strand-displacement loop (D-loop).

157 DNA polymerase holoenzyme are initiated by a strand displacement mechanism requiring gp32, the T4 sin

158 e sensor, which is based on a target-induced strand displacement mechanism, is composed of a "capture

159 dent MMR by 5' excision, by a Msh2-dependent strand displacement mechanism, or both.

160 are amplified by a continuous unidirectional strand-displacement mechanism, a linear adaptation of ro

161 may enable the helicase to unwind DNA via a "strand displacement" mechanism, which is similar to the

162 and DNA-functionalized nanotubes are mixed, strand displacement-mediated deprotection and binding al

163 Here we introduce a toehold-mediated strand-displacement methodology for transferring informa

164 y for ssDNA translocation and an alternative strand-displacement mode may explain the varying step si

165 data provide evidence for only the orthodox, strand-displacement mode of replication and reveal the p

166 The established strand-displacement model for mammalian mitochondrial DN

167 n the general validity of the "orthodox," or strand-displacement model.

168 Strand displacement occurs after ATP binding and hydroly

169 ovel finding that TRF2 inhibits WRN helicase strand displacement of HJs with telomeric repeats in dup

170 The strand displacement of the ligated product by the beacon

171 e formation of FEN1 cleavage products during strand displacement on a nontelomeric substrate, suggest

172 was coated with components of a DNA one-step strand displacement (OSD) reaction to release the walker

173 ted strand exchange reaction termed one-step strand displacement (OSD).

174 Proximity-induced intramolecular DNA strand displacement (PiDSD) is one of the key mechanisms

175 d magnetic microcarriers-assisted isothermal strand-displacement polymerase reaction (ISDPR) for quan

176 cross-opening of the two hairpins using the strand displacement principle.

177 DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstra

178 sin pore was induced by a combination of DNA strand displacement processes and enzyme-catalyzed react

179 Toehold-mediated DNA strand displacement provides unique advantages in the co

180 Further enhancement of the strand displacement rate in the presence of ATP was obse

181 r of magnitude faster than the reported bulk strand displacement rate, a discrepancy that can be acco

182 e use of specially designed toehold-mediated strand displacement reaction enables the reliable and se

183 e specificity constant (k(cat)/K(m)) for the strand displacement reaction is approximately 300-fold l

184 This toehold strand displacement reaction leads to the cyclic reuse o

185 t prevents the replicase from advancing in a strand displacement reaction on forks that do not contai

186 mics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed c

187 ond, fully complementary gammaPNA, through a strand displacement reaction, allowing translation to pr

188 nked by both nicks is then substituted, in a strand displacement reaction, by an oligonucleotide prob

189 r misassembled replication forks, blocks the strand displacement reaction, even if added to an ongoin

190 , is realized through a toehold-mediated DNA strand displacement reaction.

191 tative aptamer-ligand and aptamer-complement strand-displacement reaction.

192 By using strand displacement reactions as a primitive, we constru

193 ed, metastable states in strand exchange and strand displacement reactions for bulge loop DNA conform

194 tively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences.

195 three-way junctions substantially accelerate strand displacement reactions in this scheme, allowing f

196 Yet, recent improved understandings of DNA strand displacement reactions now provides opportunities

197 The method is based on strand displacement reactions that propagate by a hyperb

198 cases, kissing complexes can be a prelude to strand displacement reactions where the two hairpins res

199 f strand displacement, 2) dynamic control of strand displacement reactions, and 3) selective activati

200 lica beads, and their addressability through strand displacement reactions, controlled membrane orien

201 iant on using so-called toeholds to initiate strand displacement reactions, leading to the execution

202 ep change in the use of toehold-mediated DNA strand displacement reactions, where a double-stranded D

203 ation involves the use of dsRNA templates in strand displacement reactions, where the newly synthesiz

204 ligonucleotide, a series of toehold-mediated strand displacement reactions, which are reminiscent of

205 NA sequence and by performing sequential DNA strand displacement reactions.

206 ere based primarily on DNA hybridization and strand displacement reactions.

207 se enzyme-free constructions function by DNA strand displacement reactions.

208 s a method for designing fast and reversible strand displacement reactions.

209 ons, and 3) selective activation of multiple strand displacement reactions.

210 ssing-complex formation and their subsequent strand-displacement reactions are poorly understood.

211 recently been rationally designed to use DNA strand-displacement reactions, in which two strands with

212 roaches, the switching operation is based on strand-displacement reactions.

213 vely revealing toeholds required to initiate strand-displacement reactions.

214 tures, and motors, many of which rely on DNA strand-displacement reactions.

215 y shows that NEIL1 could also participate in strand displacement repair synthesis (long patch repair

216 Strand displacement replication through a DNA hairpin by

217 The strand-displacement replication mode proposed previously

218 Using a strand-displacement replication strategy, the multiple r

219 RuvAB-catalyzed strand displacement requires both RuvA and RuvB proteins

220 DNA motifs and initiates the subsequent DNA strand displacement, resulting in a binding-induced TWJ.

221 nd rationally designed two triplex-based DNA strand displacement strategies that can be triggered and

222 The strand displacement strategy overcomes this problem by o

223 Herein, we describe a binding-induced DNA strand displacement strategy that can convert protein bi

224 thermal removal of asDNA from pRNA through a strand displacement strategy.

225 We developed a sequential strand-displacement strategy for multistep DNA-templated

226 including nucleotide incorporation kinetics, strand displacement synthesis and 3'-5' exonuclease acti

227 ies that allow Pol delta-exo(-) to carry out strand displacement synthesis and discovered that it is

228 G-rich repeats, only WRN promotes sequential strand displacement synthesis and FEN1 cleavage, a criti

229 be mutagenic and that it will be removed by strand displacement synthesis and flap endonuclease proc

230 ting that altering this residue affects both strand displacement synthesis and the fidelity of DNA sy

231 18.7 nt/s) and switches its activity to slow strand displacement synthesis at DNA hairpin locations (

232 5'-flap in the nascent strand independent of strand displacement synthesis by an upstream polymerase.

233 yotic cells requires precise coordination of strand displacement synthesis by DNA polymerase delta (P

234 Finally, we show that the observed strand displacement synthesis by exonuclease-deficient P

235 PCNA eliminates flap-mediated inhibition of strand displacement synthesis by masking the secondary D

236 g Okazaki fragment maturation, the extent of strand displacement synthesis by Pol delta determines wh

237 However, Y122A is capable of inhibiting strand displacement synthesis by polymerase.

238 r excised by the flap endonuclease FEN1 with strand displacement synthesis carried out by DNA polymer

239 The presence of FEN1(RAD27) during strand displacement synthesis curtails displacement in f

240 is initiated as short-patch repair, through strand displacement synthesis from the ligation-resistan

241 s, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing the

242 ty stimulates DNA polymerase beta (pol beta) strand displacement synthesis in vitro.

243 Furthermore, we found that the rate of strand displacement synthesis is dependent on the GC con

244 This indicates that the strand displacement synthesis occurs through a mechanism

245 er with the T7 gene 4 DNA helicase, catalyze strand displacement synthesis on duplex DNA processively

246 1 substitutions displayed altered degrees of strand displacement synthesis on nicked and gapped duple

247 ive genotoxic DNA intermediates arising from strand displacement synthesis that otherwise would be re

248 B formed a ribonucleotide-containing flap by strand displacement synthesis that was cleaved by Fen1,

249 Pol epsilon is unable to carry out extended strand displacement synthesis unless its 3'-5' exonuclea

250 lored the capacity of Pol epsilon to perform strand displacement synthesis, a process that influences

251 ding RNA- and DNA-primed DNA polymerization, strand displacement synthesis, and polymerase-independen

252 DNA polymerase beta (Pol beta) carries out strand displacement synthesis, following APE1 incision o

253 activity could substitute for MCM to promote strand displacement synthesis, its presence was not esse

254 Under conditions where Pol delta carries out strand displacement synthesis, the presence of long 5'-f

255 chaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps o

256 rization, RNA cleavage, strand transfer, and strand displacement synthesis.

257 way, including normal DNA polymerization and strand displacement synthesis.

258 redoxin together with T7 helicase to mediate strand displacement synthesis.

259 rcle mechanism that exclusively uses leading strand displacement synthesis.

260 ity can function to unwind duplex DNA during strand displacement synthesis.

261 randed DNA-binding protein is more active in strand displacement synthesis.

262 type 1 (HIV-1) reverse transcriptase affect strand displacement synthesis.

263 y to be processive and to catalyze extensive strand displacement synthesis.

264 ps generated at ends of Okazaki fragments by strand displacement synthesis.

265 ases, gp41 or dda, is capable of stimulating strand displacement synthesis.

266 and C-terminal deletions on processivity and strand displacement synthesis.

267 ed processivity, and was unable to carry out strand displacement synthesis.

268 We also found that DnaE does not perform strand displacement synthesis.

269 replication complexes proceeded to carry out strand-displacement synthesis at a rate of 1.5 nt/s.

270 ve action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results

271 beta and blocks DNA polymerase beta-mediated strand-displacement synthesis in long patch BER without

272 Polymerase-catalyzed strand-displacement synthesis on DNA gaps can result in

273 unwind DNA or allow T7 polymerase to mediate strand-displacement synthesis on duplex DNA.

274 tigates the ability of the enzyme to perform strand-displacement synthesis, with important implicatio

275 e ability of gp5 and the helicase to mediate strand-displacement synthesis.

276 is able to replace gp5 and continue ongoing strand-displacement synthesis.

277 c patch of gp5 is critical for initiation of strand-displacement synthesis.

278 lease 1 (Fen-1) and blocks Pol-beta-directed strand-displacement synthesis.

279 C with DNA polymerase beta (pol-beta) blocks strand-displacement synthesis.

280 age and bacterial DNA polymerases capable of strand-displacement synthesis.

281 reviously shown using more sophisticated DNA strand displacement systems, including 1) continuously t

282 of PiDSD by combining the uses of three DNA strand displacement techniques, including a binding-indu

283 seful addition to the current toolbox of DNA strand displacement techniques.

284 n switchable functional RNA domains by using strand-displacement techniques.

285 ares favorably with the toehold-mediated DNA strand-displacement, the associative (combinative) toeho

286 er oligonucleotides, with a toehold-mediated strand displacement [TMSD] ability, helped unwind the se

287 DNA Mobius strip can be reconfigured through strand displacement to create topological objects such a

288 ts in DNA self-assembly and toehold-mediated strand displacement to develop a rewritable multi-bit DN

289 meters for PiDSD, and a toehold-mediated DNA strand displacement to generate fluorescence signals for

290 techniques, including a binding-induced DNA strand displacement to generate PiDSD, an intermolecular

291 AP is a highly faithful DNAP that can couple strand displacement to processive DNA synthesis.

292 The Visual DSD (DNA Strand Displacement) tool allows rapid prototyping and a

293 Rate constants for strand displacement upon addition of i-motif DNA (k = 1.

294 Hairpin loops may be opened by strand displacement using an opening strand that contain

295 base-pair gap, DNA synthesis and subsequent strand displacement was greatest in the presence of both

296 Kinetics of the strand displacement was monitored by the quenched Forste

297 he wild-type HSV-1 pol, although significant strand displacement was observed with exo(-) HSV-1 pol.

298 colloid system by toehold exchange-mediated strand displacement, which then triggers the consumption

299 DmBLM combines DNA strand displacement with DNA strand annealing to catalyz

300 ce to a target of interest can initiate both strand displacement within the hairpin and extension of