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

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

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

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

8 /6 binds DNA topologically with affinity for supercoiled and catenated DNA templates.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

35 ominating under the physiologically relevant supercoiled conditions.

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

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

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

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

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

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

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

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

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

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

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

93 Supercoiled DNA plasmids were exposed in the frozen stat

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

95 Supercoiled DNA polymer models for which the torsional e

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

121 stimulation because relaxation of positively supercoiled DNA was unaffected.

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

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

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

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

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

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

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

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

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

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

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

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

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

135 +/- 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with th

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

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

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

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

140 NA nuclease activity specific for nicking of supercoiled DNA.

141 ies in its preference of relaxing negatively supercoiled DNA.

142 polar region of potential energy within the supercoiled DNA.

143 icient for the production of hypernegatively supercoiled DNA.

144 y visualize and quantify protein dynamics on supercoiled DNA.

145 gative supercoils to produce hypernegatively supercoiled DNA.

146 to study complex and dynamic interactions of supercoiled DNA.

147 al role in the generation of hypernegatively supercoiled DNA.

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

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

150 es and biological interactions of negatively supercoiled DNA.

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

152 opoIIalpha-mediated relaxation of positively supercoiled DNA.

153 lity of topoisomerase I to cleave positively supercoiled DNA.

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

155 linear dsDNA and its homologous pairing with supercoiled DNA.

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

157 lar DNA has been enzymatically prepared from supercoiled DNA.

158 levels of cleavage complexes with positively supercoiled DNA.

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

160 elative cleavage enhancement with positively supercoiled DNA.

161 lexes with positively rather than negatively supercoiled DNA.

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

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

164 e reaction and preferentially cut negatively supercoiled DNA.

165 ecially the V256I variant towards positively supercoiled DNA.

166 ich is necessary for relaxation reactions of supercoiled DNA.

167 for predicting equilibrium conformations of supercoiled DNA.

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

169 ust uncover and characterize the dynamics of supercoiled DNA.

170 de atomistic insight into the flexibility of supercoiled DNA.

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

172 role in maintaining DNA topology by relaxing supercoiled DNA.

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

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

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

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

177 l Escherichia coli RNAPs as they transcribed supercoiled DNA.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

192 block twists diffusion thus trapping DNA in supercoiled domains.

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

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

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

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

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

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

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

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

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

202 karyotic genomic DNA is generally negatively supercoiled in vivo.

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

204 rgoes reduced fluctuations when bound to the supercoiled minicircle.

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

206 Surviving supercoiled molecules were separated from their degradat

207 formed between topoisomerases and positively supercoiled molecules.

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

209 approximately 3-fold faster than negatively supercoiled molecules.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

246 Supercoiled plasmids are more reactive than linear DNA;

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

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

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

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

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

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

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

254 DnaD is a primosomal protein that remodels supercoiled plasmids.

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

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

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

258 Supercoiled, relaxed covalently closed, and nicked circu

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

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

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

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

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

264 aight segments that flank a common helically supercoiled segment.

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

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

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

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

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

270 erial cells primarily exists in a negatively supercoiled state.

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

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

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

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

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 antly slower when confronted with negatively supercoiled substrates.

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

284 rates of ligation are slower with positively supercoiled substrates.

285 f DNA cleavage intermediates with positively supercoiled substrates.

286 ing enzyme preferentially relaxed positively 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.