ライフサイエンスコーパス: supercoiling

1 pression globally, likely by constrained DNA supercoiling.

2 shifts toward H-DNA with increased negative supercoiling.

3 nicircle topoisomers with defined degrees of supercoiling.

4 angement of polymerase binding sites and DNA supercoiling.

5 y the effect of mismatched base pairs on DNA supercoiling.

6 odes, is able to differentially regulate DNA supercoiling.

7 promote DNA plectoneme formation during DNA supercoiling.

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

9 suppress DNA plectoneme formation during DNA supercoiling.

10 develop a HT screen for inhibitors of gyrase supercoiling.

11 tems, induce topological changes such as DNA supercoiling.

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

13 along their duplex substrates results in DNA supercoiling.

14 ation and religation on the torque caused by supercoiling.

15 fluorophore density or reducing the level of supercoiling.

16 match those of singlets but differ in their supercoiling.

17 information on the mechanism of DNA negative supercoiling.

18 other mid genes in response to increased DNA supercoiling.

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

20 were activated in response to increased DNA supercoiling.

21 which show significant helix bending but not supercoiling.

22 poisomerase subunit while promoting positive supercoiling.

23 p2 alleviates transcription-induced positive supercoiling.

24 upstream and downstream transcription-driven supercoiling.

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

26 ation and segregation, and in regulating DNA supercoiling.

27 scuous cleavage under physiological negative supercoiling.

28 kinetics, efficiency, and extent of negative supercoiling.

29 es (>2 kb) through transcription-induced DNA supercoiling.

30 applications that exploit sensitivity to DNA supercoiling.

31 atalytic activity and increases negative DNA supercoiling.

32 scription responds to the increased negative supercoiling.

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

34 ctivated PR1-2 via transcription coupled DNA supercoiling.

35 iently relieve transcription-driven negative supercoiling.

36 ic flagella (PF) with pronounced spontaneous supercoiling.

37 e important in defining the mechanics of DNA supercoiling.

38 scale conformational transitions elicited by 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 ge and reduces DNA-stimulated ATPase and DNA supercoiling activities only 2-fold.

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

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

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

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

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

49 es with the hyperactivation of condensin DNA supercoiling activity.

50 during replication elongation by driving DNA supercoiling ahead of the fork, where supercoiling is mo

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

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

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

54 Type II topoisomerases regulate DNA supercoiling and chromosome segregation.

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

56 se that catalyzes ATP-dependent negative DNA supercoiling and DNA decatenation.

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

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

59 for the coupling between the dynamics of DNA supercoiling and gene transcription.

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

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

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

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

64 omerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation.

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

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

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

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

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

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

71 a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecul

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

73 riptional bursting is observed when both the supercoiling and the mechanical stress release due to gy

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

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

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

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

78 -DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for u

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

80 four-helix backbones with varying degrees of supercoiling around a central axis, identified those acc

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

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

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

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

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

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

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

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

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

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

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

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

93 ase I inhibitors suggest hindrance to escape supercoiling buildup at low temperatures.

94 ndicating that the rate of escaping positive supercoiling buildup is temperature and transcription ra

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

96 open complex formation, suggesting enhanced supercoiling buildup.

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

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

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

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

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

102 Negative supercoiling by DNA gyrase is essential for maintaining

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

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

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

106 s both nucleotide-dependent DNA wrapping and supercoiling by the enzyme.

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

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

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

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

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

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

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

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

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

116 , it is currently challenging to combine DNA supercoiling control with spatial manipulation and fluor

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

118 This finding suggests a mechanism by which supercoiling could regulate mitochondrial transcription

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

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

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

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

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

124 DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrati

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

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

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

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

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

130 king motif of four base pairs independent of supercoiling density.

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

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

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

134 Supercoiling describes the coiling of the axis of the DN

135 activities allows for induction of positive supercoiling despite opposing torque.

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

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

138 e timescales of transcription initiation and supercoiling dissipation (the latter may either be diffu

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

147 allows us to evaluate the energetic cost of supercoiling during transcription.

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

149 Supercoiling-enhanced looping can influence the maintena

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

151 ase hydrolyzes ATP only slowly and is a poor supercoiling enzyme and decatenase.

152 In the bursty phase, the statistics of supercoiling fluctuations at the promoter are markedly n

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

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

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

156 Overall, our findings indicate that the supercoiling generated by DNA-processing enzymes, predic

157 ent inner and outer curvatures to define the supercoiling geometry, explaining a key functional attri

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

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

160 essential for chromosome segregation and DNA supercoiling homeostasis.

161 Weakening CTD-DNA interactions slows supercoiling, impairs DNA-dependent ATP hydrolysis, and

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 uestion of the interplay of DNA demixing and supercoiling in bacterial cells.

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

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

168 ects on DNA supercoiling and the dynamics of supercoiling in molecular detail.

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 iological role of preventing excess negative supercoiling in the genome.

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

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

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

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

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

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

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

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

181 As negative supercoiling increases, bases are increasingly exposed.

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

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

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

185 eloped a stochastic mechanochemical model of supercoiling-induced transcriptional bursting in which t

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

187 ch as DNA replication and transcription, DNA supercoiling, intracellular transport, and ATP synthesis

188 The supercoiling involves the switching of coiled-coil proto

189 Supercoiling is able to induce some compaction of the ba

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

191 Supercoiling is an indicator of cell health, it modifies

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

193 ng DNA supercoiling ahead of the fork, where supercoiling is more efficiently removed by topoisomeras

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

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

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

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

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

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

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

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

202 Changes in DNA supercoiling levels during the chlamydial developmental

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

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

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

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

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 DNA binding proteins, supercoiling, macromolecular crowders, and transient DNA

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

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

212 ects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop fo

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 This method, termed Optical DNA Supercoiling (ODS), uniquely combines the ability to stu

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

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

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 cation machinery introduces intertwining and supercoiling of DNA strands as it traverses the double h

226 nfirmed PaParE inhibition of gyrase-mediated supercoiling of DNA with an IC(50) value in the low micr

227 an indirect effect promoting global negative supercoiling of DNA.

228 sential function in preventing hypernegative supercoiling of DNA.

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

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

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

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

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

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

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

236 ose maintain steady-state levels of negative supercoiling of the chromosome.

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

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

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

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

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

242 fiber is torsionally stiff, indicating that supercoiling on chromatin substrates is preferentially d

243 ime in which the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply ad

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

245 specialized functions in the control of DNA supercoiling or in DNA catenation/decatenation during re

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

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

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

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

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

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

252 DNA supercoiling plays an important role in a variety of cel

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

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

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

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

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

258 nderstanding how dynamic modification of DNA supercoiling regulates transcription.

259 Efficiency of negative supercoiling relaxation increases with the number of dom

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

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

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

263 Analysis of the degree of DNA supercoiling required for RepC nicking, and the time bet

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

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

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

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

268 This supercoiling-responsivesness is consistent with negative

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

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

271 luding those that are essential and possibly supercoiling sensitive.

272 his, since cold-shock genes exhibit atypical supercoiling-sensitivities.

273 which gyrase can evolve distinct homeostatic supercoiling setpoints in a species-specific manner.

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

275 ed into dispersed, smaller clusters when the supercoiling state of the nucleoid was perturbed.

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

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

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

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

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

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

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

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

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

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

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

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

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

291 Recent studies suggest that DNA supercoiling, which happens during transcription, might

292 nvestigate the structural basis of flagellar supercoiling, which is critical for motility, we determi

293 DNA replication in eukaryotes generates DNA supercoiling, which may intertwine (braid) daughter chro

294 ATP hydrolysis, and limits the extent of DNA supercoiling, while simultaneously enhancing decatenatio

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

298 s and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promo

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