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1 NA nuclease activity specific for nicking of supercoiled DNA.
2 G-rich sequence of this region in negatively supercoiled DNA.
3 linear dsDNA and its homologous pairing with supercoiled DNA.
4 ed double-stranded DNA, when transcribed, or supercoiled DNA.
5 lar DNA has been enzymatically prepared from supercoiled DNA.
6 levels of cleavage complexes with positively supercoiled DNA.
7 omerase I, an enzyme that relaxes negatively supercoiled DNA.
8 elative cleavage enhancement with positively supercoiled DNA.
9 lexes with positively rather than negatively supercoiled DNA.
10 only when the enzyme is bound to positively supercoiled DNA.
11 myc FUSE in vitro only in single-stranded or supercoiled DNA.
12 e reaction and preferentially cut negatively supercoiled DNA.
13 ith AMPPNP, the product is a hypernegatively supercoiled DNA.
14 u and a distant enhancer site (E) located on supercoiled DNA.
15 as well as for 4-way junction structures and supercoiled DNA.
16 vored over the longer loops, particularly on supercoiled DNA.
17 yme intermediate, resulting in relaxation of supercoiled DNA.
18 measure the curvature of apical positions in supercoiled DNA.
19 ase in the relaxation activity of negatively supercoiled DNA.
20 s a sensor of the conformational dynamics of supercoiled DNA.
21 t formation of FI*, a highly unwound form of supercoiled DNA.
22 istone-like protein HU and close the loop in supercoiled DNA.
23 ecially the V256I variant towards positively supercoiled DNA.
24 f topoisomerase IIIalpha to relax negatively supercoiled DNA.
25 ich is necessary for relaxation reactions of supercoiled DNA.
26 multiprotein complex containing GalR, HU and supercoiled DNA.
27 he effect of Mg2+on a cruciform extrusion in supercoiled DNA.
28 ith LacI's preference for binding negatively supercoiled DNA.
29 ngle-stranded DNA and cleave double-stranded supercoiled DNA.
30 ibited toward both positively and negatively supercoiled DNA.
31 n the GalR-binding sites, and (3) negatively supercoiled DNA.
32 s) about the midpoint between OE and OI, and supercoiled DNA.
33 ntal values of the diffusion coefficients of supercoiled DNA.
34 ate promoter (AdMLP) contained on negatively supercoiled DNA.
35 onstant, B, that depends on conformations of supercoiled DNA.
36 position of three sites at a branch point in supercoiled DNA.
37 nces on the tertiary structure of negatively supercoiled DNA.
38 with respect to their activities in relaxing supercoiled DNA.
39 nt models for encounters of distant sites on supercoiled DNA.
40 enzyme to catalyze relaxation of negatively supercoiled DNA.
41 ty, demonstrated by their ability to degrade supercoiled DNA.
42 a cofactor for the relaxation of negatively supercoiled DNA.
43 for predicting equilibrium conformations of supercoiled DNA.
44 ust uncover and characterize the dynamics of supercoiled DNA.
45 , we also detect exposed bases in positively supercoiled DNA.
46 de atomistic insight into the flexibility of supercoiled DNA.
47 the topology (topological linking number) of supercoiled DNA.
48 role in maintaining DNA topology by relaxing supercoiled DNA.
49 onuclease that makes single-strand breaks in supercoiled DNA.
50 the protein has a preference for binding to supercoiled DNA.
51 regions or nicks as well as relax negatively supercoiled DNA.
52 s between linear double-stranded (dsDNA) and supercoiled DNA.
53 l Escherichia coli RNAPs as they transcribed supercoiled DNA.
54 ies in its preference of relaxing negatively supercoiled DNA.
55 y visualize and quantify protein dynamics on supercoiled DNA.
56 polar region of potential energy within the supercoiled DNA.
57 icient for the production of hypernegatively supercoiled DNA.
58 to study complex and dynamic interactions of supercoiled DNA.
59 gative supercoils to produce hypernegatively supercoiled DNA.
60 al role in the generation of hypernegatively supercoiled DNA.
61 t can crosslink two separate DNA segments in supercoiled DNA.
62 amic continuum rod model of a long length of supercoiled DNA.
63 es and biological interactions of negatively supercoiled DNA.
64 tions to determine the structure of bent and supercoiled DNA.
65 opoIIalpha-mediated relaxation of positively supercoiled DNA.
66 lity of topoisomerase I to cleave positively supercoiled DNA.
67 of linear DNAs but retarded the diffusion of supercoiled DNAs.
69 ry out DNA cleavage and strand transfer from supercoiled DNA, a new picture of the disposition of DNA
70 ition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher th
72 d the formation of joint molecules between a supercoiled DNA and a linear dsDNA substrate with homolo
73 A is the product of the concentration of the supercoiled DNA and a proportionality constant, B, that
74 d III (Topo I and Topo III) relax negatively supercoiled DNA and also catenate/decatenate DNA molecul
75 po IIIbeta only partially relaxes negatively supercoiled DNA and appears incapable of generating full
76 ximately one StpA molecule per 250-300 bp of supercoiled DNA and approximately one StpA molecule per
77 tion activity of Top3beta on hypernegatively supercoiled DNA and changes the reaction from a distribu
78 thesized and tested for its ability to relax supercoiled DNA and cleave linear duplex DNA in a sequen
79 merase I (Top1p) catalyzes the relaxation of supercoiled DNA and constitutes the cellular target of c
80 acetylation of oligonucleosomes assembled on supercoiled DNA and dinucleosomes assembled on linear DN
81 Here we report that the irradiation of both supercoiled DNA and DNA oligonucleotides in the presence
82 strand scission leading to the relaxation of supercoiled DNA and formation of at least two different
83 anscriptional activation in vitro depends on supercoiled DNA and high salt concentrations, a conditio
84 s shown that a joint molecule, consisting of supercoiled DNA and homologous ODN targeted to correct t
86 Relaxation is powered by the torque in the supercoiled DNA and is constrained by friction between t
87 Progress in structural biology studies of supercoiled DNA and its complexes with regulatory protei
88 merase IV, enhanced relaxation of negatively supercoiled DNA and knotting by topoisomerase IV, which
90 es the ability of topo I to relax negatively supercoiled DNA and specifically stimulates the religati
92 extracting the cleavage pattern specific to supercoiled DNA and use this method to investigate the h
94 isomerases is required for the relaxation of supercoiled DNA and was hypothesized to be required for
95 ymus topoisomerase I (CT Topo I) on a native supercoiled DNA and, if so, whether the enzyme catalyzes
98 grase, MAP30's ability to irreversibly relax supercoiled DNA, and may be an alternative cytotoxic pat
99 es, identify local alternative structures in supercoiled DNA, and monitor structural dynamics of DNA
100 ved in experimental sedimentation studies of supercoiled DNA, and our results provide a physical expl
103 ruciform, suggesting that these positions in supercoiled DNA are under additional stress and perhaps
104 tically modifies this picture by introducing supercoiled DNA as a competing structure in addition to
105 s to assess the conformational properties of supercoiled DNA as a function of ionic conditions and su
107 d crossings, Topo IV can specifically unknot supercoiled DNA, as well as decatenate postreplicative c
108 sinusoidal variation from SfiI reactions on supercoiled DNA at 50 degreesC yielded a helical repeat
109 ve topoisomerase that is capable of relaxing supercoiled DNA at a broad range of Mg2+ concentrations;
111 or this reason, methods to prepare and study supercoiled DNA at the single-molecule level are widely
112 tein interactions in vitro may be favored on supercoiled DNA because of topological constraints.
113 is required for the relaxation of negatively supercoiled DNA behind the transcribing RNA polymerase.
116 in TFIIIB transcription factor activity with supercoiled DNA but are inactive with linear duplex DNA.
117 the proteins preferentially bind negatively supercoiled DNA but the details of the topology-dependen
120 omerase I (Top1) catalyzes the relaxation of supercoiled DNA by a conserved mechanism of transient DN
121 otic type IB enzyme, catalyzes relaxation of supercoiled DNA by cleaving and rejoining DNA strands th
122 ype IB topoisomerases catalyze relaxation of supercoiled DNA by cleaving and rejoining DNA strands vi
124 release the free energy stored in negatively supercoiled DNA by extruding the repeat as a cruciform.
125 of Rad51 protein to promote the invasion of supercoiled DNA by homologous GT-rich single-stranded DN
126 -based assay for ATP-dependent relaxation of supercoiled DNA by human TOP2A can also be used under id
128 at topo IV discriminates between (-) and (+) supercoiled DNA by recognition of the geometry of (+) SC
130 e presence of YejK, relaxation of negatively supercoiled DNA by topoisomerase IV becomes distributive
131 is-buffered solutions the Raman signature of supercoiled DNA can be obscured by Raman bands of Tris c
132 preparation, but ''ghost bands" of denatured supercoiled DNA can result if the pH is too high or the
136 topological barriers using polymer models of supercoiled DNA chains that are constrained such as to m
141 s later discovered to either relax or cleave supercoiled DNA, depending upon whether Nae I position 4
142 tomic force microscopy (AFM) for imaging the supercoiled DNA deposited at different ionic conditions.
143 have enabled researchers to obtain images of supercoiled DNAs deposited on mica surfaces in buffered
144 diffused slower when size of DNAs increased; supercoiled DNAs diffused faster than linear ones; mucus
149 nfected insect cells binds preferentially to supercoiled DNA, forming bands with lower electrophoreti
150 have simulated transfers of a 3760-basepair supercoiled DNA from solution to a surface in both 161 a
152 on is stimulated over 20-fold from linear or supercoiled DNA if CTP is present during formation of in
154 he C-terminal domain partially competes with supercoiled DNA in binding to p53, while antibodies targ
156 an exemplary member of this family, relaxes supercoiled DNA in the absence of a divalent cation or A
157 to be active in the relaxation of negatively supercoiled DNA in the absence of additional Mg(II).
160 s capable of efficiently relaxing negatively supercoiled DNA in the presence of Mg2+ but does not pos
163 scopic models of unmelted and locally melted supercoiled DNAs in 20 mM ionic strength are simulated o
165 ritten to perform Monte Carlo simulations of supercoiled DNAs in solution was modified to include a s
167 for topoisomerase II-mediated relaxation of supercoiled DNA indicate that the benzodiimidazole and d
171 nd that the affinity of DmORC for negatively supercoiled DNA is about 30-fold higher than for either
173 ow that the decrease in damage in positively supercoiled DNA is controlled at the level of thiol acti
175 demonstrate that enzyme bound to positively supercoiled DNA is in a different conformation from that
177 aposition kinetics between specific sites in supercoiled DNA is investigated at close to physiologica
179 note that although a particular site i(1) in supercoiled DNA is often in close proximity (juxtaposed)
182 s that becomes topologically linked with the supercoiled DNA is the product of the concentration of t
183 nd reform almost reversibly, indicating that supercoiled DNA is trapped in the condensed structure.
186 move linear DNA from a mixture of linear and supercoiled DNA, leaving the supercoiled form intact.
189 V have critical interactions with positively supercoiled DNA, little is known about the actions of th
190 ce-dependent denaturation in highly bent and supercoiled DNA loops, each also reveals a unique aspect
192 unt for how fluctuations in the structure of supercoiled DNA might lead to the juxtaposition of dista
193 Finally, the more complex topology of the supercoiled DNA minicircle gives rise to a secondary DNA
194 n simulated covalently bound to a negatively supercoiled DNA minicircle, and its behavior compared to
195 evaluate the looping of both linear DNA and supercoiled DNA minicircles over a broad range of DNA in
197 Transposase made double-strand breaks on a supercoiled DNA molecule containing a mini-ISY100 transp
198 binding proteins are capable of separating a supercoiled DNA molecule into distinct topological domai
199 , and lambda O protein, are able to divide a supercoiled DNA molecule into two independent topologica
200 iple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specifie
202 B is also able to stabilize writhe in single supercoiled DNA molecules and to bridge segments from tw
205 lo simulations, we investigate the shapes of supercoiled DNA molecules that are either knotted or cat
206 o, a recombinant fragment of ATAD3p bound to supercoiled DNA molecules that contained a synthetic D-l
207 gels, they caused a relaxation of positively supercoiled DNA molecules, and thus allowed a separation
211 e DNA cleavage agent, displaying significant supercoiled DNA-nicking activity at concentrations as lo
213 eometric and thermodynamic properties of the supercoiled DNAs on the surface differ significantly fro
216 rcoils), enhancer binding, and properties of supercoiled DNA play critical roles in regulating the in
217 e also observed that the addition of ParE to supercoiled DNA plus gyrase alone resulted in the format
219 wnian dynamics simulations of the packing of supercoiled DNA polymers in an elongated cell-like confi
220 Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particul
221 ducted on several DNA substrates: negatively supercoiled DNA, positively supercoiled DNA with a misma
222 decreased the overall rate of relaxation of supercoiled DNA probably because of its participation in
223 apping does not result in a more extensively supercoiled DNA product, but partially uncouples ATP tur
224 and could be disrupted by single-stranded or supercoiled DNA, properties distinct from the binding of
225 verse gyrase can completely relax positively supercoiled DNA, provided that the DNA substrate contain
226 posed by the left-handed superhelix of a (+) supercoiled DNA, rather than global topology, twist defo
227 etween DNA helices are important features of supercoiled DNA related to its biological functions.
228 lar reactions catalyzed by topoisomerase IV, supercoiled DNA relaxation, and DNA knotting but not int
229 d that the gamma complex assembles beta onto supercoiled DNA (replicative form I), but only at very l
230 affinity for sigma54-RNA polymerase, but on supercoiled DNA requires either such a bend or a high af
231 scriminate between positively and negatively supercoiled DNA requires the C-terminal domain (CTD) of
232 +/- 0.057 for linear, relaxed circular, and supercoiled DNA, respectively, in good agreement with th
234 te an overwhelming preference for negatively supercoiled DNA ((-)scDNA) as a cofactor for the hydroly
235 rimer-DNA complex crystal, p53 can recognize supercoiled DNA sequence-specifically by binding to quar
236 imm model with a scaling factor of -0.8, and supercoiled DNAs showed a reptational behavior with a sc
237 n apical position in a plectonemically wound supercoiled DNA, similar to the positioning of an A-trac
238 the full-sized topoisomerase: relaxation of supercoiled DNA, site-specific DNA transesterification,
240 synapsis that rely on ordered motions within supercoiled DNA, "slithering" or "tracking", but are com
242 tivity of PFCP, based on their protection of supercoiled DNA strand from scission by peroxyl and hydr
243 ned computational model that treats both the supercoiled DNA structural monomers and the smaller prot
245 capture one strand of underwound negatively supercoiled DNA substrate first and position the N-termi
252 lvPG promoter of Escherichia coli requires a supercoiled DNA template and occurs in the absence of sp
253 the DNA topoisomerase relaxes a negatively, supercoiled DNA template in vitro, in a reaction that re
266 ciform extrusion in the short palindromes of supercoiled DNA, thereby allowing the formation of cruci
267 topoisomerase I catalyzes the relaxation of supercoiled DNA through a concerted mechanism of DNA str
268 ons that topoisomerase II may be targeted to supercoiled DNA through the recognition of DNA cruciform
271 that Fis and E sigma38 bind cooperatively on supercoiled DNA to form a stable complex at P2 that invo
272 topoisomerases decatenate, unknot and relax supercoiled DNA to levels below equilibrium, resulting i
273 molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomera
274 y to induce cell cycle arrest and to convert supercoiled DNA to relaxed and linear forms in vitro.
276 A Mu transpososome assembled on negatively supercoiled DNA traps five supercoils by intertwining th
277 rapidly and controllably generate negatively supercoiled DNA using a standard dual-trap optical tweez
278 ODS), uniquely combines the ability to study supercoiled DNA using force spectroscopy, fluorescence i
279 merase I (Top1p) catalyzes the relaxation of supercoiled DNA via a concerted mechanism of DNA strand
280 forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick
281 eta and topoisomerase I to cleave positively supercoiled DNA was assessed in the absence or presence
284 ility of the resulting BLM analogue to relax supercoiled DNA was largely unaffected by introduction o
286 ecting successive simulated conformations of supercoiled DNA, we conclude that slithering of opposing
287 l experiments with negatively and positively supercoiled DNA, we have been able to deconvolute the ch
290 tively supercoiled (compared with negatively supercoiled) DNA, whereas topoisomerase IV generated sim
291 imposed torsional constraints on negatively supercoiled DNA, which influenced the ability of the enz
292 an p53 also displays preferential binding to supercoiled DNA, while a mutant peptide, which is unable
293 at normally represses activity on negatively supercoiled DNA, while complementation tests using mutan
294 cells, RNA polymerase (RNAP) must transcribe supercoiled DNA, whose torsional state is constantly cha
296 ates: negatively supercoiled DNA, positively supercoiled DNA with a mismatch and positively supercoil