ライフサイエンスコーパス: cruciform

1 es not bind to the four-arm junctions of the cruciform.

2 stranded components and two sizes of a novel cruciform.

3 supercoiled DNA by extruding the repeat as a cruciform.

4 requires a stem-loop to extrude as part of a cruciform.

5 hairpins or the stem-stem interactions of a cruciform.

6 alternative DNA structural transitions, like cruciforms.

7 NA secondary structures such as hairpins and cruciforms.

8 spectroscopic properties of the investigated cruciforms.

9 anipulation of the HOMO and the LUMO of such cruciforms.

10 mation of alternative DNA structures such as cruciforms.

11 quences by binding to the promoter-localized cruciforms.

12 ation of five novel phenothiazine-containing cruciforms (5-9).

13 1-PMS2) similarly decreases the level of DNA cruciforms, although the mechanism is different from tha

14 nched plectonemic molecules with an extruded cruciform and A tract localized in the terminal loops.

15 erred sites are adjacent to the loops in the cruciform and are strand-specific.

16 d strongly to bent DNA structures, including cruciform and cisplatin-modified duplexes.

17 of inverted repeats in both DNA and/or RNA (cruciform and hairpin formation).

18 The region can switch between cruciform and linear duplex.

19 ur-stranded G-quadruplex, left-handed Z-DNA, cruciform and others.

20 an topo IIalpha, causes reintegration of the cruciform and quenching of fluorescence.

21 escent signal caused by the extrusion of the cruciform and separation of the labels as gyrase progres

22 The high affinity of topoisomerase I for cruciform and specificity of topoisomerase I-cruciform s

23 ole of Rep proteins in the formation of this cruciform and the implication for its nicking and religa

24 ortant roles in the function of DNA, forming cruciforms and affecting processes such as replication a

25 ly applicable for related structures such as cruciforms and quadruplexes.

26 g DNA arms is limited compared with that for cruciforms and three-way junctions.

27 binding to linear, nucleosomal, supercoiled, cruciform, and interstrand cross-linked damaged DNA, gen

28 te consequence of slipped-strand structures, cruciforms, and intramolecular triplexes, by inactivatio

29 DNA hairpins, cruciforms, and stably unpaired regions are all effectiv

30 non-B) DNA structures (e.g., G-quadruplexes, cruciforms, and Z-DNA), which regulate many cellular pro

31 ient and versatile synthetic strategy toward cruciform anthanthrene compounds using Sonogashira coupl

32 sion of this methodology to the synthesis of cruciform architectures and the functionalization of thi

33 Cruciforms are also the models for Holliday junctions, t

34 frontier molecular orbitals (FMOs) of these cruciforms are either congruent, i.e., HOMO and LUMO occ

35 Cruciforms are not thermodynamically stable in linear DN

36 Cruciforms are resolved unidirectionally and with high e

37 Cruciforms are seen as clear-cut extrusions on the DNA f

38 work demonstrates that fluorescently labeled cruciforms are useful as general real-time indicators of

39 We found that DNA hairpins, rather than DNA cruciforms, are responsible for the replication stalling

40 ize DNA in the flip orientation, copying one cruciform arm and creating a heterocruciform intermediat

41 drome are sequentially incorporated into the cruciform arms as hairpin loops, single unpaired bases,

42 -conformation was highly mobile allowing the cruciform arms to adopt a parallel orientation.

43 n successfully compete with extension of the cruciform arms.

44 Using a supercoil-stabilized cruciform as a substrate, we have analyzed the kinetics

45 that the six o'clock construct extrudes the cruciform at a lower superhelical density than a control

46 opensity to form branched molecules with the cruciform at the end of one branch.

47 Additional ChIP experiments with the cruciform binding 2D3 antibody indicate an increased rat

48 Thus, PARP-1 differs from other cruciform-binding proteins by binding to hairpin tips ra

49 Cleavage of the cruciform by the junction resolvase T4 endonuclease VII

50 Its center was marked by a large cruciform cache containing the earliest known directiona

51 ant denaturation at the base of an imperfect cruciform can successfully compete with extension of the

52 Instead, BYDV utilizes a cruciform cap independent translation element (CITE) in

53 ation and hairpin formation, as opposed to a cruciform cleavage pathway.

54 Analysis of the kinetics of cruciform cleavage shows that cleavage of the second str

55 e that could potentially assume an alternate cruciform configuration and hence directly bind HMG1, th

56 rchange converted SP-A from a "bouquet" to a cruciform configuration.

57 propose that Hmo1 locks gene boundaries in a cruciform conformation and, with Top2, modulates the arc

58 trate that the structural transition between cruciform conformations can act as a molecular switch to

59 ossibly, interconversions between linear and cruciform conformations of the palindromes may affect pr

60 contained in a superhelical plasmid, into a cruciform containing bulged bases.

61 Using a self-limiting, cruciform-containing substrate, we demonstrate that bila

62 The time-dependent dynamics of the cruciform correlates with the structural changes reveale

63 Formation of the cruciform creates an alternative binding site for mediat

64 ator-induced extrusion of this sequence as a cruciform, creating a single-stranded region for nicking

65 (Deltamgt1), which codes for a mitochondrial cruciform-cutting endonuclease.

66 Escherichia coli and the mitochondrial CCE1 (cruciform-cuttingenzyme 1) of Saccharomyces cerevisiae.

67 olecules with the different conformations of cruciforms depends on ionic conditions.

68 sequences of target probes for capture, the cruciform design of target probes for amplification, and

69 observe the conformational transition of the cruciform directly.

70 a-helical region of CRII to be important for cruciform DNA binding and identified critical residues.

71 SbcCD cuts off the top of a cruciform DNA by making incisions on both strands and co

72 vealed two predominant non-B DNA structures: cruciform DNA formed by expanded (TA)(n) repeats that ac

73 Further analysis demonstrated that cruciform DNA has two populations of binding sites for t

74 on intermediates, followed by an increase in cruciform DNA molecules, as well as in bidirectional rep

75 e the hydroxyl radical cleavage pattern in a cruciform DNA structure formed by a 60 bp inverted repea

76 aising the possibility of the formation of a cruciform DNA structure.

77 on of TA nucleotide repeats proposed to form cruciform DNA structures, which in turn cause DNA breaks

78 CRII binds cruciform DNA with high selectivity and micromolar affin

79 d in HU's high-affinity binding to kinked or cruciform DNA, leads to less dramatically altered intera

80 a high affinity for structured DNAs such as cruciform DNA.

81 tprinting of supercoiled plasmid showed that cruciformed DSE1 is targeted by nuclear proteins more ef

82 In this report, we propose a cruciform-dumbbell model to explain the inverted dimer f

83 i.e. the reciprocal-strand-switching and the cruciform-dumbbell models) in which intermediates contai

84 gest that FS2 forms a hairpin, rather than a cruciform, during replication in cells with low levels o

85 ic skeleton comprising orthogonally arranged cruciform elements, architecturally similar to some hexa

86 e replication and the topoisomerase-like and cruciform-enhancing activities of the native protein.

87 We find that short IRs do not extrude cruciforms, even in the absence of competition.

88 Benzobisimidazole cruciforms exhibit a pronounced response to deprotonatio

89 The cruciform exists in two different conformations, an exte

90 fication assays have identified an imperfect cruciform extruded by the DSE1.

91 e major effects on the overall energetics of cruciform extrusion and on the course of this transition

92 extend this approach to include superhelical cruciform extrusion at both perfect and imperfect invert

93 l gel electrophoresis was used to detect the cruciform extrusion both in the absence and in the prese

94 Propensity for cruciform extrusion in duplex DNA correlated with stimul

95 ok a broader study of the effect of Mg2+on a cruciform extrusion in supercoiled DNA.

96 Our results show that Mg2+shifts the cruciform extrusion in the d(CCC(AT)16GGG) palindrome to

97 the short palindromes for which the unusual cruciform extrusion in the presence Mg2+was reported, we

98 These data suggest that cruciform extrusion in the short palindromes at low supe

99 it was reported that Mg2+greatly facilitates cruciform extrusion in the short palindromes of supercoi

100 Our results show that Mg2+also shifts the cruciform extrusion in this palindrome to a higher level

101 h the level of supercoiling required for the cruciform extrusion is not reduced by Mg2+, the ions red

102 gest that long palindromic sequences undergo cruciform extrusion more readily than short ones.

103 Cruciform extrusion was confirmed, and its extent was qu

104 we also find that RepC/C is able to enhance cruciform extrusion while RepC/C* cannot.

105 d origin, the modified protein cannot induce cruciform extrusion, and it is proposed that this inabil

106 includes complete coupling between DeltaLk, cruciform extrusion, formation of extrahelical bases, an

107 es algorithms to analyze B-Z transitions and cruciform extrusion.

108 ermodynamic analysis of the effect of Mg2+on cruciform extrusion.

109 rrangement has been proposed to be driven by cruciform extrusion.

110 The syntheses of three water-soluble cruciform fluorophores (XF) carrying aniline- N, N-bisac

111 We developed a series of new conjugated cruciform fluorophores (XF) featuring imine groups.

112 A series of 11 cross-conjugated cruciform fluorophores based on a benzobisimidazole nucl

113 small array was obtained from three reactive cruciform fluorophores in six different solvents.

114 oromethyl)benzene) to give the corresponding cruciform fluororphores (XF).

115 ption of intrastrand base-pairing preventing cruciform formation and protein binding to DSE1 is respo

116 to an apical position increases the rate of cruciform formation and reduces the superhelical energy

117 ow that the susceptibilities of these IRs to cruciform formation correspond closely with their observ

118 for self-catalyzed depurination mediated by cruciform formation in plasmid DNA in vitro.

119 Hairpin/cruciform formation is not observed in free solution, pr

120 tion start sites in eukaryotes suggests that cruciform formation is rarely involved in mechanisms of

121 li cells was assessed from the efficiency of cruciform formation upstream of a regulated promoter.

122 supercoiling upon promoter induction led to cruciform formation, which was quantitatively measured b

123 kage and subsequent deletions at hairpin and cruciform forming (AT/TA)n sequences, with little to no

124 solution mapping that PARP-1 may bind to the cruciform-forming regions of its own promoter.

125 By placing a cruciform-forming sequence at varying distances from the

126 d atomic force microscopy (AFM) to visualize cruciform geometry in plasmid DNA with different superhe

127 that PARP-1 binds to stem/loop boundaries of cruciform hairpins.

128 percoiled DNA through the recognition of DNA cruciforms, helix-helix crossovers and hairpins.

129 organization of pericentric chromatin into a cruciform in mitosis such that centromere-flanking DNA a

130 consistent with the presence of the extruded cruciform in the supercoiled plasmid and not in the line

131 mechanism is initiated by SbcCD cleavage of cruciforms in duplex DNA followed by RecA-independent si

132 ce Microscopy (AFM) was applied to visualize cruciforms in negatively supercoiled plasmid DNA.

133 particular, we found a strong enrichment of cruciforms in the termination region of operons; this en

134 bitals (HOMOs) are localized (24-99%) in all cruciforms, in contrast to the lowest unoccupied molecul

135 markably, the overall integrity of the 5BSL3 cruciform is not an absolute requirement for the kissing

136 In the absence of this, we find that a cruciform junction is no longer subject to bilateral cle

137 In supercoiled TH promoter, DSE1 assumes a cruciform-like conformation i.e., it binds cruciform-spe

138 ed to their ability to fold into hairpin- or cruciform-like DNA structures interfering with DNA repli

139 Cruciform-like molecules with two orthogonally placed pi

140 spatial DNA organization, follow the order: cruciform<or=hairpin<<loop.

141 rbitals (FMOs) along different axes of these cruciforms makes them promising as sensing platforms, si

142 DSE1 cruciform may act as a target site for activator (BAMC c

143 Therefore, structural transitions of the cruciform may play a key role in these processes.

144 synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene)

145 ong edges with aromatic rings forming rigid, cruciform molecules.

146 onships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increase

147 DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA compl

148 Mus81-Mms4 cleavage of cruciforms occurs at divergently but not convergently tr

149 genomic instability is believed to be due to cruciform or hairpin formation and subsequent cleavage o

150 es and IRs with short spacers can extrude as cruciforms or fold into hairpins on the lagging strand d

151 equences that can form intrastrand hairpins (cruciforms) or four-stranded structures (G-quadruplex or

152 lded conformations (i.e. slipped structures, cruciforms, or triplexes) at or near the breakpoints was

153 Unusual DNA conformations including cruciforms play an important role in gene regulation and

154 ARCAL1 and FANCM directly unwind TA-rich DNA cruciforms, preventing catastrophic chromosome breakage

155 induces the palindrome to reconfigure into a cruciform prior to fork assembly.

156 ted higher than additive effects in in vitro cruciform processing, suggesting that WRN and the MMR pr

157 UV/vis absorption and emission spectroscopy: cruciforms' protonation results in hypsochromic and bath

158 In addition, cruciforms provide a model system for structural studies

159 stalled replication forks, DNA hairpins and cruciforms, R-loops, and DNA G-quadruplexes (G4 DNA).

160 erfect and quasi-palindromes, which involves cruciform resolution during the G2 phase of the cell cyc

161 Cruciform resolution produces double-strand breaks (DSBs

162 X-ray diffraction studies of three selected cruciforms revealed the expected ~90 degrees angle betwe

163 obular complex of PCBP2 interacting with the cruciform RNA via KH domains and featuring a prominent G

164 d the expected ~90 degrees angle between the cruciform's substituents, and crystal packing patterns d

165 We report the synthesis of nine conjugated cruciform-shaped molecules based on the central benzo[1,

166 sing platforms, since analyte binding to the cruciform should mandate a change in the HOMO-LUMO gap a

167 Use of the cruciform site has been shown to correlate with activate

168 th sequence-specific and structure (possibly cruciform)-specific recognition for activity.

169 a cruciform-like conformation i.e., it binds cruciform-specific 2D3 antibody, and S1 nuclease-cleavag

170 te element analysis was used to optimize the cruciform specimen geometry so that stresses within the

171 and suggest that the helical geometry of the cruciform stem differs from that of the normal duplex fo

172 in length and is part of a larger predicted cruciform structure (5BSL3).

173 orm a one-stranded hairpin or a two-stranded cruciform structure and have analyzed recombinants at th

174 ted repeats (IRs) that can form a hairpin or cruciform structure are common in the human genome and m

175 the stem if the strands were to fold into a cruciform structure are required for activity, suggestin

176 cruciform and specificity of topoisomerase I-cruciform structure interaction were confirmed by compet

177 nergy of supercoiling and the free energy of cruciform structure per se.

178 ive analysis of our immobile HJs and a model cruciform structure sheds new light on the issue of the

179 verted DNA sequences at the nick site form a cruciform structure that facilitates DNA cleavage.

180 location, we proposed that the PATRR forms a cruciform structure that induces the genomic instability

181 This cruciform structure then acts as a substrate for structu

182 an inverted repeat that is likely to form a cruciform structure, providing convenient tags for creat

183 yme and results in symmetrical cleavage of a cruciform structure, thus, Mus81-Eme1 can ensure coordin

184 ile many Ln-1 molecules assumed the expected cruciform structure, unexpected dynamic movements of the

185 m a double-stranded linear amplicon, or to a cruciform structure, which is then resolved to yield the

186 repeat, which could form an extremely stable cruciform structure.

187 Mg2+, the ions reduce the free energy of the cruciform structure.

188 ate the high affinity of topoisomerase I for cruciform structure.

189 otif with the potential to form a hairpin or cruciform structure.

190 wo of the arms across a four-way junction or cruciform structure.

191 CRISPR repeats and at sequences adjacent to cruciform structures abutting AT-rich regions, similar t

192 responsible for cleavage of the hairpin and cruciform structures and generation of double-strand bre

193 g 2D3 antibody indicate an increased rate of cruciform structures at PATRR regions in both mitotic an

194 ication pathway controls the accumulation of cruciform structures at stalled forks.

195 ligands are attached to the PCR primers, the cruciform structures can be detected by standard immunoc

196 Cruciform structures exist in vivo and they are critical

197 Cruciform structures generated with oligonucleotides wer

198 tential of forming single-stranded stem-loop cruciform structures have been reported to be essential

199 oiled DNA, thereby allowing the formation of cruciform structures in vivo.

200 king palindrome and incapable of forming any cruciform structures invariably yielded progeny viruses

201 The high specificity of Rif1 for cruciform structures is significant given the role of th

202 romosomes 11 and 22, suggesting that hairpin/cruciform structures mediate double-strand breaks leadin

203 rm recognizes single-stranded spacers within cruciform structures that also have a role in chromatin

204 Palindromic sequences can form hairpin and cruciform structures that pose a threat to genome integr

205 TA repeats are particularly prone to form cruciform structures, explaining why these DNA sequences

206 helicase can efficiently and directly unfold cruciform structures, thereby preventing their cleavage

207 uences have the potential to form hairpin or cruciform structures, which are putative substrates for

208 nhibits branch migration and produces stable cruciform structures.

209 omic DNA sample anneal to form four-stranded cruciform structures.

210 AT-rich regions and sequences that can form cruciform structures.

211 1 integrases within the stems of plasmid DNA cruciform structures.

212 epetitive elements that can form hairpin and cruciform structures.

213 tentially through the formation of secondary cruciform structures.

214 ic DNA binding protein with a preference for cruciform structures.

215 Cruciforms' substituents were varied pairwise among the

216 y delocalized across the molecule, except in cruciforms substituted with electron-withdrawing groups

217 We have used a supercoil-stabilized cruciform substrate to probe the simultaneity of cleavag

218 Using a supercoil-stabilised cruciform substrate we demonstrate that an active subuni

219 mer; this has been confirmed by the use of a cruciform substrate.

220 akes transferred on a flexible polycarbonate cruciform substrate.

221 formation of an alternative DNA structure, a cruciform, suggesting that these positions in supercoile

222 ind to mixed base sequences that cannot form cruciforms, suggesting that recognition is a general phe

223 Three of the cruciform tetramers assemble into a triangular dodecamer

224 drogen-bonded beta-sheets that assemble into cruciform tetramers consisting of eight beta-strands in

225 fic conditions, the inverted repeat formed a cruciform that was used as a marker for the unambiguous

226 for having the nicking site at the tip of a cruciform: the need to provide the functional initiator

227 Two novel donor-acceptor cruciform topologies are efficiently synthesized by site

228 orene to produce molecules with well-defined cruciform topologies, extended pi-conjugated aromatic co

229 een folded and unfolded conformations of the cruciform toward the folded one.

230 ently, we showed that the inverted repeat-to-cruciform transition acts as a molecular switch, influen

231 rect repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively

232 ve (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine qua

233 A structures (slipped structures with loops, cruciforms, triplexes and tetraplexes) as well as microh

234 n adopt alternative conformations, including cruciforms, triplexes, and quadruplexes.

235 concentrations of ethidium suggest that the cruciforms undergo a transition under torsional stress.

236 The affinity of topoisomerase I for cruciform was found to be an order of magnitude higher a

237 The photophysics of the cruciforms was investigated upon addition of either an e

238 , 1,4-distyryl-2,5-bis(ethynylaryl)benzenes (cruciforms) was investigated; their fluorescence quantum

239 equence, and thus its ability to fold into a cruciform, was dispensable for origin function, as was t

240 oth folded and unfolded conformations of the cruciform were identified, and the data showed that DNA

241 When the A tract and cruciform were placed diametrically opposite, this yield

242 cted of a resolvase activity, the artificial cruciforms were degraded.

243 t long inverted repeats can form hairpins or cruciforms when they are located within a region of the

244 erted repeats promote the formation of a DNA cruciform which is processed by an endonuclease into a l

245 One alternative DNA conformation is the cruciform, which has been shown to have a critical role

246 e., the HOMO is located on one branch of the cruciform while the LUMO is located on the second one.

247 synthetic circular DNA molecules containing cruciforms with immobile or tetramobile branched junctio

248 each cleave the phosphodiester backbone of a cruciform within the lifetime of the DNA-protein complex

249 l 1,4-distyryl-2,5-bisphenylethynylbenzenes (cruciforms, XF) have been prepared by a sequential Horne

250 Last, we found that cleavage of an extruded cruciform yielded a product, which after treatment with

251 ONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structu

252 ender sequence-dependent structures, such as cruciforms, Z-DNA, or H-DNA, even though they are not fa