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 the protein is involved in sequestration of supercoils.

4 upercoils, rather than induction of negative supercoils.

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

6 pid removal of transcription driven negative supercoils.

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

8 Bacterial plasmids are negatively supercoiled.

9 atalytic activity and increases negative DNA supercoiling.

10 e important in defining the mechanics of DNA supercoiling.

11 pression globally, likely by constrained DNA supercoiling.

12 scription responds to the increased negative supercoiling.

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

14 ctivated PR1-2 via transcription coupled DNA supercoiling.

15 iently relieve transcription-driven negative supercoiling.

16 ic flagella (PF) with pronounced spontaneous supercoiling.

17 scale conformational transitions elicited by supercoiling.

18 along their duplex substrates results in DNA supercoiling.

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

20 shifts toward H-DNA with increased negative supercoiling.

21 nicircle topoisomers with defined degrees of supercoiling.

22 angement of polymerase binding sites and DNA supercoiling.

23 odes, is able to differentially regulate DNA supercoiling.

24 promote DNA plectoneme formation during DNA supercoiling.

25 scuous cleavage under physiological negative supercoiling.

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

27 fluorophore density or reducing the level of supercoiling.

28 kinetics, efficiency, and extent of negative supercoiling.

29 applications that exploit sensitivity to DNA supercoiling.

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

31 rescently labeled protospacer insertion in a supercoiled 3-kb plasmid harboring a minimal CRISPR locu

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

33 ive supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA p

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

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

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

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

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

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

40 es with the hyperactivation of condensin DNA supercoiling activity.

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

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

43 cient DNA-stimulated ATPases and efficiently supercoil and decatenate DNA.

44 /6 binds DNA topologically with affinity for supercoiled and catenated DNA templates.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

70 tenanes between sister chromatids as well as supercoils associated with the over- or under-winding of

71 Negative supercoil at gene boundaries prevents supercoil diffusio

72 Top2 and Hmo1 preserve negative supercoil at gene boundaries, while Top1 acts at coding

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

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

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

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

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

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

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

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

81 open complex formation, suggesting enhanced supercoiling buildup.

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

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

84 Negative supercoiling by DNA gyrase is essential for maintaining

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

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

87 Topoisomerase I (Top1) resolves supercoils by nicking one DNA strand and facilitating re

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

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

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

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

92 nhibitor and bovine aprotinin that they nick supercoiled, circular plasmid DNA.

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

94 ominating under the physiologically relevant supercoiled conditions.

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

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

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

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

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

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

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

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

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

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

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

106 Supercoiling describes the coiling of the axis of the DN

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

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

109 gative supercoil at gene boundaries prevents supercoil diffusion and nucleosome repositioning at codi

110 boundaries simply through the inhibition of supercoil diffusion.

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

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

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

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

115 or this reason, methods to prepare and study supercoiled DNA at the single-molecule level are widely

116 is required for the relaxation of negatively supercoiled DNA behind the transcribing RNA polymerase.

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

118 topological barriers using polymer models of supercoiled DNA chains that are constrained such as to m

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

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

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

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

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

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

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

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

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

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

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

130 Supercoiled DNA polymer models for which the torsional e

131 apping does not result in a more extensively supercoiled DNA product, but partially uncouples ATP tur

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

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

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

135 ion and replication, resulting in a range of supercoiled DNA structures.

136 capture one strand of underwound negatively supercoiled DNA substrate first and position the N-termi

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

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

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

140 rapidly and controllably generate negatively supercoiled DNA using a standard dual-trap optical tweez

141 ODS), uniquely combines the ability to study supercoiled DNA using force spectroscopy, fluorescence i

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

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

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

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

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

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

148 In addition, double-stranded supercoiled DNA-cleavage experiments with shishijimicin

149 ecially the V256I variant towards positively supercoiled DNA.

150 ich is necessary for relaxation reactions of supercoiled DNA.

151 for predicting equilibrium conformations of supercoiled DNA.

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

153 de atomistic insight into the flexibility of supercoiled DNA.

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

155 role in maintaining DNA topology by relaxing supercoiled DNA.

156 NA nuclease activity specific for nicking of supercoiled DNA.

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

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

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

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

161 ust uncover and characterize the dynamics of supercoiled DNA.

162 y visualize and quantify protein dynamics on supercoiled DNA.

163 to study complex and dynamic interactions of supercoiled DNA.

164 es and biological interactions of negatively supercoiled DNA.

165 During transcription, RNA polymerase (RNAP) supercoils DNA as it translocates.

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

167 NA-processing enzymes, predicted by the twin-supercoiled domain model, can be largely accommodated by

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

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

170 However, supercoil dynamics are difficult to access because of th

171 undamental step in plectoneme nucleation and supercoil dynamics, which are critical for the processin

172 iences significant drag and thereby obscures supercoil dynamics.

173 ess and thereby advance our understanding of supercoil dynamics.

174 Motility is powered by the rotation of supercoiled 'endoflagella' that wrap around the cell bod

175 Supercoiling-enhanced looping can influence the maintena

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

177 s from twist changes for twisted, coiled, or supercoiled fibers, including those of natural rubber, n

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

179 tructure, subsequently culminating with over-supercoiled form through in-path intermediates.

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

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

182 essential for chromosome segregation and DNA supercoiling homeostasis.

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

184 Supercoiling imposes stress on a DNA molecule that can d

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

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

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

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

189 iological role of preventing excess negative supercoiling in the genome.

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

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

192 opoisomerases capable of generating positive supercoils in DNA.

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

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

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

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

197 As negative supercoiling increases, bases are increasingly exposed.

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

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

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

201 Bacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive sup

202 al bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accu

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

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

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

206 ls into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by

207 rapping by the CTD provides one limit to DNA supercoil introduction, beyond which strand passage comp

208 Supercoiling is able to induce some compaction of the ba

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

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

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

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

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

214 Removal of these positive supercoils is essential for replication fork progression

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

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

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

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

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

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

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

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

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

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

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

226 rgoes reduced fluctuations when bound to the supercoiled minicircle.

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

228 approximately 3-fold faster than negatively supercoiled molecules.

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

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

231 te chiralities of twist and coiling produces supercoiled natural rubber fibers and coiled fishing lin

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

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

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

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

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

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

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

239 an indirect effect promoting global negative supercoiling of DNA.

240 sential function in preventing hypernegative supercoiling of DNA.

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

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

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

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

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

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

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

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

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

250 ncation mutants reveal that integration to a supercoiled plasmid increases without the outer monomer

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

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

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

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

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

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

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

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

259 nt with these catalyzing processive positive supercoil relaxation in front of the progressing repliso

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

261 le simultaneously enhancing decatenation and supercoil relaxation.

262 h strand passage competes with ATP-dependent supercoil relaxation.

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

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

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

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

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

268 This supercoiling-responsivesness is consistent with negative

269 Both supercoil retention assays and binding measurement by fl

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

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

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

273 ly enhanced in DNA molecules that maintain a supercoiled state with constant torsional tension.

274 erial cells primarily exists in a negatively supercoiled state.

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

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

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

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

279 ique can be used to generate a wide range of supercoiled states, with between <5 and 70% lower helica

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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