ライフサイエンスコーパス: supercoiling

1 atalytic activity and increases negative DNA supercoiling.

2 develop a HT screen for inhibitors of gyrase supercoiling.

3 and left-handed Z-form DNA under controlled supercoiling.

4 tems, induce topological changes such as DNA supercoiling.

5 e to temperature and to the imposed level of supercoiling.

6 ctivated PR1-2 via transcription coupled DNA supercoiling.

7 ation and religation on the torque caused by supercoiling.

8 iently relieve transcription-driven negative supercoiling.

9 match those of singlets but differ in their supercoiling.

10 information on the mechanism of DNA negative supercoiling.

11 other mid genes in response to increased DNA supercoiling.

12 leoid and/or to promote negative or positive supercoiling.

13 were activated in response to increased DNA supercoiling.

14 which show significant helix bending but not supercoiling.

15 poisomerase subunit while promoting positive supercoiling.

16 p2 alleviates transcription-induced positive supercoiling.

17 upstream and downstream transcription-driven supercoiling.

18 ms slipped-strand DNA from the energy of DNA supercoiling.

19 ation and segregation, and in regulating DNA supercoiling.

20 ic flagella (PF) with pronounced spontaneous supercoiling.

21 regation and in regulating intracellular DNA supercoiling.

22 rium of histones H3/H4 and its effect on DNA supercoiling.

23 ner that depends on its surrounding negative supercoiling.

24 heir effects on either total or unrestrained supercoiling.

25 sion, it should be nearly independent of DNA supercoiling.

26 f the corresponding increase of the template supercoiling.

27 rotein to the apex of the loop, and negative supercoiling.

28 not depend on the level of unconstrained DNA supercoiling.

29 n for lesions in gyrase that reduce negative supercoiling.

30 scale conformational transitions elicited by supercoiling.

31 scription responds to the increased negative supercoiling.

32 shifts toward H-DNA with increased negative supercoiling.

33 nicircle topoisomers with defined degrees of supercoiling.

34 angement of polymerase binding sites and DNA supercoiling.

35 odes, is able to differentially regulate DNA supercoiling.

36 promote DNA plectoneme formation during DNA supercoiling.

37 ct relationship between H-NS binding and DNA supercoiling.

38 suppress DNA plectoneme formation during DNA supercoiling.

39 th DNA gyrase and/or transcription equalizes supercoiling across the chromosome.

40 lpsoralen intercalation to map the extent of supercoiling across the Escherichia coli chromosome duri

41 conformational transitions that arise due to supercoiling across the full range of supercoiling densi

42 We propose that polyamines and DNA supercoiling act synergistically to regulate expression

43 idual actin filaments poorly in vitro, often supercoiling actin into plectonemes.

44 ge and reduces DNA-stimulated ATPase and DNA supercoiling activities only 2-fold.

45 We also showed evidence for the existence of supercoiling activity in A. thaliana and that the plant

46 However, the DNA supercoiling activity is inefficient and requires an exc

47 Recently, a severe loss of supercoiling activity of Escherichia coli gyrase upon de

48 RecA has no effect on the supercoiling activity of gyrase but stimulates the relax

49 in a baculovirus expression system and shown supercoiling activity of the partially purified enzyme.

50 BBZ compounds inhibited S. aureus DNA gyrase supercoiling activity with IC(50) values in the range of

51 th changes in its localisation, dynamics and supercoiling activity.

52 GyrA D82G gyrase exhibits a reduced supercoiling activity.

53 es with the hyperactivation of condensin DNA supercoiling activity.

54 These results suggest that negative supercoiling alone is not sufficient to drive G-quadrupl

55 s the free energy of hydrolysis to drive DNA supercoiling, an energetically unfavourable process.

56 efficiency of arrest increases with negative supercoiling and also with multiple rounds of transcript

57 en the insert and GyrA more modestly impairs supercoiling and ATP turnover, and does not affect DNA b

58 Type II topoisomerases regulate DNA supercoiling and chromosome segregation.

59 of nucleosomal DNA, accumulation of negative supercoiling and conversion of multiple regions of genom

60 (ii) understand the mechanistic role of DNA-supercoiling and DNA-bending cofactors in both prokaryot

61 the insert greatly reduces the DNA binding, supercoiling and DNA-stimulated ATPase activities of gyr

62 n intramolecular reaction, removing positive supercoiling and introducing negative supercoiling into

63 SpORC to ars1 DNA is facilitated by negative supercoiling and is accompanied by changes in DNA topolo

64 Topoisomerase I (Top1) regulates DNA supercoiling and is the target of camptothecin and inden

65 Top3-Hel112 complex does not induce positive supercoiling and is thus likely to play different roles.

66 DNA topoisomerases manage chromosome supercoiling and organization in all cells.

67 DNA topoisomerases manage chromosome supercoiling and organization in all forms of life.

68 cA protein can influence the balance between supercoiling and relaxation activities either by interfe

69 amic effects are due to an imbalance between supercoiling and relaxation activities, which appears to

70 entire experimental setup that measures DNA supercoiling and relaxation via single molecule magnetic

71 enzymes that use ATP to maintain chromosome supercoiling and remove links between sister chromosomes

72 By reducing negative supercoiling and resolving R loops, TOP3B promotes trans

73 Type IIA topoisomerases control DNA supercoiling and separate newly replicated chromosomes u

74 l conformers that are formed under different supercoiling and solution conditions.

75 e potency of ciprofloxacin for inhibition of supercoiling and stabilization of cleaved complex was in

76 tein conformation depending on the degree of supercoiling and the interoperator length.

77 The potency of AZD0914 for inhibition of supercoiling and the stabilization of cleaved complex by

78 minated the reciprocal relationships between supercoiling and transcription, an illustration of mecha

79 The arrest required negative supercoiling and was much more pronounced when the pyrim

80 Type II topoisomerases modify DNA supercoiling, and crystal structures suggest that they s

81 o a reduction in DNA complexity (catenation, supercoiling, and knotting) below the level expected at

82 n (G3T)n sequences, this was not affected by supercoiling, and permanganate failed to detect exposed

83 A and pgk, were responsive to alterations in supercoiling, and promoter activity could be regulated m

84 wist and writhe to the chromosome's negative supercoiling are in good correspondence with experimenta

85 Our results identify DNA supercoiling as a novel mechanism controlling Cas9 bindi

86 Moreover, we introduce DNA supercoiling as a quantitative tool to explore the seque

87 A gyrB mutant strain with decreased negative supercoiling, as predicted.

88 at MG_149 osmoinduction was regulated by DNA supercoiling, as the presence of novobiocin decreased MG

89 The factors that provoke such supercoiling, as well as the role that PF coiling plays

90 By using supercoiling assay, we show that the transient template

91 ro, but not H3 nucleosomes, as measured by a supercoiling assay.

92 Functional supercoiling assays reveal that both hyper- and hypo-pho

93 Interestingly, in vitro plasmid supercoiling assays revealed that treatment of either hi

94 topoisomerases (Top1Bs) relax excessive DNA supercoiling associated with replication and transcripti

95 d pathways involved in the management of DNA supercoiling associated with transcription.

96 t that directs the reaction towards negative supercoiling, bacterial gyrase complexes bound to 137- o

97 force it to swivel and diffuse this positive supercoiling behind the fork where topoisomerase IV woul

98 logical domains and prevented the passage of supercoiling between them.

99 We showed that positive supercoiling buildup on a DNA segment by transcription s

100 how here that K(+) ions are required for DNA supercoiling but are dispensable for ATP-independent DNA

101 and it interfered with gyrase-dependent DNA supercoiling but not DNA relaxation.

102 Gc phrB mutant showed increased negative DNA supercoiling, but while the protein bound double-strande

103 id to enable real-time monitoring of plasmid supercoiling by a bacterial topoisomerase, Escherichia c

104 I topoisomerases that can introduce negative supercoiling by creating a wrap of DNA before strand pas

105 are shown to be appropriate for assaying DNA supercoiling by Escherichia coli DNA gyrase and DNA rela

106 Topoisomerase I (Top1) relaxes DNA supercoiling by forming transient cleavage complexes (To

107 Top1mt relaxes mitochondrial DNA (mtDNA) supercoiling by introducing transient cleavage complexes

108 tes, we demonstrated that efficient positive supercoiling by reverse gyrase requires a bubble size la

109 which we mechanically relieved the positive supercoiling by rotating the external magnetic field at

110 e shown DNA-dependent ATP hydrolysis and DNA supercoiling by this protein, indicative of a DNA transl

111 t transcription, in which the free energy of supercoiling can circumvent the need for a subset of bas

112 gand binding play an important role and that supercoiling can instigate additional ligand-DNA contact

113 f individual promoters to alterations in DNA supercoiling can provide a mechanism for global patterns

114 Previously we have shown that DNA supercoiling can strongly facilitate E-P communication o

115 rase holoenzyme is markedly impaired for DNA supercoiling capacity, but displays normal ATPase functi

116 quencing, show that tethering induces global supercoiling changes, which are likely incompatible with

117 ase (RNAP) initiation and termination sites, supercoiling characteristics were similar to poorly tran

118 lis, smc null mutations cause defects in DNA supercoiling, chromosome compaction, and chromosome part

119 tion of DNA damage, transcription-associated supercoiling, collision between replication forks and th

120 Topoisomerases are central regulators of DNA supercoiling commonly thought to act independently in th

121 a topA mutant strain with increased negative supercoiling compared with wild-type levels, and the cat

122 e conformational transitions result in three supercoiling conformational regimes that are governed by

123 e might relate to a polar filament that upon supercoiling could be packaged into virions.

124 oisomerases were investigated using in vitro supercoiling, decatenation, DNA binding, and DNA cleavag

125 DNA binding to ATP hydrolysis, and leads to supercoiling deficiency.

126 g activity is passive and dependent upon the supercoiling degree of the DNA substrate.

127 coupling efficiency between ATP turnover and supercoiling, demonstrating that CTD functions can be fi

128 They occur for supercoiling densities and forces that are typically enc

129 d DNA molecules at greater length scales and supercoiling densities than previously explored by simul

130 due to supercoiling across the full range of supercoiling densities that are commonly explored by liv

131 model in which modifications at the level of supercoiling density caused by changes in the osmotic pr

132 An increase in supercoiling density of plasmid DNA was observed as the

133 At a critical supercoiling density, the DNA extension decreases abrupt

134 We hypothesize that expression of these supercoiling-dependent early genes is upregulated by inc

135 ion blockage in an orientation-, length- and supercoiling-dependent manner.

136 ented in our study by three early genes, had supercoiling-dependent promoters that were transcribed a

137 The extent of supercoiling differs between regions of the chromosome,

138 The chirality of supercoiling directs rotational direction, and the short

139 The complex was capable of supercoiling DNA-gp3 as observed previously for gp16 alo

140 cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it tra

141 have been described in vitro and include DNA supercoiling, DNA replication, RNA splicing, and transcr

142 oes not require ATP, but is dependent on DNA supercoiling: DNA with positive torsional stress is comp

143 or an average of two Fis-binding regions per supercoiling domain in the chromosome of exponentially g

144 del in which H-NS-constrained changes in DNA supercoiling driven by transcription promote pausing at

145 Since changes in DNA supercoiling during chlamydial development have been pro

146 romoters and the increased level of negative supercoiling during mid time points in the developmental

147 ssential mammalian enzyme that regulates DNA supercoiling during transcription and replication.

148 y adaptable to other enzymes that change DNA supercoiling (e.g. restriction enzymes) and are suitable

149 ectorial strand transport independent of the supercoiling energy stored in the DNA molecule.

150 Supercoiling-enhanced looping can influence the maintena

151 op traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping.

152 ed not to affect the direction and extent of supercoiling for variants H3.1 and H3.3.

153 Monte Carlo simulations of the supercoiling free energies of solution DNAs, and also of

154 ist energy parameter, E(T), that governs the supercoiling free energy, and also with atomic force mic

155 ist energy parameter, E(T), that governs the supercoiling free energy.

156 with topological constraints directed by DNA supercoiling, functions to regulate Hin synaptic complex

157 Topoisomerase I (Top1) is known to relax DNA supercoiling generated by transcription, replication, an

158 e use of various techniques, the role of DNA supercoiling has not been studied systematically.

159 Homologous pairing and braiding (supercoiling) have crucial effects on genome organizatio

160 Precise control of supercoiling homeostasis is critical to DNA-dependent pr

161 essential for chromosome segregation and DNA supercoiling homeostasis.

162 Supercoiling imposes stress on a DNA molecule that can d

163 The enzyme specifically introduces negative supercoiling in a process that must coordinate fuel cons

164 Topo-1 removes excess supercoiling in an ATP-independent reaction and works wi

165 rboring gyrA751 displayed decreased negative supercoiling in cells.

166 by RNA polymerase can stimulate negative DNA supercoiling in Escherichia coli topA strains.

167 ictions, among them different degrees of DNA supercoiling in fibers with L = 10n and 10n + 5 bp, diff

168 type II topoisomerases and positive plasmid supercoiling in hyperthermophilic bacteria and archea.

169 ng development and the ability to adjust DNA supercoiling in response to osmotic stress.

170 redict that this force would create negative supercoiling in the DNA duplex region between the anchor

171 plasmid thus points to the potential role of supercoiling in the G-quadruplex formation in promoter s

172 We conclude that levels of positive supercoiling in the range of 0.025-0.051 (most probably

173 due to compensatory accumulation of positive supercoiling in the rest of the template, we carried out

174 rial DNA (mtDNA) displays increased negative supercoiling in TOP1mt knockout cells and murine tissues

175 The importance of DNA supercoiling in transcriptional regulation has been know

176 reas the wild-type HU generated negative DNA supercoiling in vitro, an engineered heterodimer with an

177 two subsets based on their responses to DNA supercoiling in vitro.

178 s or nucleoid-associated proteins affect DNA supercoiling in vivo.

179 trol the topology of DNA (e.g., the level of supercoiling) in all cells.

180 the regulation of gene expression in situ by supercoiling, in the case of the former gene, as well as

181 ant features of RPA-bubble structures at low supercoiling, including the existence of multiple bubble

182 As negative supercoiling increases, bases are increasingly exposed.

183 around the histone core implied by positive supercoiling indicates that centromere nucleosomes are u

184 in has no effect on the formation of plasmid supercoiling, indicating that acrolein-protein adduct fo

185 atly twisted superhelical rope, with unusual supercoiling induced by parallel triple-helix interactio

186 nes had promoters that were transcribed in a supercoiling-insensitive manner over the physiologic ran

187 sitive supercoiling and introducing negative supercoiling into circular DNA using free energy derived

188 The supercoiling involves the switching of coiled-coil proto

189 tion and consequent increase in negative DNA supercoiling is an important physiological function of t

190 Supercoiling is an indicator of cell health, it modifies

191 Since negative supercoiling is known to facilitate the formation of alt

192 However, supercoiling is not just a by-product of DNA metabolism.

193 the chlamydial gyrase promoter by increased supercoiling is unorthodox compared with the relaxation-

194 Thus, we propose that DNA supercoiling is utilized in Chlamydia as a general mecha

195 (TopA), a regulator of global and local DNA supercoiling, is modified by Nepsilon-Lysine acetylation

196 ct geometric classes, one of which resembles supercoiling known from DNA.

197 in a d(GAC)6.d(GAC)6 duplex induces negative supercoiling, leading to a local B-to-Z DNA transition.

198 rial, we demonstrate that Rdh54-mediated DNA supercoiling leads to transient DNA strand opening.

199 and rebinding to a DNA segment, changing the supercoiling level of the segment.

200 To understand how chlamydial supercoiling levels are regulated, we purified and analy

201 Changes in DNA supercoiling levels during the chlamydial developmental

202 We present a model in which supercoiling levels during the intracellular chlamydial

203 rases, an approach that may be used to alter supercoiling levels for responding to changes in cellula

204 genes is upregulated by increased chlamydial supercoiling levels in midcycle via their supercoiling-r

205 nsitive manner over the physiologic range of supercoiling levels that have been measured in Chlamydia

206 To obtain a measure of how DNA supercoiling levels vary during the chlamydial developme

207 s proposed to be regulated by changes in DNA supercoiling levels.

208 n DNA under tensions that may occur in vivo, supercoiling lowered the free energy of loop formation a

209 ct that the process of transcription affects supercoiling makes it difficult to elucidate the effects

210 gene phenotypes and provide insight into how supercoiling may modulate epigenetic effects on chromoso

211 The DNA gyrase negative supercoiling mechanism involves the assembly of a large

212 enotype in Salmonella, showing disruption of supercoiling near the terminus and replicon failure at 4

213 We suggest that HU establishes higher supercoiling near the terminus of the chromosome during

214 In Escherichia coli crosstalk between DNA supercoiling, nucleoid-associated proteins and major RNA

215 otonic relationship of size versus degree of supercoiling observed in experimental sedimentation stud

216 rrelated, we interpret this as evidence that supercoiling occludes AGT binding sites.

217 Positive supercoiling occurs by a poorly understood mechanism inv

218 When mitotic positive supercoiling occurs on decatenated DNA, it is rapidly re

219 with crossed and open linker DNAs and global supercoiling of arrays into left- and right-handed coils

220 show that the mechanism responsible for the supercoiling of bacterial flagellar filaments cannot app

221 ing single-stranded DNA circles and positive supercoiling of bubble substrate demonstrate that revers

222 yme reverse gyrase, which catalyzes positive supercoiling of DNA and was suggested to play a role in

223 DNA gyrase catalyzes ATP-dependent negative supercoiling of DNA by a strand passage mechanism that r

224 e I is required for preventing hypernegative supercoiling of DNA during transcription.

225 , which catalyses the ATP-dependent negative supercoiling of DNA.

226 an indirect effect promoting global negative supercoiling of DNA.

227 sential function in preventing hypernegative supercoiling of DNA.

228 study the effect of HU on the stiffness and supercoiling of double-stranded DNA.

229 esponsible for preventing the hyper-negative supercoiling of genomic DNA.

230 grained Monte Carlo simulations to model the supercoiling of linear DNA molecules under tension.

231 our results demonstrated that hypernegative supercoiling of plasmid DNA by T7 RNA polymerase did not

232 ted that transcription-coupled hypernegative supercoiling of plasmid DNA did not need the expression

233 of DNA and was capable of reducing negative supercoiling of plasmids containing biotinylated chromat

234 A gyrase is inhibited, whereas the extent of supercoiling of relaxed DNA is limited.

235 he MSL complex reduces the level of negative supercoiling of the deoxyribonucleic acid of compensated

236 This change is characterized by positive supercoiling of the DNA and requires mitotic spindles an

237 ory, protein-mediated loops in DNA may sense supercoiling of the genome in which they are embedded.

238 We investigated the correlation between supercoiling of the protofilaments and molecular dynamic

239 Our results provide strong support that supercoiling of the protofilaments in the flagellar fila

240 quence; the blockage increased with negative supercoiling of the template DNA.

241 The effects of chromatin assembly and DNA supercoiling on the communication are quantitatively sim

242 length, as well as the presence of negative supercoiling or breaks in the non-template DNA strand.

243 ion does not require accessory proteins, DNA supercoiling or particular metal-ion cofactors and is th

244 DNA is generated in the presence of negative supercoiling or upon binding proteins that absorb the hi

245 Here, we observed that HU induces supercoiling over a similar time span as the measured ch

246 Escherichia coli gyrase is known to favor supercoiling over decatenation, whereas the opposite has

247 en together, these results indicate that DNA supercoiling participates in controlling MG_149 expressi

248 nstraints, such as those associated with DNA supercoiling, play an integral role in genomic regulatio

249 In addition, we show that negative supercoiling positively regulates the expression of the

250 yzes the peculiar ATP-dependent DNA-positive supercoiling reaction and might be involved in the physi

251 d that these compounds are inhibitors of the supercoiling reaction catalyzed by M. tuberculosis gyras

252 cer was efficient at all levels of negative supercoiling, recombination at mwr became markedly less

253 The length scales and supercoiling regimes investigated here coincide with tho

254 nderstanding how dynamic modification of DNA supercoiling regulates transcription.

255 erium tuberculosis and needs to catalyse DNA supercoiling, relaxation and decatenation reactions in o

256 ch maintain chromosome topology by variously supercoiling, relaxing, and disentangling DNA.

257 tantly changing, but how RNAP deals with DNA supercoiling remains elusive.

258 ll (<50 bp), there are no host factor or DNA supercoiling requirements, and they are strongly directi

259 Furthermore, the type of supercoiling response correlated with the in vivo expres

260 the circadian cycle are similar to those of supercoiling-responsive genes in Escherichia coli.

261 al supercoiling levels in midcycle via their supercoiling-responsive promoters in a manner similar to

262 This supercoiling-responsivesness is consistent with negative

263 s, which allows dissipation of the excessive supercoiling resulting from Top1 inhibition, spontaneous

264 ct induces R-loops, indicating hypernegative supercoiling [(-)sc] in the region - precisely the oppos

265 g the first evidence that dctA expression is supercoiling sensitive and uncovering a simple metabolic

266 luding those that are essential and possibly supercoiling sensitive.

267 roquine titration, psoralen crosslinking and supercoiling-sensitive reporter assays show that the eff

268 ere identified, and the data showed that DNA supercoiling shifts the equilibrium between folded and u

269 a correlation between the responsiveness to supercoiling shown by the two midcycle promoters and the

270 processes are intimately related to the DNA supercoiling state and thus suggest a direct relationshi

271 te of DNA in cyanobacteria, we show that the supercoiling status of this plasmid changes in a circadi

272 ting the initial DNA wrapping and subsequent supercoiling steps in the reaction cycle.

273 y regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism.

274 of the cellular processes that generate DNA supercoiling, such as transcription and replication.

275 The changes in DNA structure that accompany supercoiling suggest a number of mechanisms whereby chan

276 maS, resulted in twisting of the tubules and supercoiling, suggesting a rotatory movement of the heli

277 However, when positive supercoiling takes place in catenated plasmid, topoisome

278 ameters regulating transcription-coupled DNA supercoiling (TCDS) in E.coli still remain elusive.

279 r strength affects transcription-coupled DNA supercoiling (TCDS), we developed a two-plasmid system i

280 commenced elongation but preserved negative supercoiling that assists promoter melting at start site

281 ow a differential response to changes in DNA supercoiling that correlates with the temporal expressio

282 viously unrecognized role in maintaining DNA supercoiling that is important for normal cell physiolog

283 opoisomerases are essential for removing the supercoiling that normally builds up ahead of replicatio

284 l perturbations (e.g., linear stretching and supercoiling) that can affect the operation of other DNA

285 For negative supercoiling, this regime lies between bubble-dominated

286 Beyond a sharp supercoiling threshold, we also detect exposed bases in

287 We show the importance of supercoiling through an evaluation of the regulation of

288 Here, we use single-molecule DNA supercoiling to directly observe and quantify the dynami

289 und synaptic complex that harnesses negative supercoiling to drive the forward reaction and promote r

290 synapses were observed, using relaxation of supercoiling to report on cleavage and rotation events.

291 in DNA tension have no detectable effect on supercoiling velocity, but the enzyme becomes markedly l

292 The effect of increased and decreased supercoiling was also investigated.

293 came markedly less efficient as the level of supercoiling was reduced.

294 he mechanical interplay between H-NS and DNA supercoiling which provides insights to H-NS organizatio

295 olicus GyrB subunit is capable of supporting supercoiling with Escherichia coli GyrA, but not DNA rel

296 ccupancy of Cse4 at STB induces positive DNA supercoiling, with a linking difference (DeltaLk) contri

297 tA, and ltuB, were relatively insensitive to supercoiling, with promoter activity varying by no more

298 E. coli cells display a gradient of negative supercoiling, with the terminus being more negatively su

299 e torsion in front of the polymerase induces supercoiling (writhe) and is largely resolved by Top2.

300 activity in relieving transcription-induced supercoiling, yeast genes encoding rRNA were visualized