ライフサイエンスコーパス: superhelical

1 p-DNA interactions result in condensation of superhelical and B-DNA, displacement of intercalated eth

2 witches between VlsE's native and non-native superhelical and beta-sheet structures readily occur (pH

3 CRM1 exists in equilibrium between extended, superhelical and compact, ring-like conformations.

4 ly, in the Raman difference spectrum between superhelical and relaxed DNA are proposed as markers of

5 Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to r

6 distant sites localizes certain sequences to superhelical apices.

7 sed of eight alpha-helices in a right-handed superhelical arrangement and exhibits structural similar

8 g agent and cryoTEM) elucidate the resulting superhelical arrangement that precisely matches the a pr

9 teins that form an intertwined anti-parallel superhelical assembly, which docks intracellularly onto

10 rther approximately 90 degrees to orient its superhelical axis almost parallel to the pulling axis.

11 However, the superhelical axis in the DNA molecules used here will be

12 e chain at positions that project toward the superhelical axis produces tighter packing, as determine

13 When stretched along the superhelical axis, all superhelices show elastic, plasti

14 p apart to a particular alignment across the superhelical axis, but the juxtaposition of sites in lin

15 tire Rap protein is compressed along the TPR superhelical axis, generating new intramolecular contact

16 ng-pitch helix of F-actin to form continuous superhelical cables that wrap around the actin filaments

17 ication both influence and are influenced by superhelical changes in DNA.

18 ow motifs that typify tropomyosin's twisting superhelical coiled-coil to the wide and tapering tropom

19 anizing 147 base pairs of DNA into two tight superhelical coils, the nucleosome generates an architec

20 We analyze the superhelical competition between B-Z transitions and den

21 ucture at the base-step level and the global superhelical conformation observed for nucleosome-bound

22 ned during the simulation, including (1) the superhelical conformation of the antiparallel apolipopro

23 RM1 exhibits an overall extended and pitched superhelical conformation.

24 at deviates substantially from the canonical superhelical conformation.

25 sequence to assume the required left-handed superhelical conformation.

26 ch N- and C-terminal regions adhere to a 7/2 superhelical conformation.

27 e DNA trajectories in both structures assume superhelical conformations.

28 this pattern results from the effects of the superhelical context on gene expression coupled with the

29 es responsible for recognizing and resolving superhelical crossings and topological tangles in DNA.

30 Here we extend this approach to include superhelical cruciform extrusion at both perfect and imp

31 tatistical mechanical procedure in which the superhelical deformation is partitioned between strand s

32 Molecules with higher superhelical densities are preferentially selected for a

33 is report, we use topoisomer sets of defined superhelical densities as DNA templates in a purified in

34 iform geometry in plasmid DNA with different superhelical densities at various ionic conditions.

35 SSB activates transcription at physiological superhelical densities by stabilizing the template-stran

36 repeats extrude as hairpins at physiological superhelical densities in a Mg(II)-dependent manner.

37 hairpin extrusion can occur at physiological superhelical densities in a Mg2+-dependent manner.

38 ry effect of DNA supercoiling occurs between superhelical densities of 0 to -0.02 suggesting that, wh

39 using a series of topoisomers with different superhelical densities ranging from totally relaxed to m

40 ation structure might be favorable at higher superhelical densities since it relaxes more supercoils.

41 redict how changing guide RNA sequences, DNA superhelical densities, Cas9 and crRNA expression levels

42 However, even at high superhelical densities, DNA strands within the presumabl

43 probing analysis indicated that, at moderate superhelical densities, the (ATTCT)(n).(AGAAT)(n) repeat

44 eases over the entire range of physiological superhelical densities, whereas transcription initiation

45 tivity to structural probes at different DNA superhelical densities, with extrusion at P2 being more

46 ty of five chlamydial promoters at different superhelical densities.

47 ion of a locally condensed structure at high superhelical densities.

48 jacent A+T-rich flanking sequences at higher superhelical densities.

49 where structural transitions occurred at low superhelical densities.

50 r repeat tracts in plasmids at physiological superhelical densities.

51 mparable in linking number (Lk(0) = 258) and superhelical density (sigma = -0.05) to the moderate sup

52 Loss of Top1 resulted in increased negative superhelical density (two to six times the normal value)

53 an genome are affected by cellular levels of superhelical density and spermine.

54 triplex DNA within the Py.Pu tract at native superhelical density as isolated from Escherichia coli.

55 The superhelical density at which the transition occurred wa

56 nd twisted with magnetic tweezers, levels of superhelical density confined in CI-mediated DNA loops r

57 The increase in superhelical density did not diminish replication arrest

58 ng growth and to an inferred gradient of DNA superhelical density from the origin to the terminus.

59 n occurs under high salt conditions when the superhelical density is above -0.03.

60 ers juxtaposition mechanisms, especially for superhelical density magnitude greater than around 0.04.

61 supercoiled at midcycle, with an approximate superhelical density of -0.07.

62 During heat shock, the superhelical density of a plasmid with the heat-inducibl

63 ncrease of approximately 1 degrees /bp (or a superhelical density of Deltasigma approximately +0.03)

64 silent mating type locus by determining the superhelical density of mini-circles excised from HML (H

65 As the global superhelical density of the chromosome is controlled by

66 ependence of transcription in vitro with the superhelical density of the plasmid template.

67 lex length, sequence, salt concentration and superhelical density on the conformation of DNA nanocirc

68 The influence of negative superhelical density on the genetic instabilities of lon

69 presence and absence of IHF at any given DNA superhelical density remains the same.

70 ypersensitivity assay and by determining the superhelical density required for stable DNA unwinding,

71 At the superhelical density sufficient to locally unwind DNA, a

72 construct extrudes the cruciform at a lower superhelical density than a control plasmid without the

73 transcription, displayed specific optima of superhelical density while others did not.

74 By altering the superhelical density, gyrase may regulate expression of

75 trusion, induced by Mg(II) and physiological superhelical density, is essential to provide the correc

76 topology, i.e. the lowering of the negative superhelical density, repressed the formation of the sti

77 In topoisomers with low superhelical density, the population of the folded confo

78 ation added, whereas in the sample with high superhelical density, this population is as high as 98-1

79 each histone significantly decreases plasmid superhelical density, which probably reflects a release

80 shown to exist up to moderate values of the superhelical density.

81 ends followed by compensatory adjustments in superhelical density.

82 hibits a broad optimum at a midphysiological superhelical density.

83 th extrusion at P2 being more favored at low superhelical density.

84 the small promoter hairpins at physiological superhelical density.

85 cycle retained SIR-dependent differences in superhelical density.

86 cted to act as sinks for the accumulation of superhelical density.

87 independent topological domains of distinct superhelical density.

88 ding on the crowder volume ratio and the DNA superhelical density.

89 n vitro response of T3S promoters to altered superhelical density.

90 e T3S genes were not sensitive to changes in superhelical density.

91 ferent times after infection and assayed its superhelical density.

92 stant Z-DNA-forming site to compete with the superhelical destabilization that is required for integr

93 With superhelical DNA and a homologous single-stranded oligon

94 formation of displacement loops (D-loops) in superhelical DNA and by strand exchange between colinear

95 A negatively superhelical DNA can be modeled to wrap around this left

96 n the presence of IHF, the same increases in superhelical DNA densities result in larger increases in

97 the crossover structures that differentiate superhelical DNA from linear DNA.

98 ge-based techniques to structures present in superhelical DNA has been hindered by the fact that the

99 trongly suggest that linker histone binds to superhelical DNA in a negatively cooperative mode.

100 preference of the linker histones to bind to superhelical DNA in comparison with linear or relaxed mo

101 The structure also suggests that superhelical DNA induced at the origin of plasmid F by f

102 ve cooperativity by which linker histone and superhelical DNA interact.

103 "persistence length", and argues that long, superhelical DNA may be regarded at once as locally stif

104 nt structural transitions in kilobase length superhelical DNA molecules.

105 We show that MukB stimulates the superhelical DNA relaxation activity of wild-type Topo I

106 hich was highly proficient for ATP-dependent superhelical DNA relaxation and decatenation of interloc

107 ivity, that the ability of p63DBD to bind to superhelical DNA suggests that it is capable of binding

108 ved behavior of binding of linker histone to superhelical DNA that is consistent with both the divale

109 Topoisomerase I (TOP1) relaxes superhelical DNA through a breakage/rejoining reaction i

110 direct competition, linker histone binds to superhelical DNA to the complete exclusion of linear DNA

111 for the promoter region of the PARP gene in superhelical DNA where the dyad symmetry elements likely

112 bility of DNA gyrase to constrain a positive superhelical DNA wrap, and also suggest that the particu

113 try caused by bubble formation as well as by superhelical DNA wrapping.

114 are enzymes of quintessence to the upkeep of superhelical DNA, and are vital for replication, transcr

115 HsRad52 catalyzed D-loop formation in superhelical DNA, as well as strand exchange among oligo

116 rotein catalyzed the formation of D-loops in superhelical DNA, as well as strand exchange between sin

117 though aggregation can be made to occur with superhelical DNA, it can do so only at near-saturation l

118 ity and promotes the formation of D-loops in superhelical DNA.

119 een strand separation and B-Z transitions in superhelical DNA.

120 cal equilibrium model of R-loop formation in superhelical DNA.

121 quilibration behind the relaxation of native superhelical DNAs suggests that it may require cleavage

122 contains a predicted beta-barrel porin and a superhelical domain containing tetratricopeptide repeats

123 n initiation from promoter sites in the same superhelical domain.

124 of DNA sequences near the terminal loop of a superhelical domain.

125 ition among these three transitions within a superhelical domain.

126 er properties that organize the structure of superhelical domains apart from intrinsic bending and ma

127 on of linker histone H1 with both linear and superhelical double-stranded DNA has been investigated a

128 This IHF-mediated translocation of superhelical energy facilitates duplex destabilization i

129 Fis binding results in the translocation of superhelical energy from the promoter-distal portion of

130 Fis-mediated translocation of superhelical energy from upstream binding sites to the p

131 rate of cruciform formation and reduces the superhelical energy required to drive the transition.

132 The superhelical energy required to initiate duplex unpairin

133 The chiral superhelical fibers show reversible disassembly to monom

134 The assemblies consist of superhelical fibers with length greater than 1 mum and w

135 Single-protein-chain superhelical filaments are obtained from monomeric repea

136 ts play a major role in the formation of the superhelical gene V protein-single-stranded nucleic acid

137 that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion

138 lters its local coiled-coil conformation and superhelical geometry.

139 rigid cylinder carrying a positively charged superhelical groove that accommodates 1.7 turns of DNA.

140 binding site is located on the inside of the superhelical gyre of DNA, just inside the periphery of t

141 units (Cdc16, Cdc23 and Cdc27) share related superhelical homo-dimeric architectures that assemble to

142 We show that the formation of superhelical ICP8-ssDNA filaments is required for anneal

143 ps that form a DNA-binding surface at either superhelical location (SHL) +/-2.5 (LRS) or SHL +/-0.5 (

144 f CHD4 binds and distorts nucleosomal DNA at superhelical location (SHL) +2, supporting the 'twist de

145 TBP can bind to superhelical location (SHL) -6, which contains a TATA-li

146 , forms a super-stable nucleosome complex at superhelical location +5 (SHL+5) with similar affinity a

147 , INO80 places its ATPase subunit, Ino80, at superhelical location -2 (SHL -2), in contrast to SHL -6

148 o play a greater role in reacting with AP at superhelical location 1.5, but other amino acids (e.g.,

149 XD or ATPase domain was found to contact the superhelical location 2 (SHL2) of the nucleosome, provid

150 factors can bind and locally distort DNA at superhelical location 2.

151 , most of these sequence changes occurred at superhelical locations (SHLs) +/-4, +/-1, and +/- 2, whe

152 te DNA-sequence-independent stabilization of superhelical locations 0-1 and 3.5-4.5.

153 At such ionic conditions, superhelical loops are typically separated by regions of

154 ry significantly to achieve the most favored superhelical packing arrangement.

155 imizing the fiber energy with respect to the superhelical parameters, we found two types of topologic

156 Four superhelical parameters-inclination of nucleosomes, twis

157 nding topology, torsion angles, helical, and superhelical parameters.

158 g the local peptide conformation and certain superhelical parameters.

159 bending forces along the DNA to maintain the superhelical path required for nucleosome wrapping.

160 ake in nucleosomes along various left-handed superhelical pathways and to deduce the features of sequ

161 ficant flexibility, sampling structures with superhelical pitch and radius complementary to the major

162 ges in triple-helical structure, in terms of superhelical pitch, hydrogen bonding pattern, and hydrat

163 d structure inducing local relaxation of the superhelical pitch.

164 ty of the enzyme to unwind D-loops formed on superhelical plasmid DNA by the E. coli recombinase RecA

165 unit composition stimulate the conversion of superhelical plasmid DNA to the relaxed form.

166 ons of vaccinia virus DNA and contained in a superhelical plasmid, into a cruciform containing bulged

167 ect of histone H1 binding on the cleavage of superhelical plasmids by single-strand-specific nuclease

168 ngle-stranded DNAs as assisting DNAs to open superhelical plasmids, allowing the DNA-cleaving DNAzyme

169 strate scope of DNAzymes to double-stranded, superhelical plasmids.

170 non-imino acid-containing region adopts 10/3 superhelical properties, whereas the imino acid rich N-

171 terion is the AMP's ability to assemble into superhelical protofibril scaffolds.

172 and anti-parallel structures; (2) preferred superhelical radii, which depend linearly on the oligome

173 d to bend DNA into axial conformity with the superhelical ramp at physiological salt concentration ca

174 source of the free energy holding DNA to the superhelical ramp on the histone octamer surface is obta

175 Top3 alone, this complex displays increased superhelical relaxation activity.

176 cture of the trimer reveals a neatly twisted superhelical rope, with unusual supercoiling induced by

177 een domain organization provides an extended superhelical scaffold allowing for protein-protein as we

178 ino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of con

179 nformation with a design well matched to its superhelical shape on F-actin.

180 the 'glue' to allow assembly of an extended superhelical solenoid structure.

181 The observation of a superhelical spiral in the present structure and that of

182 allel alpha-helices that can stack to form a superhelical spiral.

183 ortion of Nup157 shows that it projects as a superhelical stack from the compact C-shaped portion of

184 cryptic plasmid (pANS) as a reporter of the superhelical state of DNA in cyanobacteria, we show that

185 the three terbenzimidazole analogues on the superhelical state of plasmid DNA depends on the [total

186 of transcription, are known to depend on the superhelical state of the DNA substrate.

187 m for ensuring the formation of a particular superhelical state over an extended region of the DNA.

188 percentages but promotes the formation of a superhelical state upon further additions.

189 Furthermore, perturbation of superhelical status within the physiological range elici

190 ses have the essential role of relieving the superhelical strain by removing these structures.

191 ed replication forks of molecules with a (+) superhelical strain have the additional option of regres

192 ses a positive linking number difference, or superhelical strain, to build up around the elongating r

193 igh base unpairing propensity under negative superhelical strain.

194 rgetically favorable, such as the removal of superhelical strain; why ATP is required for such reacti

195 on, a phenomenon that is exacerbated by both superhelical stress and increased tract length.

196 B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of

197 ir position -92 is, in fact, destabilized by superhelical stress and that this duplex destabilization

198 nges in B-DNA secondary structure induced by superhelical stress and to identify putative Raman marke

199 A DNA molecule under negative superhelical stress becomes susceptible to transitions t

200 After relaxation of superhelical stress by various methods not involving top

201 at cells may use to nonenzymatically relieve superhelical stress during transcription.

202 Superhelical stress in circular plasmids can generate se

203 Transcription generates superhelical stress in DNA that poses problems for genom

204 We observe that negative superhelical stress induces local variation in the canon

205 vitro with purified components and in vivo, superhelical stress is distributed throughout the entire

206 base sequence, on which a specified level of superhelical stress is imposed.

207 We propose that latent superhelical stress is normally absorbed by the intrinsi

208 th transcriptional activity, suggesting that superhelical stress is obscured from Top2 within chromat

209 to extremophiles, we estimate the effects of superhelical stress on the stability of the basepair ste

210 aused at least in part by alterations in the superhelical stress upon bis-intercalation.

211 This in turn creates a positive superhelical stress, a (+)-DeltaLk, that must be relaxed

212 s implicated in the controlled relaxation of superhelical stress, also displays an increased number o

213 Such stem-loops can form in duplex DNA under superhelical stress, and their critical sequence feature

214 tiation element is intrinsically unstable to superhelical stress, permitting entry of the polymerase,

215 where the duplex becomes destabilized under superhelical stress.

216 tructure is largely conserved under moderate superhelical stress.

217 s that prevails after the initial release of superhelical stress.

218 duced in each base-pair of a DNA molecule by superhelical stresses are used to analyze several genomi

219 d Escherichia coli genes are destabilized by superhelical stresses, whereas closely related sequences

220 The observed superhelical structure establishes a mechanism for the s

221 The looser superhelical structure of the non-imino acid region of c

222 mers wrap around the RNA molecule creating a superhelical structure that could not only shield the po

223 : addition of MeOH induces a transition to a superhelical structure that is followed by conversion to

224 The other interface promotes a superhelical structure within the crystal that may refle

225 lex shows that Cand1 adopts a highly sinuous superhelical structure, clamping around the elongated SC

226 Since unbound TALEs retain superhelical structure, it seems likely that DNA binding

227 whereas subsequent additions of TFE induce a superhelical structure.

228 d in three alpha-helices, build an elongated superhelical structure.

229 angle neutron scattering supported a double superhelical structure.

230 ile the C-terminal region is a more regular, superhelical structure.

231 They form superhelical structures around which DNA is wrapped.

232 These receptors are highly flexible superhelical structures composed of HEAT-repeat motifs t

233 histone dimers can multimerize into extended superhelical structures that mediate gene expression cha

234 f helical nanowires that further bundle into superhelical structures.

235 Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages

236 n oligomers with coincident C(2) to C(8) and superhelical symmetry axes that can be readily extended

237 dues, the peptide still adopts a typical 7/2 superhelical symmetry similar to that observed in other

238 puckering, our structure still adopts a 7/2 superhelical symmetry similar to that observed in other

239 l twisting, both of which depart from strict superhelical symmetry.

240 gamma ori DNA occurred in both strands of a superhelical template upon the combined addition of wt p

241 However, at higher superhelical tension an H-y5 structure forms in the Py.P

242 Human topoisomerase I relaxes superhelical tension associated with DNA replication, tr

243 mechanism proposed for the relaxation of DNA superhelical tension by human topoisomerase I.

244 poisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-s

245 ates results in the accumulation of positive superhelical tension by the elongating polymerase, which

246 ogether show that the relaxation of positive superhelical tension by these enzymes was the key proper

247 Negative superhelical tension can drive local transitions to alte

248 al enzymes that are responsible for relaxing superhelical tension in DNA by forming a transient coval

249 rand nick that the enzyme creates to relieve superhelical tension in duplex DNA.

250 logical changes, possibly by accumulation of superhelical tension in the newly synthesized DNA, that

251 lity of Rad54 to hydrolyze ATP and introduce superhelical tension into covalently closed circular pla

252 both the potential length of the triplex and superhelical tension of intramolecular triplex formation

253 in chromosomal stability by relaxing the DNA superhelical tension that arises from a variety of nucle

254 DNA superhelical tension, an important feature of genomic or

255 tin templates results in the accumulation of superhelical tension, making the relaxation activity of

256 ch of which relax both positive and negative superhelical tension, reverse the transcriptional repres

257 terial topo I, which can relax only negative superhelical tension, the transcription is repressed on

258 In the absence of superhelical tension, we found that the efficiency of st

259 beling procedure does not interfere with the superhelical tension-driven formation of alternative DNA

260 leotide uptake by plasmid DNA under negative superhelical tension.

261 es, which increased with increasing negative superhelical tension.

262 chicken blood extract to relax unrestrained superhelical tension.

263 at intramolecular triplexes form with modest superhelical tensions for all the tracts examined.

264 spectrometry (H/DX-MS), we find that the DNA superhelical termini within each nucleosome are loosely

265 mination factor MTERF1, which has a modular, superhelical topology complementary to DNA.

266 ical secondary structure that has an overall superhelical topology remotely homologous to the MIF4G h

267 m driven by intrinsic dynamics of the MTERF1 superhelical topology.

268 se the energy of ATP hydrolysis to introduce superhelical torsion into DNA, which suggests a common m

269 g-range effects of histone H1 binding on the superhelical torsion of the plasmid.

270 ernal loop of newly synthesized RpL4 via its superhelical TPR domain, thereby restricting RpL4 loop i

271 In contrast, a GC spacers abolishes the DNA superhelical trajectory and exhibits less bent DNA, sugg

272 ement with overlapping half-sites, maintains superhelical trajectory and reveals two interacting p63D

273 local anisotropic bending of DNA define its superhelical trajectory in chromatin.

274 with that containing a TA spacer, exhibiting superhelical trajectory.

275 eviously developed algorithms, which studied superhelical transitions to a single alternate conformat

276 For TALEs forming less than one superhelical turn around DNA, partly folded states inhib

277 unit of chromatin in which approximately two superhelical turns of 147 bp double-stranded DNA are wra

278 y important for regulating the number of DNA superhelical turns that are removed during the lifetime

279 e proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromati

280 -helical bundle proteins with a right-handed superhelical twist is described.

281 Thus, in the presence of IHF, the negative superhelical twist normally absorbed by this DNA structu

282 The monomeric helix has a superhelical twist similar to that of right-handed coile

283 pha-helices wrapped around each other with a superhelical twist.

284 idue pairs that generate a rare right-handed superhelical twist.

285 rcoils >10-fold faster than it does negative superhelical twists.

286 al results are not consistent with extensive superhelical wrapping of DNA on either complex as has be

287 le generation, with very little derived from superhelical wrapping.