ライフサイエンスコーパス: DNA conformation

1 as maintained except for local deviations in DNA conformation.

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

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

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

5 of spermidine, a small polyamine influencing DNA conformation.

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

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

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

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

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

11 vator protein that introduces changes in the DNA conformation.

12 contacts with RNA polymerase and changes in DNA conformation.

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

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

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

16 er chromatin structure through modulation of DNA conformation.

17 long range effect of cytosine methylation on DNA conformation.

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

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

20 fragile zones are predominantly in a duplex 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 ecules at high-affinity sites regulates oriC DNA conformation.

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

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

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

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

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

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

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

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

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

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

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

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

36 he DNA that allow formation of complementary DNA conformations.

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

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

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

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

41 force field that preferentially stabilizes B-DNA conformations.

42 of the switching between lying and standing DNA conformations.

43 mulations of the equilibrium distribution of DNA conformations.

44 er is the primary determinant of supercoiled DNA conformations.

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

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

47 structures thus far involve targeting single DNA conformations.

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

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

50 sed as spectroscopic probes to examine local DNA conformations.

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

52 sitively or negatively writhed and denatured DNA conformations.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

92 1,10-phenanthroline copper confirms that the DNA conformation at the position of the right-side ligan

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

163 Unusual DNA conformations including cruciforms play an important

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

190 The determination of DNA conformations on surfaces and hybridization behavior

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

228 We conclude that alternative DNA conformations trigger genomic rearrangements through

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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