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1 stranded components and two sizes of a novel cruciform.
2 supercoiled DNA by extruding the repeat as a cruciform.
3 requires a stem-loop to extrude as part of a cruciform.
4 hairpins or the stem-stem interactions of a cruciform.
5 es not bind to the four-arm junctions of the 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.
13 nched plectonemic molecules with an extruded cruciform and A tract localized in the terminal loops.
19 escent signal caused by the extrusion of the cruciform and separation of the labels as gyrase progres
20 The high affinity of topoisomerase I for cruciform and specificity of topoisomerase I-cruciform s
21 ole of Rep proteins in the formation of this cruciform and the implication for its nicking and religa
22 ortant roles in the function of DNA, forming cruciforms and affecting processes such as replication a
25 te consequence of slipped-strand structures, cruciforms, and intramolecular triplexes, by inactivatio
27 ient and versatile synthetic strategy toward cruciform anthanthrene compounds using Sonogashira coupl
28 sion of this methodology to the synthesis of cruciform architectures and the functionalization of thi
30 frontier molecular orbitals (FMOs) of these cruciforms are either congruent, i.e., HOMO and LUMO occ
34 work demonstrates that fluorescently labeled cruciforms are useful as general real-time indicators of
35 We found that DNA hairpins, rather than DNA cruciforms, are responsible for the replication stalling
36 ize DNA in the flip orientation, copying one cruciform arm and creating a heterocruciform intermediat
37 drome are sequentially incorporated into the cruciform arms as hairpin loops, single unpaired bases,
41 that the six o'clock construct extrudes the cruciform at a lower superhelical density than a control
45 ant denaturation at the base of an imperfect cruciform can successfully compete with extension of the
48 e that could potentially assume an alternate cruciform configuration and hence directly bind HMG1, th
50 trate that the structural transition between cruciform conformations can act as a molecular switch to
51 ossibly, interconversions between linear and cruciform conformations of the palindromes may affect pr
56 ator-induced extrusion of this sequence as a cruciform, creating a single-stranded region for nicking
58 Escherichia coli and the mitochondrial CCE1 (cruciform-cuttingenzyme 1) of Saccharomyces cerevisiae.
60 sequences of target probes for capture, the cruciform design of target probes for amplification, and
62 a-helical region of CRII to be important for cruciform DNA binding and identified critical residues.
65 on intermediates, followed by an increase in cruciform DNA molecules, as well as in bidirectional rep
66 e the hydroxyl radical cleavage pattern in a cruciform DNA structure formed by a 60 bp inverted repea
70 tprinting of supercoiled plasmid showed that cruciformed DSE1 is targeted by nuclear proteins more ef
72 i.e. the reciprocal-strand-switching and the cruciform-dumbbell models) in which intermediates contai
73 gest that FS2 forms a hairpin, rather than a cruciform, during replication in cells with low levels o
74 e replication and the topoisomerase-like and cruciform-enhancing activities of the native protein.
79 e major effects on the overall energetics of cruciform extrusion and on the course of this transition
80 extend this approach to include superhelical cruciform extrusion at both perfect and imperfect invert
81 l gel electrophoresis was used to detect the cruciform extrusion both in the absence and in the prese
85 the short palindromes for which the unusual cruciform extrusion in the presence Mg2+was reported, we
87 it was reported that Mg2+greatly facilitates cruciform extrusion in the short palindromes of supercoi
88 Our results show that Mg2+also shifts the cruciform extrusion in this palindrome to a higher level
89 h the level of supercoiling required for the cruciform extrusion is not reduced by Mg2+, the ions red
93 d origin, the modified protein cannot induce cruciform extrusion, and it is proposed that this inabil
94 includes complete coupling between DeltaLk, cruciform extrusion, formation of extrahelical bases, an
103 ption of intrastrand base-pairing preventing cruciform formation and protein binding to DSE1 is respo
104 to an apical position increases the rate of cruciform formation and reduces the superhelical energy
105 ow that the susceptibilities of these IRs to cruciform formation correspond closely with their observ
108 tion start sites in eukaryotes suggests that cruciform formation is rarely involved in mechanisms of
109 li cells was assessed from the efficiency of cruciform formation upstream of a regulated promoter.
110 supercoiling upon promoter induction led to cruciform formation, which was quantitatively measured b
113 d atomic force microscopy (AFM) to visualize cruciform geometry in plasmid DNA with different superhe
116 organization of pericentric chromatin into a cruciform in mitosis such that centromere-flanking DNA a
117 consistent with the presence of the extruded cruciform in the supercoiled plasmid and not in the line
118 mechanism is initiated by SbcCD cleavage of cruciforms in duplex DNA followed by RecA-independent si
120 particular, we found a strong enrichment of cruciforms in the termination region of operons; this en
121 bitals (HOMOs) are localized (24-99%) in all cruciforms, in contrast to the lowest unoccupied molecul
122 markably, the overall integrity of the 5BSL3 cruciform is not an absolute requirement for the kissing
124 In supercoiled TH promoter, DSE1 assumes a cruciform-like conformation i.e., it binds cruciform-spe
125 ed to their ability to fold into hairpin- or cruciform-like DNA structures interfering with DNA repli
128 rbitals (FMOs) along different axes of these cruciforms makes them promising as sensing platforms, si
131 synthetic protocols for a large selection of cruciform molecules based on oligo(phenyleneethynylene)
133 onships from SAMs of series of OPE3 and OPE5 cruciform molecules; the conductance of the SAM increase
134 genomic instability is believed to be due to cruciform or hairpin formation and subsequent cleavage o
135 es and IRs with short spacers can extrude as cruciforms or fold into hairpins on the lagging strand d
136 lded conformations (i.e. slipped structures, cruciforms, or triplexes) at or near the breakpoints was
139 UV/vis absorption and emission spectroscopy: cruciforms' protonation results in hypsochromic and bath
142 X-ray diffraction studies of three selected cruciforms revealed the expected ~90 degrees angle betwe
143 d the expected ~90 degrees angle between the cruciform's substituents, and crystal packing patterns d
144 We report the synthesis of nine conjugated cruciform-shaped molecules based on the central benzo[1,
145 sing platforms, since analyte binding to the cruciform should mandate a change in the HOMO-LUMO gap a
148 a cruciform-like conformation i.e., it binds cruciform-specific 2D3 antibody, and S1 nuclease-cleavag
149 te element analysis was used to optimize the cruciform specimen geometry so that stresses within the
150 and suggest that the helical geometry of the cruciform stem differs from that of the normal duplex fo
152 orm a one-stranded hairpin or a two-stranded cruciform structure and have analyzed recombinants at th
153 ted repeats (IRs) that can form a hairpin or cruciform structure are common in the human genome and m
154 the stem if the strands were to fold into a cruciform structure are required for activity, suggestin
155 cruciform and specificity of topoisomerase I-cruciform structure interaction were confirmed by compet
157 ive analysis of our immobile HJs and a model cruciform structure sheds new light on the issue of the
159 location, we proposed that the PATRR forms a cruciform structure that induces the genomic instability
161 an inverted repeat that is likely to form a cruciform structure, providing convenient tags for creat
162 yme and results in symmetrical cleavage of a cruciform structure, thus, Mus81-Eme1 can ensure coordin
163 ile many Ln-1 molecules assumed the expected cruciform structure, unexpected dynamic movements of the
164 m a double-stranded linear amplicon, or to a cruciform structure, which is then resolved to yield the
170 CRISPR repeats and at sequences adjacent to cruciform structures abutting AT-rich regions, similar t
172 ligands are attached to the PCR primers, the cruciform structures can be detected by standard immunoc
175 tential of forming single-stranded stem-loop cruciform structures have been reported to be essential
177 king palindrome and incapable of forming any cruciform structures invariably yielded progeny viruses
179 romosomes 11 and 22, suggesting that hairpin/cruciform structures mediate double-strand breaks leadin
180 rm recognizes single-stranded spacers within cruciform structures that also have a role in chromatin
181 Palindromic sequences can form hairpin and cruciform structures that pose a threat to genome integr
182 uences have the potential to form hairpin or cruciform structures, which are putative substrates for
189 y delocalized across the molecule, except in cruciforms substituted with electron-withdrawing groups
193 formation of an alternative DNA structure, a cruciform, suggesting that these positions in supercoile
194 ind to mixed base sequences that cannot form cruciforms, suggesting that recognition is a general phe
196 drogen-bonded beta-sheets that assemble into cruciform tetramers consisting of eight beta-strands in
197 fic conditions, the inverted repeat formed a cruciform that was used as a marker for the unambiguous
198 for having the nicking site at the tip of a cruciform: the need to provide the functional initiator
199 orene to produce molecules with well-defined cruciform topologies, extended pi-conjugated aromatic co
201 ently, we showed that the inverted repeat-to-cruciform transition acts as a molecular switch, influen
202 rect repeats and their associated subsets of cruciforms, triplex and slipped structures, respectively
203 ect repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several
204 A structures (slipped structures with loops, cruciforms, triplexes and tetraplexes) as well as microh
205 concentrations of ethidium suggest that the cruciforms undergo a transition under torsional stress.
208 , 1,4-distyryl-2,5-bis(ethynylaryl)benzenes (cruciforms) was investigated; their fluorescence quantum
209 equence, and thus its ability to fold into a cruciform, was dispensable for origin function, as was t
210 oth folded and unfolded conformations of the cruciform were identified, and the data showed that DNA
213 t long inverted repeats can form hairpins or cruciforms when they are located within a region of the
214 erted repeats promote the formation of a DNA cruciform which is processed by an endonuclease into a l
216 e., the HOMO is located on one branch of the cruciform while the LUMO is located on the second one.
217 synthetic circular DNA molecules containing cruciforms with immobile or tetramobile branched junctio
218 each cleave the phosphodiester backbone of a cruciform within the lifetime of the DNA-protein complex
219 l 1,4-distyryl-2,5-bisphenylethynylbenzenes (cruciforms, XF) have been prepared by a sequential Horne
220 Last, we found that cleavage of an extruded cruciform yielded a product, which after treatment with
221 ONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structu
222 ender sequence-dependent structures, such as cruciforms, Z-DNA, or H-DNA, even though they are not fa
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