ライフサイエンスコーパス: supercoiled

1 d the right-handed conformer (DNA positively supercoiled).

2 nal start site even when the DNA template is supercoiled.

3 Bacterial plasmids are negatively supercoiled.

4 Supercoiled (3)H-pUC19 plasmid samples were irradiated w

5 nucleosome positioning sequence, MP2, into a supercoiled AID target plasmid to determine where around

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

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

8 e spermidine-induced bias is seen equally on supercoiled and linear excisive recombination junction i

9 ular transfer of active Tnp occurs with both supercoiled and linear non-specific DNA.

10 the presence of increasing concentrations of supercoiled and linear pUC19.

11 c DNA in vitro and in situ; on duplex DNA in supercoiled and linearized plasmids; and on oligonucleot

12 rination was contingent on the plasmid being supercoiled and was not observed in linearized plasmids,

13 ed the left-handed conformer (DNA negatively supercoiled), and mutations within the globular region p

14 ffusion coefficients D for relaxed circular, supercoiled, and linear DNA molecules of length L rangin

15 with different configurations, e.g., linear, supercoiled, and relaxed or DNA of different length, e.g

16 of circular plasmids, become positively (+) supercoiled, and the unlinking of such catenanes by type

17 The chlamydial plasmid was most negatively supercoiled at midcycle, with an approximate superhelica

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

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

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

21 ciently than the unlinking of negatively (-) supercoiled catenanes.

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

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

24 Site-specific recombination on supercoiled circular DNA molecules can yield a variety o

25 Site-specific recombination on supercoiled circular DNA yields a variety of knotted or

26 d to estimate torsional rigidities of weakly supercoiled circular DNAs.

27 tes, including linear, relaxed circular, and supercoiled circular forms.

28 maged complexes of RdgC with both linear and supercoiled circular plasmid DNA using atomic force micr

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

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

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

32 ominating under the physiologically relevant supercoiled conditions.

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

34 presumably before the reverse shift to the B-supercoiled conformation.

35 uplication is in a stable low linking number supercoiled conformation.

36 ndertaken to confirm the identity of a minor supercoiled dimeric concatamer observed by both approach

37 te an overwhelming preference for negatively supercoiled DNA ((-)scDNA) as a cofactor for the hydroly

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

39 d III (Topo I and Topo III) relax negatively supercoiled DNA and also catenate/decatenate DNA molecul

40 po IIIbeta only partially relaxes negatively supercoiled DNA and appears incapable of generating full

41 ximately one StpA molecule per 250-300 bp of supercoiled DNA and approximately one StpA molecule per

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

43 Relaxation is powered by the torque in the supercoiled DNA and is constrained by friction between t

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

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

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

47 isomerases is required for the relaxation of supercoiled DNA and was hypothesized to be required for

48 ymus topoisomerase I (CT Topo I) on a native supercoiled DNA and, if so, whether the enzyme catalyzes

49 ruciform, suggesting that these positions in supercoiled DNA are under additional stress and perhaps

50 tically modifies this picture by introducing supercoiled DNA as a competing structure in addition to

51 ve topoisomerase that is capable of relaxing supercoiled DNA at a broad range of Mg2+ concentrations;

52 th the Hin synaptic complex at the base of a supercoiled DNA branch.

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

54 omerase I (Top1) catalyzes the relaxation of supercoiled DNA by a conserved mechanism of transient DN

55 ype IB topoisomerases catalyze relaxation of supercoiled DNA by cleaving and rejoining DNA strands vi

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

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

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

59 atively supercoiled compared with positively supercoiled DNA by MukB.

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

61 preparation, but ''ghost bands" of denatured supercoiled DNA can result if the pH is too high or the

62 ve any advantage to (+) supercoiled over (-) supercoiled DNA catenanes for unlinking.

63 We showed that in (-) supercoiled DNA catenanes this protein-bound bent segmen

64 ter simulation, conformational properties of supercoiled DNA catenanes.

65 partially relaxed molecules with a D-loop or supercoiled DNA circles.

66 tion barrier against the merge of oppositely supercoiled DNA domains.

67 BapE fragments chromosomes by cleaving supercoiled DNA in a sequence-nonspecific manner, thereb

68 old decrease in processivity was observed on supercoiled DNA in comparison with linear DNA.

69 ATA box-directed transcription of linear and supercoiled DNA in the absence of Bdp1.

70 s capable of efficiently relaxing negatively supercoiled DNA in the presence of Mg2+ but does not pos

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

72 Enhanced drug efficacy on positively supercoiled DNA is due primarily to an increase in basel

73 demonstrate that enzyme bound to positively supercoiled DNA is in a different conformation from that

74 Supercoiled DNA is known to favor transient separation o

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

76 nd relaxed or DNA of different length, e.g., supercoiled DNA ladder.

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

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

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

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

81 evaluate the looping of both linear DNA and supercoiled DNA minicircles over a broad range of DNA in

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

83 Transposase made double-strand breaks on a supercoiled DNA molecule containing a mini-ISY100 transp

84 binding proteins are capable of separating a supercoiled DNA molecule into distinct topological domai

85 , and lambda O protein, are able to divide a supercoiled DNA molecule into two independent topologica

86 iple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specifie

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

88 We have recently shown that apexes of supercoiled DNA molecules are sites that can promote the

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

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

91 o, a recombinant fragment of ATAD3p bound to supercoiled DNA molecules that contained a synthetic D-l

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

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

94 Supercoiled DNA plasmids were exposed in the frozen stat

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

96 Supercoiled DNA polymer models for which the torsional e

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

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

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

100 rimer-DNA complex crystal, p53 can recognize supercoiled DNA sequence-specifically by binding to quar

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

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

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

104 fied GAS RNA polymerase and either linear or supercoiled DNA template.

105 i.e., low salt concentrations or negatively supercoiled DNA templates.

106 t full-length Tnp interacts efficiently with supercoiled DNA that does not contain ESes.

107 o transcription assays for the first time on supercoiled DNA that mimics in vivo situation.

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

109 topoisomerases decatenate, unknot and relax supercoiled DNA to levels below equilibrium, resulting i

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

111 y to induce cell cycle arrest and to convert supercoiled DNA to relaxed and linear forms in vitro.

112 From supercoiled DNA to the tight loops of DNA formed by some

113 merase I (Top1p) catalyzes the relaxation of supercoiled DNA via a concerted mechanism of DNA strand

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

115 eta and topoisomerase I to cleave positively supercoiled DNA was assessed in the absence or presence

116 ss-linked species of topo IV when positively supercoiled DNA was in the reaction.

117 stimulation because relaxation of positively supercoiled DNA was unaffected.

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

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

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

121 Unwinding the supercoiled DNA with ethidium bromide also made DNA resi

122 HMO2 binds supercoiled DNA with higher affinity than linear DNA and

123 The reaction pathway for FokI on a supercoiled DNA with two sites was dissected by fast kin

124 Moreover, cleavage of supercoiled DNA, and estimates of strand-specific cleava

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

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

127 Whereas DnaD opens up supercoiled DNA, DnaB acts as a lateral compaction prote

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

129 move linear DNA from a mixture of linear and supercoiled DNA, leaving the supercoiled form intact.

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

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

132 verse gyrase can completely relax positively supercoiled DNA, provided that the DNA substrate contain

133 +/- 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with th

134 Once translocation is impeded on supercoiled DNA, the DNA is cleaved.

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

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

137 e DNA cleavage agent, displaying significant supercoiled DNA-nicking activity at concentrations as lo

138 icient for the production of hypernegatively supercoiled DNA.

139 ecially the V256I variant towards positively supercoiled DNA.

140 gative supercoils to produce hypernegatively supercoiled DNA.

141 al role in the generation of hypernegatively supercoiled DNA.

142 t can crosslink two separate DNA segments in supercoiled DNA.

143 amic continuum rod model of a long length of supercoiled DNA.

144 tions to determine the structure of bent and supercoiled DNA.

145 opoIIalpha-mediated relaxation of positively supercoiled DNA.

146 lity of topoisomerase I to cleave positively supercoiled DNA.

147 G-rich sequence of this region in negatively supercoiled DNA.

148 linear dsDNA and its homologous pairing with supercoiled DNA.

149 ich is necessary for relaxation reactions of supercoiled DNA.

150 ed double-stranded DNA, when transcribed, or supercoiled DNA.

151 lar DNA has been enzymatically prepared from supercoiled DNA.

152 levels of cleavage complexes with positively supercoiled DNA.

153 omerase I, an enzyme that relaxes negatively supercoiled DNA.

154 elative cleavage enhancement with positively supercoiled DNA.

155 lexes with positively rather than negatively supercoiled DNA.

156 only when the enzyme is bound to positively supercoiled DNA.

157 myc FUSE in vitro only in single-stranded or supercoiled DNA.

158 e reaction and preferentially cut negatively supercoiled DNA.

159 for predicting equilibrium conformations of supercoiled DNA.

160 ith AMPPNP, the product is a hypernegatively supercoiled DNA.

161 u and a distant enhancer site (E) located on supercoiled DNA.

162 as well as for 4-way junction structures and supercoiled DNA.

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

164 de atomistic insight into the flexibility of supercoiled DNA.

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

166 role in maintaining DNA topology by relaxing supercoiled DNA.

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

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

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

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

171 l Escherichia coli RNAPs as they transcribed supercoiled DNA.

172 ies in its preference of relaxing negatively supercoiled DNA.

173 polar region of potential energy within the supercoiled DNA.

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

175 diffused slower when size of DNAs increased; supercoiled DNAs diffused faster than linear ones; mucus

176 imm model with a scaling factor of -0.8, and supercoiled DNAs showed a reptational behavior with a sc

177 of linear DNAs but retarded the diffusion of supercoiled DNAs.

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

179 A gyrase selectively converts the positively supercoiled domain into negative supercoils to produce h

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

181 pts in vivo, precisely predicted by the twin-supercoiled-domain model of transcription.

182 his phenomenon has been explained by a "twin-supercoiled-domain" model of transcription in which posi

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

184 Our results can be explained by the "twin-supercoiled-domain" model of transcription where the fri

185 of selectively linearizing one or the other supercoiled domains created by the DNA*DNA associated re

186 The diffusional merge of these oppositely supercoiled domains is not significantly affected by the

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

188 block twists diffusion thus trapping DNA in supercoiled domains.

189 es, such as G-quadruplexes, can be formed in supercoiled duplex DNA and DNA in chromatin in vivo unde

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

191 e of linear and supercoiled DNA, leaving the supercoiled form intact.

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

193 It binds to supercoiled forms and converts them to open forms withou

194 Although DNA is frequently bent and supercoiled in the cell, much of the available informati

195 karyotic genomic DNA is generally negatively supercoiled in vivo.

196 ported tendency of the repeat to unpair when supercoiled is probably related simply to GC content rat

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

198 somes and examined the lengths of individual supercoiled loops by electron microscopy.

199 rgoes reduced fluctuations when bound to the supercoiled minicircle.

200 is found in the cell largely as a negatively supercoiled molecule.

201 Surviving supercoiled molecules were separated from their degradat

202 formed between topoisomerases and positively supercoiled molecules.

203 led plasmids >10-fold faster than negatively supercoiled molecules.

204 ls of DNA cleavage complexes with positively supercoiled molecules.

205 approximately 3-fold faster than negatively supercoiled molecules.

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

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

208 ly supercoiled substrates but not positively supercoiled or linear DNA.

209 eparations of circular plasmid DNA in either supercoiled or nicked circular form often are contaminat

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

211 utation in the mtRNAP subunit Mtf1; and 4) a supercoiled or pre-melted promoter DNA template restores

212 dynamic interplay among Fis, IHF and DnaA on supercoiled oriC templates.

213 ties per se do not give any advantage to (+) supercoiled over (-) supercoiled DNA catenanes for unlin

214 underwent a phase transition from B-form to supercoiled P-form.

215 The action of CT Topo I on supercoiled p30delta DNA was examined over a range of ti

216 al) straight region and a lower (C-terminal) supercoiled part.

217 he presence of the extruded cruciform in the supercoiled plasmid and not in the linear one.

218 We also use a novel combination of the supercoiled plasmid assay with T4 Endonuclease V treatme

219 selectively denatured without damage to the supercoiled plasmid by alkaline denaturation in an argin

220 tach a fluorochrome sequence-specifically to supercoiled plasmid DNA (pDNA) without perturbing transg

221 ficity for single-stranded DNA and converted supercoiled plasmid DNA (replicative form I, RFI) into t

222 tudies with DNase I and S1 nucleases using a supercoiled plasmid DNA containing the human VEGF promot

223 rBCP was also found to protect supercoiled plasmid DNA from oxidative damage (i.e., nic

224 Protein complexes with supercoiled plasmid DNA further enabled us to study the

225 -dialkynylimidazoles do not cause nicking of supercoiled plasmid DNA or cleavage of bovine serum albu

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

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

228 nalyzed the modulation of DNA synthesis on a supercoiled plasmid DNA template by DNA polymerases (pol

229 to target ssDNA, oligonucleotide dsDNA, and supercoiled plasmid DNA under physiological-like ionic a

230 The gel assay, which used supercoiled plasmid DNA, was sensitive to both SSBs and

231 y junctions and DNA nodes, within negatively supercoiled plasmid DNA.

232 gly induced the formation of hypernegatively supercoiled plasmid DNA.

233 o competing activities can act together on a supercoiled plasmid forming two topologically distinct p

234 While conjugate 2 selectively protected supercoiled plasmid from cleavage by EcoRI and DraI enzy

235 s, we demonstrate a structural transition in supercoiled plasmid molecules containing homologous segm

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

237 Studies using the supercoiled plasmid relaxation assay revealed a ss:ds ra

238 By combining the supercoiled plasmid relaxation assay with AFM imaging, w

239 which have recently been shown to form in a supercoiled plasmid system in aqueous solution.

240 When these sequences were transcribed on supercoiled plasmid templates, termination occurred almo

241 formation of the Myc1234 G-quadruplex in the supercoiled plasmid thus points to the potential role of

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

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

244 on-B-form DNA secondary structure within the supercoiled plasmid.

245 n the c-Myc promoter was incorporated into a supercoiled plasmid.

246 man topoisomerase IIalpha relaxes positively supercoiled plasmids >10-fold faster than negatively sup

247 Supercoiled plasmids are more reactive than linear DNA;

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

249 hotolyase to mark the sites of UV lesions in supercoiled plasmids for detection and quantification by

250 hese assays exploit the fact that negatively supercoiled plasmids form intermolecular triplexes more

251 LacR and that loops formed within negatively supercoiled plasmids induce the V-shaped structure.

252 o relax and cleave negatively and positively supercoiled plasmids was assessed.

253 ) of UVB directly relax 95% and 78% of pUC18 supercoiled plasmids, respectively.

254 d also of the structures of surface-confined supercoiled plasmids, were performed using different tri

255 DnaD is a primosomal protein that remodels supercoiled plasmids.

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

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

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

259 Supercoiled, relaxed covalently closed, and nicked circu

260 hat conformational properties of (+) and (-) supercoiled replication catenanes are very different, th

261 cement to create topological objects such as supercoiled ring and catenane structures.

262 raction is required for the stability of the supercoiled RNA.

263 ) from mammalian cells and extraction of the supercoiled (sc) form of plasmid DNA (pDNA) from agarose

264 that migrates independently from the intact supercoiled (SC) form.

265 aight segments that flank a common helically supercoiled segment.

266 o-end extension of a mechanically stretched, supercoiled, single DNA molecule, we have been able dire

267 ical number of end-rotations above which the supercoiled solution is preferred and below which toroid

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

269 n over a distance and functionally mimic the supercoiled state characteristic for prokaryotic DNA.

270 erial cells primarily exists in a negatively supercoiled state.

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

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

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

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

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

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

277 a 500-bp linear substrate, or a 4.3-kilobase supercoiled substrate in the presence of calcium ions.

278 levels of cleavage complexes with positively supercoiled substrates and displayed an even more dramat

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

280 oisomerase I-mediated cleavage of negatively supercoiled substrates but not positively supercoiled or

281 age with positively as opposed to negatively supercoiled substrates in the absence or presence of ant

282 ng the lifetime of the covalent complex with supercoiled substrates.

283 rates of ligation are slower with positively supercoiled substrates.

284 f DNA cleavage intermediates with positively supercoiled substrates.

285 ing enzyme preferentially relaxed positively supercoiled substrates.

286 antly slower when confronted with negatively supercoiled substrates.

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

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

289 rotate, resulting in relaxation of initially supercoiled target DNA.

290 were transcribed at higher levels from more-supercoiled templates, which is the response observed fo

291 should be approximately 100 times higher in supercoiled than in relaxed DNA.

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

293 If the substrate is supercoiled, these circles can be unlinked or form multi

294 ircle intermediates during the conversion of supercoiled to linear DNA, indicating that the enzyme cl

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

296 than protein-free DNA to exist as negatively supercoiled topoisomers, suggesting a potential role of

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

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

299 f catenated DNA and relaxation of positively supercoiled [(+)ve sc] DNA, but inhibited relaxation of

300 DNA, but inhibited relaxation of negatively supercoiled [(-)ve sc] DNA.