ライフサイエンスコーパス: DNA conformation

1 as a minimally perturbing method for probing DNA conformation.

2 as maintained except for local deviations in DNA conformation.

3 ine tracts, which are associated with a bent DNA conformation.

4 single-stranded character and hence a non-B DNA conformation.

5 r assay in Escherichia coli for this unusual DNA conformation.

6 of spermidine, a small polyamine influencing DNA conformation.

7 smatch are important for binding in a kinked DNA conformation.

8 that the bases pair as designed, but in a Z-DNA conformation.

9 The central four base pairs adopt the B-DNA conformation.

10 as found to act as an allosteric effector of DNA conformation.

11 in addition to base sequence, can influence DNA conformation.

12 vator protein that introduces changes in the DNA conformation.

13 contacts with RNA polymerase and changes in DNA conformation.

14 h of the ssDNA strand in the double-stranded DNA conformation.

15 nt interbase hydrogen bond network in the TA-DNA conformation.

16 d the histone octamer creates a unique local DNA conformation.

17 er chromatin structure through modulation of DNA conformation.

18 long range effect of cytosine methylation on DNA conformation.

19 cts of methylation and spermine binding on A-DNA conformation.

20 h a 5'-purine, unexpectedly stabilizes the A-DNA conformation.

21 , with 20% of d(CG)4, and 90% of d(CG)5 in Z-DNA conformation.

22 fold, suggesting an important role for local DNA conformation.

23 is an important aspect of sequence-dependent DNA conformation.

24 owth by mimicking the effects of hormones on DNA conformation.

25 res much less DNA, and is independent of the DNA conformation.

26 ch sequences but is selective for a straight DNA conformation.

27 he SV40 origin the AT tract is in a straight DNA conformation.

28 GCGCGC) was found to be in the left-handed Z-DNA conformation.

29 gnition and, consequently, on the underlying DNA conformation.

30 rimidine repeats can adopt the left-handed Z-DNA conformation.

31 an intermediate state into the highly kinked DNA conformation.

32 al4 domain while allosterically altering the DNA conformation.

33 fragile zones are predominantly in a duplex DNA conformation.

34 ring initiation by stabilizing the scrunched DNA conformation.

35 ecules at high-affinity sites regulates oriC DNA conformation.

36 hiometry, site-site interactions and induced DNA conformation.

37 of the MOR gene promoter by adopting a non-B DNA conformation.

38 achieve a high degree of control over local DNA conformation.

39 in the absence of other proteins and alters DNA conformation.

40 roduces no substantial change in the local B-DNA conformation.

41 structures thus far involve targeting single DNA conformations.

42 promoter, perhaps by stabilizing non-B-form DNA conformations.

43 he DNA that allow formation of complementary DNA conformations.

44 f gapped DNA molecules contains a variety of DNA conformations.

45 the entire range between canonical A- and B-DNA conformations.

46 minor and major grooves around both A and B-DNA conformations.

47 e -20.9-kb DHS were shown not to adopt non-B-DNA conformations.

48 force field that preferentially stabilizes B-DNA conformations.

49 mulations of the equilibrium distribution of DNA conformations.

50 er is the primary determinant of supercoiled DNA conformations.

51 are in dynamic equilibrium between B- and Z-DNA conformations.

52 ty to adopt negative supercoil induced non-B DNA conformations.

53 of the switching between lying and standing DNA conformations.

54 ntly than aSyn, and do not stabilize similar DNA conformations.

55 redict a lower elastic energy of highly bent DNA conformations.

56 ng in polypurine strand-nicked and catenated DNA conformations.

57 sed as spectroscopic probes to examine local DNA conformations.

58 hat favor the transition from B-DNA to non-B-DNA conformations.

59 sitively or negatively writhed and denatured DNA conformations.

60 bone modifications --> partial transition of DNA conformations (A to B form).

61 butions to the relative stability of various DNA conformations (A, B, C, Z, and single-stranded (ss)

62 develop, test, and apply a method to follow DNA conformations acting in the Escherichia coli mismatc

63 s apparent specificity for the left-handed Z-DNA conformation adopted by alternating (dGdC) polymers

64 wist per dimer, are nearly identical to this DNA conformation, allowing a close comparison of the two

65 This gel assay is sensitive to DNA conformation and Al3+ ions were found to alter the c

66 mblies that may themselves induce changes in DNA conformation and chromatin structure.

67 tional groups) and indirect readout (sensing DNA conformation and deformability).

68 xes is important to decipher the role of the DNA conformation and dynamics in protein recognition and

69 facilitate the examination of the role of 3D DNA conformation and dynamics in protein-DNA interaction

70 ides a novel and accurate approach to assess DNA conformation and dynamics in solution.

71 DNA conformation and E2-DNA contacts are similar in both

72 DNA distortion mutually 'locks' protein and DNA conformation and enables substrate verification with

73 The AT-tract alters DNA conformation and enhances contacts between the DNA b

74 d narrow distance distributions sensitive to DNA conformation and flexibility.

75 Thus, GATC sites at oriC affect the DNA conformation and GATCs, in conjunction with the prot

76 Thus, the observed DNA conformation and hydration allows for the formulatio

77 r comes from both binding-induced changes in DNA conformation and interactions with additional compon

78 ning the origins of the different effects on DNA conformation and packing exerted by individual metal

79 ed fit model is proposed that depends on the DNA conformation and provides a mechanism for nonlocal c

80 are sensitive to the sequence context, local DNA conformation and solvent environment of the probe ba

81 te that the ability of H1(0) to alter linker DNA conformation and stabilize condensed chromatin struc

82 be used to garner diverse information about DNA conformation and structure, and potentially be exten

83 ty of the GAA.TTC tracts to adopt the sticky DNA conformation and the inhibition of intramolecular re

84 ry proteins may directly link alterations in DNA conformation and topology with changes in gene expre

85 tly probe DNA binding by H-NS, its impact on DNA conformation and topology, and its competition with

86 te that could structurally couple changes in DNA conformation and transcription during the streptomyc

87 rmal interactions with genomic DNA, altering DNA conformation and transcription factor binding.

88 This may indicate a more extended DNA conformation and, therefore, enhancement of transien

89 regions of a number of biologically relevant DNA conformations and in structured single-stranded DNA.

90 We discuss the importance of replicating DNA conformations and the roles of topoisomerases, focus

91 est that many sequence-dependent features of DNA conformation are mediated by site specific binding o

92 o unbent DNA and then deforms it, or if bent DNA conformations are 'captured' by protein binding.

93 Hence, non-B DNA conformations are critical for these mutagenesis mec

94 cations for the stabilization of A-DNA and B-DNA conformations are discussed.

95 Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chro

96 nduced bending) or, alternatively, "prebent" DNA conformations are thermally accessible, which the pr

97 xhibit sequence-induced curvature, adopt a B-DNA conformation as a function of increasing temperature

98 idine/polypurine region (PPy/u) can adopt ss DNA conformation, as demonstrated by S1 nuclease sensiti

99 resence of base-modified nucleotides affects DNA conformation, as determined by the helical rise per

100 ex DNA, with the duplex form regaining the B-DNA conformation at high concentrations (approximately 2

101 gle-loop structure with an unusual unstacked DNA conformation at its downstream edge was observed whe

102 ition, formation of the specific unbent MutS-DNA conformation at mismatches appears to be required fo

103 e specific adduct conformation and the local DNA conformation at that nucleotide.

104 1,10-phenanthroline copper confirms that the DNA conformation at the position of the right-side ligan

105 rtial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity.

106 n a similar base-pair sequence, and that the DNA conformation averaged over all stereospecific methyl

107 tograms can give layered insight into global DNA conformation, binding interactions, and molecular di

108 de-repeat sequence that is able to adopt a Z-DNA conformation both in vitro and in vivo and interacts

109 ingle-stranded character and, hence, a non-B DNA conformation both in vivo and in vitro.

110 expression in Escherichia coli, which affect DNA conformation by bending, wrapping and bridging the D

111 This distortion of DNA conformation by M.EcoRI is shown to be important for

112 ffectively converted from the B-DNA to the A-DNA conformation by neomycin, spermine and Co(NH3)6(3+).

113 the sequence-specific stabilization of bent DNA conformations by cations localized within the narrow

114 the expansion process the formation of non-B DNA conformations by the repeat sequence has previously

115 Thus, DNA conformation can have a profound impact on substrate

116 of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals.

117 resolution, which can be used to analyze the DNA conformation changes, providing one solution for det

118 KDM6B induces an overlapped linker DNA conformation consistent with function in a compact c

119 models for Holliday junctions, the transient DNA conformations critically involved in DNA homologous

120 s perspectives and thereby gain insight into DNA conformation, deformability and interactions in diff

121 This detailed analysis suggests significant DNA conformation dependence of the interaction.

122 metallo-base pair is compatible with Z- or B-DNA conformations, depending on the duplex sequence.

123 on found in isolation, the TnsC-bound target DNA conformation differs markedly in the transpososome.

124 probably result from the change in the local DNA conformation due to protein(s) binding in this regio

125 Differences in global DNA conformation (duplex, hairpin, single strand), as we

126 the current study provides new insights into DNA conformation during epigenetic regulation.

127 Unexpectedly, this non-B DNA conformation elicited the formation of a TRS-length

128 this may reflect differences in the precise DNA conformation, especially with regard to width and de

129 that the enzyme recognizes its substrates by DNA conformation exclusion and offer a simple explanatio

130 tion-dependent transition from B- to a non-B-DNA conformation expanding from 3' end toward the 5' of

131 sed by the cyclohexane ring of OX affect the DNA conformations explored by OX-GG adduct compared to t

132 inuous versus discrete models of large-scale DNA conformation, focusing on issues of relevance to mol

133 n the enzyme binding interactions and in the DNA conformation for each unique substrate molecule.

134 es in the basal transcriptional activity and DNA conformation for several genes.

135 Finally, the importance of preserving the B-DNA conformation for the diagnosis of cancer is put forw

136 y similar, suggesting a dominant role of the DNA conformation for UNG function.

137 ular DNA.DNA-associated region of the sticky-DNA conformation formed by long GAA.TTC repeats.

138 Alternative DNA conformation formed by sequences called flipons are

139 We conclude that the unusual DNA conformations formed by the PKD1 poly(R.Y) tract und

140 repeating sequences per se, or of the non-B DNA conformations formed by these sequences, in the muta

141 pe1 has the ability to incise at AP sites in DNA conformations formed during DNA replication, transcr

142 first begin by elucidating the main forms of DNA conformation found in nature and the general structu

143 ch is known to be the dominant binary enzyme-DNA conformation from solution and crystallographic stud

144 TG sites by adopting particular preferred BR-DNA conformations, from which they derive differences in

145 polymerlike structure that has assumed the Z-DNA conformation further strengthened by the long inner

146 ned the impact of parameters which influence DNA conformation (gel temperature, gel composition, and

147 gers-Oseen problem for an equilibrium set of DNA conformations generated for each condition by the Me

148 tributed to the enzyme-induced change in the DNA conformation, going from a rod-like to a bent shape.

149 Interest to the left-handed DNA conformation has been recently boosted by the findin

150 The effect of electrostatic interactions on DNA conformation has now been investigated further, usin

151 Approaches for measuring changes in DNA conformation have been developed, based on the princ

152 ters, or regions with the ability to adopt Z-DNA conformation, have been hypothesized to enhance reco

153 loor appears to be relatively insensitive to DNA conformation (helical twist and propeller twist).

154 strand displacement reactions for bulge loop DNA conformations, here referred to as Omega-DNAs.

155 critique on infrared spectroscopy applied to DNA conformation highlighting pivotal studies on isolate

156 ion data offers detailed characterization of DNA conformation, hydration and electrostatics.

157 Higher levels of -sigma stabilize non-B DNA conformations (i.e. triplexes, sticky DNA, flexible

158 two br5C-modified DNA nonamers are in the Z-DNA conformation in 50% methanol solution.

159 elled protein binding on DNA with changes in DNA conformation in a relatively high-throughput manner.

160 In deoxycytidine, chi adopts an A-DNA conformation in both the north and south energy mini

161 r the structure and function of this unusual DNA conformation in Friedreich's ataxia.

162 The DNA conformation in our multimeric Sac7d/DNA model has t

163 pectroscopy has made to the understanding of DNA conformation in relation to hydration and its potent

164 turn, have an unclear accuracy to represent DNA conformation in solution.

165 greater linking deficiency and 40% greater Z-DNA conformation in the alternating d(CG) region.

166 on permits accurate definition of the kinked DNA conformation in the CAP-DNA complex.

167 The effects of hydration on the DNA conformation in the colon biopsy tissues at differen

168 dine-protein interactions, or by influencing DNA conformation in the core region.

169 changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-bi

170 Z-DNA conformation in the d(CG)n sequences was assayed by

171 The triplex DNA, however, remained in a Psi-DNA conformation in the resolubilized state.

172 em-loop structure in vitro with a hybrid A/B-DNA conformation in the stem area.

173 binding of the arm, which appears to affect DNA conformation in this region.

174 itional nonspecific interactions and altered DNA conformation in this structure account for the stron

175 e further infer that the main determinant of DNA conformation in this system is protein-DNA interacti

176 o recombination data favor this as the major DNA conformation in vivo as well.

177 ly, the base-pair steps which exhibit pure A-DNA conformations in the crystal complexes follow the sc

178 ally the fraction of time spent in different DNA conformations in the vicinity of the adduct, for CP-

179 ide evidence for an extended E-motif DNA (eE-DNA) conformation in short d[GCC](n).d[GCC](n) repeat fr

180 plex segment retains a minimally perturbed B-DNA conformation including Watson-Crick hydrogen-bonding

181 Unusual DNA conformations including cruciforms play an important

182 to bind to and stabilize a number of altered DNA conformations, including left-handed Z-DNA.

183 Dynamic interchange between DNA conformations, including metastable states, can be o

184 ts as a scaffold to stabilize three distinct DNA conformations, including the final extruded state.

185 re a greater degree of interactions with the DNA conformations induced by small insertion/deletion mi

186 We provide evidence that linker DNA conformation is a key determinant of H1 CTD structur

187 Exciton coupling between AT pairs in native DNA conformation is estimated by applying these sum rule

188 A-DNA conformation is favored by guanine-rich sequences, s

189 We found that an extended DNA conformation is maintained throughout the transition

190 tion mutants suggests that an appropriate BR-DNA conformation is necessary but not sufficient for myo

191 One alternative DNA conformation is the cruciform, which has been shown

192 imply that the elastic energy of highly bent DNA conformations is lower than predicted by classical e

193 e then show that this dynamic equilibrium of DNA conformations is reflected as shifts in hydrodynamic

194 quencies point towards biological changes in DNA conformation, lipid oxidation and accumulation and s

195 bulkiness of the W1 region implies that the DNA conformation may be distorted upon PF0610 binding.

196 These differences in DNA conformation may help explain decreases in relative

197 that the transition from the B-DNA to non-B-DNA conformation may play an important role in bcl-2 tra

198 ructure of our data files to support complex DNA conformations, multiple DNA-protein complexes within

199 It reveals sequence-dependent DNA conformations not seen previously, including kinking

200 calculated energy required to achieve the TA-DNA conformation of DNA that is observed in the complex

201 s may increase transcription by altering the DNA conformation of genes harboring long GAA.TTC repeats

202 ither the Watson-Crick base pairing or the A-DNA conformation of the backbone.

203 rmations on the stability of the canonical B-DNA conformation of the Dickerson-Drew dodecamer duplex

204 consistent with considerable changes in the DNA conformation of the nucleoprotein complex.

205 ction can accommodate perturbations to the B-DNA conformation of the stacked duplex arms associated w

206 the DNA can have a significant impact on the DNA conformation often leading to localized coiling, whi

207 of binding-site sequences and the effects of DNA conformation on calicheamicin-induced DNA cleavage s

208 enzymes induce a marked change in the global DNA conformation on the binding of a single dimer.

209 These local and transient DNA conformations on both sides of ssDNA-dsDNA junctions

210 The determination of DNA conformations on surfaces and hybridization behavior

211 tochore formation take place at the level of DNA conformation or epigenetic mechanisms rather than DN

212 d screened for mutations using single-strand DNA conformation polymorphism analysis, denaturing high-

213 Our results suggest that DNA conformation probing with acoustic wave sensors is a

214 ted by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in com

215 ins, possibly by stabilizing single-stranded DNA conformations required for interaction with enhancer

216 Once formed, these DNA conformations resist h-FEN1.

217 alization of DNA-binding proteins, different DNA conformations, restriction enzymes, and other DNA mo

218 f the TpA step gives rise to two alternative DNA conformations, resulting in different interactions w

219 es are caused by the existence of an unusual DNA conformation(s) within the TRS, during the in vitro

220 tance of this glutamate residue in sigma(54).DNA conformation sensing, permitting the identification

221 Analysis of the equilibrium sets of DNA conformations showed that shortening of DNA extensio

222 ysis, based on the Monte Carlo simulation of DNA conformations, showed that if the rate of loop forma

223 e and OsO4, which is consistent with a non-B-DNA conformation similar to that of left-handed Z-DNA an

224 e, has been widely used as a probe for local DNA conformation, since excitation and emission characte

225 omplex of Pdx1 and BETA2/NeuroD1 maintains a DNA conformation such that distal regions of the gene ar

226 ulting in interconversions between different DNA conformations such as B-DNA, Z-DNA and S-DNA.

227 The role of alternate DNA conformations such as Z-DNA in the regulation of tra

228 nition steps of MMR: MutL does not trap bent DNA conformations, suggesting migrating MutL or MutS/Mut

229 ular dynamics simulations to investigate how DNA conformation, TF properties, and protein-protein int

230 ures helps to distinguish distortions of the DNA conformation that are inherent to the cross-overs of

231 groove modification of DNA causes changes in DNA conformation that are recognized by DNA-binding prot

232 is a fragile site, because it adopts a non-B DNA conformation that can be cleaved by the RAG complex.

233 ucleic Acid Database) to identify details of DNA conformation that correlate with specific Raman reco

234 ue, at least in part, to the need to adopt a DNA conformation that facilitates protein contacts with

235 cleavage site and to its stabilization of a DNA conformation that is required for catalysis.

236 fined model for the effect that TFIIA has on DNA conformation that takes into account potential chang

237 g frequently require transient or metastable DNA conformations that are biologically important but ch

238 This genome architecture favors DNA conformations that are conducive to genes spatial co

239 ng within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, da

240 ity of the amino group may permit particular DNA conformations that enforce hydrogen-amino contacts t

241 dopt multiple inter and intramolecular non-B-DNA conformations that may play an important role in bio

242 be induced by heat treatment to adopt novel DNA conformations that migrate faster than the correspon

243 en the sensitivity of calicheamicin to local DNA conformation, this observation is consistent with ot

244 quid crystalline lipid phase(L(alpha)) and B DNA conformation throughout the temperature range (5 deg

245 The bcl-2 Mbr assumes a non-B DNA conformation, thus explaining its distinctive fragil

246 Thus, AlkD acts by sculpting the global DNA conformation to achieve lesion expulsion from DNA.

247 indicate that the contribution of the local DNA conformation to the rate of repair at a particular n

248 ntributions of adduct conformation and local DNA conformation to the rate of repair, we compared the

249 e used Monte Carlo simulation of supercoiled DNA conformations to study the effect of supercoiling an

250 tributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding.

251 revealed significant unanticipated shifts in DNA conformation, to create an endonuclease that specifi

252 We conclude that alternative DNA conformations trigger genomic rearrangements through

253 Furthermore, changes in DNA conformation upon zinc finger protein binding may af

254 s were performed starting from two different DNA conformations using AMBER v8.0.

255 s were made based on circular and linearized DNA conformations using two genomes from each domain: De

256 dichroism measurements to the study of local DNA conformations, using the guanine base analog 6-methy

257 ofound effect in conferring stability to a Z-DNA conformation via electrostatic complementarity and h

258 A typical B-DNA conformation was adopted by the promoter DNA.

259 Surprisingly, the role of DNA conformation was never considered in this context.

260 Only small perturbation of the DNA conformation was observed upon binding of the cHMGI

261 ergy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of

262 These Crp/DNA conformations were asymmetrical (non-palindromic).

263 the previous analysis of the DNA structure B-DNA conformations were found with the AMBER force-field

264 sm for regulating transcription, sensing the DNA conformation where transcription bubble formation in

265 shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes

266 n process invoke an important role for non-B DNA conformations which may be adopted by these repeat s

267 nstrated that CGG runs adopt a left-handed Z-DNA conformation, whose features remain uncertain becaus

268 plex segment retains a minimally perturbed B-DNA conformation with all base pairs, including the junc

269 and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was

270 that binds specifically to the left-handed Z-DNA conformation with high affinity (KD = 4 nM).

271 tral eight base pairs of the decamer adopt A-DNA conformation with the two terminal nucleotides flipp

272 Sequential NOEs expected for a B-type DNA conformation with typical Watson-Crick base pairing

273 plex segment retains a minimally perturbed B-DNA conformation with Watson-Crick hydrogen-bonding reta

274 were found with the AMBER force-field and A-DNA conformations with CHARMM parameters.

275 ring and TR-FRET to correlate changes in the DNA conformations with composition of the histone core d

276 Equilibrium sets of DNA conformations with one segment of the double helix w

277 DNA structures are in a very similar, A-type DNA conformation, with helical axes curving towards the

278 erpret the sedimentation results in terms of DNA conformations, with particular emphasis on the marke

279 ions revealed the existence of similar non-B-DNA conformation within a d(TG/AC)28 repeat of the endog

280 angle X-ray scattering (CVSAXS) reports the DNA conformation within protein-DNA complexes and here i

281 nding on single DNA molecules and changes in DNA conformation without protein labeling.

282 We conclude that alternative DNA conformations, WRN deficiency and lung tumorigenesis