ライフサイエンスコーパス: strand displacement

1 to compete with the grafted strands through strand displacement.

2 be efficiently reversed via toehold-mediated strand displacement.

3 mismatched base pairs as kinetic barriers to strand displacement.

4 gering another round of primer extension and strand displacement.

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

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

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

8 ture can be used as a toehold for initiating strand displacement.

9 lies exclusively on sequence recognition and strand displacement.

10 target RNA's secondary structure to initiate strand displacement.

11 and disrupts the duplex via toehold-mediated strand displacement.

12 olymerase enzyme that couples synthesis with strand displacement.

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

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

15 eotide reversibly using toehold-mediated DNA strand-displacement.

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

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

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

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

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

21 The strand displacement activity is distinguished from the s

22 Such strand displacement activity is highly unusual for a DNA

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

24 The strand displacement activity of DNA polymerase delta is

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

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

27 1, a 5'-3' helicase, not only stimulates the strand displacement activity of Pol delta but it also al

28 The strand displacement activity of POLN was higher than exo

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

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

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

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

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

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

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

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

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

38 such as rolling circle amplification (RCA), strand displacement amplification (SDA) and isothermal e

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

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

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

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

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

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

45 NAAT" platform, even in biplexed isothermal strand displacement amplification reactions containing 1

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

47 ponential amplification in two directions by strand-displacement amplification, designated hybridizat

48 ination of a hairpin probe hybridization and strand-displacement amplification.

49 Dynamic strand displacement and errors were elucidated thermodyn

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

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

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

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

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

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

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

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

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

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

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

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

62 Strand displacement assays were conducted by mixing (DMA

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

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

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

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

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

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

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

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

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

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

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

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

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

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

77 ld exchange reactions, which are competitive strand displacement between oligonucleotides.

78 The strand displacement burst synthesis rate for Escherichia

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

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

81 demonstrate continued primer extension with strand displacement by employing activated 3'-aminonucle

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

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

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

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

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

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

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

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

90 Strand displacement cascades are commonly used to make d

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

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

93 d, with possible applications to speeding up strand displacement cascades in nucleic acid nanotechnol

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

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

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

97 DNA devices that operate through associative strand-displacement cascades.

98 Strand displacement characteristics of the polymerase sh

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

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

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

102 uccessfully design and construct complex DNA strand displacement circuits.

103 Encapsulating DNA strand-displacement circuits further allows their use in

104 odularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular co

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

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

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

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

109 itioned nucleosome, are strong blocks to the strand displacement DNA synthesis activity of DNA polyme

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

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

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

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

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

115 Furthermore, Pif1 increases strand-displacement DNA synthesis by DNA polymerase delt

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

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

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

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

120 Toehold-mediated DNA strand displacement (DSD) is a powerful strategy to engi

121 Strand displacement, during which a single strand displa

122 Thus associative strand displacement enables robust thermal cycling of DN

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

124 cleaving the short 5' tails generated during strand displacement, FEN1 eliminates the entry point for

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

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

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

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

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

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

131 Inspired by nanotechnologies based on DNA strand displacement, herein we demonstrate that syntheti

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

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

134 these variants are specifically deficient in strand displacement in the absence of RecA filament.

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

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

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

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

139 DNA strand displacement is a key reaction in DNA homologous

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

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

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

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

144 Kinetic control of strand displacement is particularly important in autonom

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

146 Toehold-mediated strand displacement is the most abundantly used method t

147 ation, designated hybridization cascade plus strand-displacement isothermal amplification (HyCaSD).

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

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

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

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

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

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

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

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

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

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

158 d regions with a profile consistent with the strand displacement model of mtDNA replication, whereas

159 and quantitative evidence for the asymmetric strand displacement model of mtDNA replication.

160 nitiated by replication fork stalling during strand displacement mtDNA synthesis.

161 Moreover, based on DNA strand displacement, nanopores can also be utilized to c

162 ists, including software to reliably program strand-displacement nucleic acid circuits.

163 Strand displacement occurs after ATP binding and hydroly

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

165 The strand displacement of the ligated product by the beacon

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

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

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

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

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

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

172 Strand-displacement principles have also been applied in

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

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

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

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

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

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

179 A DNA strand displacement reaction in a crowded environment is

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

181 nformational transformation-mediated toehold strand displacement reaction is designed to protect MIC

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

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

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

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

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

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

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

189 m duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without signi

190 de a helpful tool for the rational design of strand-displacement reaction networks.

191 We also demonstrated a hierarchical strand-displacement reaction on meta-DNA to transfer the

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

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

194 The ATP-fueled ligation biases strand displacement reactions by increasing the toehold

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

196 Despite the widespread use of strand displacement reactions for realizing dynamic DNA

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

198 Since then, toehold-mediated strand displacement reactions have been used with ever i

199 of quantitatively describing the kinetics of strand displacement reactions in the presence of mismatc

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

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

202 itiate branch migration, the rate with which strand displacement reactions proceed can be varied by m

203 this was provided in the year 2000, in which strand displacement reactions were employed to drive a D

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

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

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

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

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

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

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

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

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

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

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

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

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

217 Strand-displacement reactions generally proceed by three

218 Strand-displacement reactions have been combined with ot

219 for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing f

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

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

222 operate through a series of toehold-mediated strand-displacement reactions.

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

224 th the study and application of nucleic acid strand-displacement reactions.

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

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

227 Strand displacement replication through a DNA hairpin by

228 The strand-displacement replication mode proposed previously

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

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

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

232 The strand displacement strategy overcomes this problem by o

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

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

235 A strand-displacement strategy can enhance the hybridizati

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

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

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

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

240 18.7 nt/s) and switches its activity to slow strand displacement synthesis at DNA hairpin locations (

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

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

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

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

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

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

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

248 report a prebiotically plausible approach to strand displacement synthesis in which short 'invader' o

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

264 rcle mechanism that exclusively uses leading strand displacement synthesis.

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

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

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

268 avage is impaired, we observe a reduction in strand-displacement synthesis as opposed to the widespre

269 context of 5' flap structures generated via strand-displacement synthesis by DNA polymerase delta.

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

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

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

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

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

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

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

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

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

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

280 e fundamental properties of polymerase-based strand displacement systems.

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

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

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

284 oligonucleotides that drive toehold-mediated strand displacement, the probes reset to the real-time s

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 Kinetics of the strand displacement was monitored by the quenched Forste

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

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

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

299 igonucleotides that undergo toehold-mediated strand displacement with the aptamer.

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