ライフサイエンスコーパス: supercoil

1 coils per second (average burst size was 6.2 supercoils).

2 ha-helical secondary structures wrapped in a supercoil.

3 amphipathic alpha-helices that twist into a supercoil.

4 a 'coil of coiled coils', form a plectonemic supercoil.

5 pid removal of transcription driven negative supercoils.

6 ase I (Top1) catalyzes the relaxation of DNA supercoils.

7 omosomes and preferentially relaxes positive supercoils.

8 upercoils, rather than induction of negative supercoils.

9 the protein is involved in sequestration of supercoils.

10 ls, extended plectonemes, and branched hyper-supercoils.

11 Bacterial plasmids are negatively supercoiled.

12 shifts toward H-DNA with increased negative supercoiling.

13 nicircle topoisomers with defined degrees of supercoiling.

14 angement of polymerase binding sites and DNA supercoiling.

15 odes, is able to differentially regulate DNA supercoiling.

16 promote DNA plectoneme formation during DNA supercoiling.

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

18 atalytic activity and increases negative DNA supercoiling.

19 suppress DNA plectoneme formation during DNA supercoiling.

20 develop a HT screen for inhibitors of gyrase supercoiling.

21 scription responds to the increased negative supercoiling.

22 tems, induce topological changes such as DNA supercoiling.

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

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

25 ctivated PR1-2 via transcription coupled DNA supercoiling.

26 iently relieve transcription-driven negative supercoiling.

27 ic flagella (PF) with pronounced spontaneous supercoiling.

28 scale conformational transitions elicited by supercoiling.

29 DNA gyrase essentially failed to negatively supercoil 35% stiffer DAP DNA.

30 an isoforms, preferentially relaxes positive supercoils, a feature shared with Escherichia coli topoi

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

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

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

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

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

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

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

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

39 es with the hyperactivation of condensin DNA supercoiling activity.

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

41 ue, we measured the relaxation of individual supercoiled and "braided" DNA molecules by htopo IIalpha

42 element that inhibits activity on negatively supercoiled and catenated substrates, as well as a disti

43 Type II topoisomerases regulate DNA supercoiling and chromosome segregation.

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

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

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

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

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

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

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

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

52 poisomerase topo IV rapidly removes positive supercoils and catenanes from DNA but is significantly s

53 in their shape and the capacity to constrain supercoils and compact the DNA.

54 completely suppressed by removal of negative supercoils and further aggravated by expression of mutan

55 We found that mechanical stress induces supercoils and plectonemes in the sensory axons of spect

56 po IIA) are essential enzymes that relax DNA supercoils and remove links joining replicated chromosom

57 MukB condenses DNA by sequestering negative supercoils and stabilizing topologically isolated loops

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

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

60 Gyrase removed positive supercoils approximately 10-fold more rapidly and more p

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

62 y low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-en

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

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

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

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

67 able tape-like structures that, in turn, are supercoiled at the microscale.

68 ntitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent qualit

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

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

71 des the anticipated accumulation of positive supercoils between head-on-conflicting polymerases.

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

73 supercoil that is converted into a negative supercoil by strand passage.

74 n bacteria, these catenated molecules become supercoiled by DNA gyrase before they undergo a complete

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

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

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

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

79 MukB stimulates the relaxation of negative supercoils by topo IV; to understand the mechanism of th

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

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

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

83 Supercoil chirality, twist density, and tension determin

84 within the nucleosome unit and higher-order supercoiled chromatin leading to neutralization of the n

85 r(-)sc emerges in the middle of a positively supercoiled chromosomal domain is a mystery that require

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

87 opological reconfiguration of the negatively supercoiled compared with positively supercoiled DNA by

88 or either bent compared with straight DNA or supercoiled compared with relaxed DNA, and untwists DNA

89 levels of cleavage complexes with positively supercoiled (compared with negatively supercoiled) DNA,

90 ominating under the physiologically relevant supercoiled conditions.

91 that confinement leads to "freezing" of the supercoiled configuration.

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

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

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

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

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

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

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

99 oresis of DNA topoisomers did not detect any supercoil-dependent structural transitions.

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

101 boundaries simply through the inhibition of supercoil diffusion.

102 urnover is why M. tuberculosis gyrase cannot supercoil DNA to the same extent as its gamma-proteobact

103 Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particul

104 tion activity of Top3beta on hypernegatively supercoiled DNA and changes the reaction from a distribu

105 merase IV, enhanced relaxation of negatively supercoiled DNA and knotting by topoisomerase IV, which

106 TOP3B relaxes negative supercoiled DNA and reduces transcription-generated R lo

107 Nicking by RepC occurred only in negatively supercoiled DNA and was force- and twist-dependent.

108 the proteins preferentially bind negatively supercoiled DNA but the details of the topology-dependen

109 Relaxation of negatively supercoiled DNA by DNA gyrase is inhibited, whereas the

110 release the free energy stored in negatively supercoiled DNA by extruding the repeat as a cruciform.

111 -based assay for ATP-dependent relaxation of supercoiled DNA by human TOP2A can also be used under id

112 atively supercoiled compared with positively supercoiled DNA by MukB.

113 e presence of YejK, relaxation of negatively supercoiled DNA by topoisomerase IV becomes distributive

114 can induce the formation of hypernegatively supercoiled DNA in vitro and in vivo.

115 stributive, whereas relaxation of positively supercoiled DNA is stimulated.

116 nzyme relaxes both negatively and positively supercoiled DNA like the eukaryotic enzymes.

117 ce-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect

118 Finally, the more complex topology of the supercoiled DNA minicircle gives rise to a secondary DNA

119 n simulated covalently bound to a negatively supercoiled DNA minicircle, and its behavior compared to

120 essor protein to distal recognition sites on supercoiled DNA minicircles using MD simulations.

121 B is also able to stabilize writhe in single supercoiled DNA molecules and to bridge segments from tw

122 Our methodology enables the study of supercoiled DNA molecules at greater length scales and s

123 lo simulations, we investigate the shapes of supercoiled DNA molecules that are either knotted or cat

124 ng on right-handed plectonemes in negatively supercoiled DNA molecules.

125 opo IV is also involved in the unknotting of supercoiled DNA molecules.

126 ted G-quadruplex formation within negatively supercoiled DNA plasmids.

127 Supercoiled DNA polymer models for which the torsional e

128 wnian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confi

129 lar reactions catalyzed by topoisomerase IV, supercoiled DNA relaxation, and DNA knotting but not int

130 scriminate between positively and negatively supercoiled DNA requires the C-terminal domain (CTD) of

131 tivity of PFCP, based on their protection of supercoiled DNA strand from scission by peroxyl and hydr

132 ned computational model that treats both the supercoiled DNA structural monomers and the smaller prot

133 se promoters had higher activity from a more supercoiled DNA template.

134 tations and simulate the dynamic response of supercoiled DNA to a single strand nick.

135 molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomera

136 forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick

137 stimulation because relaxation of positively supercoiled DNA was unaffected.

138 oisomerase IV to relax and cleave positively supercoiled DNA were analyzed.

139 percoiled DNA with a mismatch and positively supercoiled DNA with a bulge.

140 ates: negatively supercoiled DNA, positively supercoiled DNA with a mismatch and positively supercoil

141 ved in experimental sedimentation studies of supercoiled DNA, and our results provide a physical expl

142 d crossings, Topo IV can specifically unknot supercoiled DNA, as well as decatenate postreplicative c

143 ever, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown.

144 V have critical interactions with positively supercoiled DNA, little is known about the actions of th

145 ducted on several DNA substrates: negatively supercoiled DNA, positively supercoiled DNA with a misma

146 at normally represses activity on negatively supercoiled DNA, while complementation tests using mutan

147 cells, RNA polymerase (RNAP) must transcribe supercoiled DNA, whose torsional state is constantly cha

148 , we also detect exposed bases in positively supercoiled DNA.

149 de atomistic insight into the flexibility of supercoiled DNA.

150 the topology (topological linking number) of supercoiled DNA.

151 role in maintaining DNA topology by relaxing supercoiled DNA.

152 onuclease that makes single-strand breaks in supercoiled DNA.

153 the protein has a preference for binding to supercoiled DNA.

154 regions or nicks as well as relax negatively supercoiled DNA.

155 s between linear double-stranded (dsDNA) and supercoiled DNA.

156 l Escherichia coli RNAPs as they transcribed supercoiled DNA.

157 ies in its preference of relaxing negatively supercoiled DNA.

158 polar region of potential energy within the supercoiled DNA.

159 icient for the production of hypernegatively supercoiled DNA.

160 ecially the V256I variant towards positively supercoiled DNA.

161 ich is necessary for relaxation reactions of supercoiled DNA.

162 for predicting equilibrium conformations of supercoiled DNA.

163 tively supercoiled (compared with negatively supercoiled) DNA, whereas topoisomerase IV generated sim

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

165 ahead of the RNA polymerase and a negatively supercoiled domain behind it.

166 n" model of transcription where a positively supercoiled domain is generated ahead of the RNA polymer

167 nomenon has been nicely explained by a "twin-supercoiled-domain" model of transcription where a posit

168 etically suggestive of the physically folded supercoiled domains, along with a method for predicting

169 block twists diffusion thus trapping DNA in supercoiled domains.

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

171 otein and demonstrated to bind and nick both supercoiled duplex DNA and oligonucleotides in vitro in

172 iences significant drag and thereby obscures supercoil dynamics.

173 Supercoiling-enhanced looping can influence the maintena

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

175 ition may facilitate persistence of negative supercoils, exposing the coding single strand and possib

176 ked"), and covalently closed circular (ccc, "supercoiled") form.

177 Compared with relaxed DNA, the presence of supercoils greatly enhances juxtaposition probability.

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

179 essential for chromosome segregation and DNA supercoiling homeostasis.

180 Supercoiling imposes stress on a DNA molecule that can d

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

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

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

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

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

186 ates or pauses during relaxation of positive supercoils in DAP-substituted versus normal DNA were dis

187 A) to recognize the accumulation of negative supercoils in duplex DNA.

188 that HMGB1 specifically introduces negative supercoils in ICL-containing plasmids in HeLa cell extra

189 s shown to bind ssDNA and stabilize negative supercoils in plasmid DNA.

190 e in binding to DNA and maintaining negative supercoils in the latter.

191 , or produces extensive build-up of negative supercoils in the newly synthesized DNA.

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

193 As negative supercoiling increases, bases are increasingly exposed.

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

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

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

197 I DNA topoisomerase that introduces negative supercoils into DNA in an ATP-dependent reaction.

198 ore processively than it introduced negative supercoils into relaxed DNA.

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

200 Supercoiling is an indicator of cell health, it modifies

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

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

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

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

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

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

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

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

209 Changes in DNA supercoiling levels during the chlamydial developmental

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

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

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

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

214 We conclude that the chromosome structure is supercoiled locally and elongated at large length scales

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

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

217 rgoes reduced fluctuations when bound to the supercoiled minicircle.

218 approximately 3-fold faster than negatively supercoiled molecules.

219 e helix, three peptides self-assemble into a supercoiled motif with a one-amino-acid offset between t

220 In particular, in negatively supercoiled, multiply interlinked, right-handed catenane

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

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

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

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

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

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

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

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

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

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

235 ss is compacted more quickly than negatively supercoiled or nicked DNAs.

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

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

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

239 nd DNA with burst rates of approximately 100 supercoils per second (average burst size was 6.2 superc

240 BLM is more potent than deglycoBLM in supercoiled plasmid DNA relaxation, while the analogue h

241 copper-induced LDL-cholesterol oxidation and supercoiled plasmid DNA strand breakage inhibition induc

242 ng a different binding mechanism between the supercoiled plasmid on one hand and the oc and linear is

243 eported on the chromatographic separation of supercoiled plasmid topoisomers on cinchona-alkaloid mod

244 a two-plasmid system in which a linear, non-supercoiled plasmid was used to express lac repressor co

245 In negatively supercoiled plasmids containing head-to-tail sites, the

246 DHX9 associated with H-DNA in the context of supercoiled plasmids.

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

248 patial domains that are probably composed of supercoiled plectonemes arrayed into a bottle brush-like

249 efficiency were observed around 300 kHz for supercoiled pUC18 and 100 kHz for linear lambdaDNA.

250 evolved to promote rapid removal of positive supercoils, rather than induction of negative supercoils

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

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

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

254 nderstanding how dynamic modification of DNA supercoiling regulates transcription.

255 emical properties by magnetic tweezers-based supercoil relaxation and classical DNA relaxation assays

256 these experiments, indirect measurements of supercoil relaxation are obtained by observing the motio

257 Here, we used a single-molecule DNA supercoil relaxation assay to measure the torque depende

258 ral discrimination and tension dependence of supercoil relaxation by human topoisomerase IIalpha.

259 analyses, we also show that Lam-D slows down supercoil relaxation of Top1mt and strongly inhibits Top

260 important for DNA bending, DNA cleavage and supercoil relaxation.

261 irst, extension is a poor dynamic measure of supercoil relaxation; in fact, the linking number relaxe

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

263 Efficient positive supercoil removal required the GyrA-box, which is necess

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

265 This supercoiling-responsivesness is consistent with negative

266 Both supercoil retention assays and binding measurement by fl

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

268 luding those that are essential and possibly supercoiling sensitive.

269 ution facilitates topoisomer separation, the supercoiled species are eluting as a single peak upon el

270 erial cells primarily exists in a negatively supercoiled state.

271 of the CI-operator structure in its natural, supercoiled state.

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

273 flagellin-which can switch between different supercoiled states in a highly cooperative manner.

274 Various supercoiled states of the filament exist, which are form

275 single protein can switch between different supercoiled states with high cooperativity.

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

277 all of which possess filamentous coiled-coil/supercoiled structures.

278 The presence of the more realistic supercoiled substrate facilitates the formation of large

279 during strand passage and relaxed positively supercoiled substrates approximately 3-fold faster than

280 antly slower when confronted with negatively supercoiled substrates.

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

282 bda switch is significantly increased in the supercoiled system compared with a linear assay, increas

283 Protospacer DNA with free 3'-OH ends and supercoiled target DNA are required, and integration occ

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

285 ing, with the terminus being more negatively supercoiled than the origin of replication, and that suc

286 As a result, DNA is bound as a positive supercoil that is converted into a negative supercoil by

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

288 n topoisomerase IV to safely remove positive supercoils that accumulate ahead of replication forks.

289 proceed first via the formation of negative supercoils that are sequestered by the protein followed

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

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

292 These insertions strain the supercoil to the breaking point, causing the local forma

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

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

295 ism to achieve separation of isoforms and/or supercoiled topoisomers using the very same chromatograp

296 evant to transcription-coupled remodeling of supercoiled topological domains, and we discuss possible

297 previously not seen triangular, square, and supercoiled topologies.

298 Some type II topoisomerases relax supercoils, unknot and decatenate DNA to below thermodyn

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

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