ライフサイエンスコーパス: linear DNA

1 Integration of HIV-1 linear DNA into the host chromatin is an essential step

2 ic cell, before DNA replication, contains 46 linear DNA molecules, each of the order of centimeters i

3 oid topological entanglements between the 92 linear DNA molecules following replication?

4 A linear DNA (lambda DNA, 48.5 Kb), anchored at one end to

5 ws an RNA polymerase molecule moving along a linear DNA.

6 llobleomycins, supercoiled plasmid DNA and a linear DNA duplex were employed as substrates for Co(III

7 actors (TBP and TFB1), RNA polymerase, and a linear DNA fragment containing a strong promoter.

8 tablished that in Saccharomyces cerevisiae a linear DNA palindrome is efficiently formed from a singl

9 ct of DNA topology on gene expression from a linear DNA molecule in a bacterium.

10 sented to assemble a gene of interest into a linear DNA template with all the components necessary fo

11 which is processed by an endonuclease into a linear DNA with two hairpin loops at its ends.

12 RCA is a linear DNA amplification technique that can use specific

13 nd integrate the normal U3 LTR terminus of a linear DNA independently of an aberrant U5 LTR terminus.

14 binant IN catalyzed correct integration of a linear DNA into a supercoiled target plasmid.

15 This assay consists of a linear DNA probe labeled with a fluorophore in the middl

16 ds that can stably pair to both strands of a linear DNA target in a RecA-dependent reaction with ATP

17 intact after elongating to the very end of a linear DNA template and that such complexes catalyzed th

18 Escherichia coli RNA polymerase (RNAP) on a linear DNA template with two convergently aligned lambda

19 upply functions that protect and recombine a linear DNA targeting cassette with its substrate sequenc

20 e gyrase-DNA complex that was converted to a linear DNA form upon addition of sodium dodecyl sulphate

21 hrough a single point (small molecule), to a linear DNA tag containing a combination of alternating d

22 is recruited to the promoter, transcribes a linear DNA template, then terminates transcription and d

23 ed substrate into primarily nicked, but also linear, DNA at enzyme/DNA molar ratios of 5:1 or greater

24 T4 large terminase subunit gp17 by analyzing linear DNAs that are translocated in vitro.

25 clease activities and uses both circular and linear DNA as substrates.

26 litated transfection using both circular and linear DNA in P. falciparum thereby serving as an altern

27 quinone-treated enzyme to bind circular and linear DNA molecules and (2) the generation of salt-stab

28 ell extracts was compared using circular and linear DNA substrates.

29 lasts repaired AP sites on both circular and linear DNA.

30 tant enzyme binds both covalently closed and linear DNA with greater avidity than the wild type enzym

31 The kinetics of nicked and linear DNA formation are comparable, both being associat

32 mus 29 plasmid DNA to afford both nicked and linear DNA.

33 relative amounts of supercoiled, nicked, and linear DNA present show that there is one double-strand

34 alculates the energy of both nucleosomal and linear DNA of the given sequence.

35 rated to cleave both supercoiled plasmid and linear DNA substrates.

36 the looping interactions on supercoiled and linear DNA, a series of plasmids was constructed with le

37 On both supercoiled and linear DNA, the stabilities of the complexes spanning tw

38 omoters glnAp2 and glnHp2 on supercoiled and linear DNA.

39 nts D for relaxed circular, supercoiled, and linear DNA molecules of length L ranging from approximat

40 We find that TopBP1 binds to circular and linear DNAs with comparable affinities and that these DN

41 Any linear DNA can be packaged in vitro into purified procap

42 The transpovirons are linear DNA elements of ~7 kb that encompass six to eight

43 d-type DrHU, deltaDrHU distinguishes between linear DNA and DNA with nicks or gaps.

44 n efficient homologous recombination between linear DNA fragments and circular plasmids in Escherichi

45 required for recombination in vitro between linear DNA molecules with overlapping homologous ends.

46 ation intermediates is unchanged by blocking linear DNA processing with a recBCD mutation or by block

47 For both linear DNA and circular DNA, these contributions are muc

48 nd computations evaluate the looping of both linear DNA and supercoiled DNA minicircles over a broad

49 The affinity of Hlp for 76 bp linear DNA is higher, K d = 0.037 +/- 0.001 nM, compared

50 Here, we describe an approach for building linear DNA templates that contain a single, site-specifi

51 In cells infected by linear DNA containing viruses the transcriptional templa

52 nalysis of a merRA double mutant produced by linear DNA recombination demonstrated merHp promoter act

53 tence of Acinetobacter for transformation by linear DNA has allowed the development of a powerful new

54 Telomeres are DNA-protein complexes that cap linear DNA strands, protecting DNA from damage.

55 l repair rather than on the RecBCD-catalyzed linear DNA degradation.

56 at all four DNA quarter-sites does not cause linear DNA to bend.

57 cular DNAs or at the termini of circularized linear DNAs.

58 A method was developed to clone linear DNAs by overexpressing T4 phage DNA ligase in viv

59 T4 DNA ligase strains are useful for cloning linear DNAs in vivo by transformation or transduction of

60 e potential to serve as junctions to connect linear DNA segments into complex 3D lattices.

61 in plasmid sized and torsionally-constrained linear DNA molecules.

62 dy we showed that virus particles containing linear DNA of the duck hepatitis B virus (DHBV) could in

63 Catenanes were formed by cyclizing linear DNA with long cohesive ends in the presence of su

64 AN was found to degrade linear DNA at alkaline pH, preferred Mg(2+) over Mn(2+),

65 e-stranded (ds)DNA exonuclease that destroys linear DNA produced by restriction of foreign DNA.

66 is applicable to membrane protein diffusion, linear DNA chain dynamics, and mechanics of intracellula

67 terogeneity of solutions of chromosomal DNA, linear DNA, and circular double-stranded DNA over a wide

68 d either by transcription of promoter-driven linear DNA templates or by stepwise chemical synthesis o

69 Duplex linear DNA is made when initiation of synthesis occurs a

70 in relaxed circular DNA, some contain duplex linear DNA.

71 A small fraction of viruses make duplex linear DNA after initiating plus-strand DNA synthesis fr

72 mall fraction of viruses instead make duplex linear DNA after initiating plus-strand DNA synthesis fr

73 the pathway leading to production of duplex linear DNA is favored, whereas primer translocation is f

74 ulting in two different end products; duplex linear DNA or relaxed circular DNA.

75 r DNA, while the other pathway yields duplex linear DNA.

76 r DNA, while the other pathway yields duplex linear DNA.

77 that protect and recombine an electroporated linear DNA substrate in the bacterial cell.

78 in Escherichia coli by using electroporated linear DNA.

79 DNA minicircles in the presence of equimolar linear DNA, and has little effect on the affinity for th

80 ular 100-bp DNA compared with the equivalent linear DNA, indicating that alteration of the conformati

81 -way DNA junctions in the presence of excess linear DNA competitor, and binds more tightly than GI to

82 h matching and nonmatching ends of exogenous linear DNA substrates with high efficiency and fidelity.

83 SceI endonuclease generates extrachromosomal linear DNA molecules in vivo.

84 However, we find linear DNAs flanked by loxP sites recombine efficiently

85 allows standard plasmid isolation following linear DNA transformation of the strains containing high

86 For linear DNA modeled as a wormlike chain, the distribution

87 They exhibit high affinity for linear DNA and even higher affinity for microcircular DN

88 model reveals that the most stable loops for linear DNA occur when LacI adopts the extended conformat

89 ration for circular DNA and more rapidly for linear DNA, but more slowly than predicted by theory.

90 Our results show that Tap is required for linear DNA replication in Streptomyces and suggest that

91 es with concentration more significantly for linear DNA than circular DNA.

92 ondrial DEB activity was highly specific for linear DNA.

93 uclease implicated in degradation of foreign linear DNA and in RecA-dependent recombinational repair

94 further cleaved on the second strand to form linear DNA.

95 rane proteins can be expressed directly from linear DNA templates within 90 min, eliminating the need

96 and EcoR124I leads to HsdR dissociation from linear DNA but not from circular DNA.

97 res that differentiate superhelical DNA from linear DNA.

98 A; separation of circular DNA molecules from linear DNA molecules; and separation of circular plus an

99 tRNA(Cys) or the variant COX2 promoter from linear DNA templates.

100 e-sensitive for selective transcription from linear DNA templates containing the 14S rRNA, COX2, and

101 ecific restriction endonucleases to generate linear DNA inserts with defined termini and requires DNA

102 ave plasmid DNA targets in vitro, generating linear DNA products with an activity that is dependent o

103 Transfer of total genomic linear DNA containing amplified DHFR genes into DHFR(-)

104 the binding of these proteins to immobilized linear DNA fragments in Xenopus egg extracts.

105 a 222-bp DNA fragment, which was isolated in linear (DNA(L222)) and circular (DNA(C222)) forms.

106 s, which had been experimentally detected in linear DNA molecules.

107 for the generation of closed hairpin ends in linear DNA.

108 enerated torsion melts FUSE in vitro even in linear DNA, and FBP/FBP Interacting Repressor (FIR) regu

109 specific and essential role for tpg genes in linear DNA replication.

110 formations of immobile Holliday junctions in linear DNA molecules have been analyzed with the use of

111 ical axis, but the juxtaposition of sites in linear DNA or far apart in supercoiled DNA may occur wit

112 uciforms are not thermodynamically stable in linear DNA due to branch point migration, which makes th

113 on entry, though by 72 hours after infection linear DNAs accumulated and early as well as late lytic

114 acquisition in vivo and for integration into linear DNA in vitro.

115 te amino acid side chains intercalating into linear DNA to form a bend.

116 DNA into the scrunched state, and introduces linear DNA tension as a potential regulatory quantity fo

117 equires ATP hydrolysis when the substrate is linear DNA, but is independent of hydrolysis when negati

118 gene for both bulk damaged DNA and isolated linear DNA.

119 In contrast, the isolated linear DNA containing site-specific DSBs had an unusuall

120 that the Rad50/Mre11/Xrs2 complex juxtaposes linear DNA molecules via their ends to form oligomers an

121 The 192-kb linear DNA genome of vaccinia virus has covalently close

122 ssembled in vitro +/- histone H5 on a 6.3 kb linear DNA fragment in 90 mM NaCl using the polyglutamic

123 ers were the host cell chromosome and a 4-kb linear DNA fragment containing the cat gene, with flanki

124 of gene transfer (transformation with 6.5-kb linear DNA fragments) as an experimental model for conju

125 (5)-CPG-C(2), cleaved a 5'-(32)P end labeled linear DNA duplex with a sequence selectivity identical

126 d as a generic methodology for end-labelling linear DNA for studying DNA-protein interactions by AFM.

127 ble for direct in vivo manipulation of large linear DNA including the N15 and PY54 prophages and line

128 synthesis of either strong-stop, full-length linear DNA or 2-LTR circles was observed with R10A/K11A

129 minant DNA species, such as the full-length, linear DNA.

130 es, which have been examined at four levels: linear DNA structure; the distribution of constitutive c

131 binase protomers does not occur on un-nicked linear DNA.

132 non-specific nicking endonuclease on normal linear DNA.

133 variety of branched DNA substrates, but not linear DNA, and had the highest affinity for a Holliday

134 the spirochete genus Borrelia carry numerous linear DNA replicons with covalently closed hairpin telo

135 ically manipulated by the direct addition of linear DNA constructs to log-phase cultures.

136 This assay directly measures the amount of linear DNA present in preparations of supercoiled (CCC)

137 A procedure for precise assembly of linear DNA constructs as long as 20 kb is proposed.

138 uences that enable the efficient assembly of linear DNA fragments, using reactions developed by Gibso

139 rameter which best explains the behaviour of linear DNA on mica.

140 rcular DNA, was formed by circularization of linear DNA by nonhomologous recombination between the tw

141 We quantified the compaction of linear DNA by measuring the end-to-end distance of the D

142 lta::red strains with high concentrations of linear DNA fragments (derived from plasmid digests) gave

143 knot formation during random cyclization of linear DNA molecules.

144 measures ADP produced following digestion of linear DNA by an ATP-dependent deoxyribonuclease.

145 Digestion of linear DNA by type I restriction endonucleases is genera

146 death is mostly prevented by elimination of linear DNA degradation activity of ExoV, suggesting that

147 along dsDNA and dissociates from the end of linear DNA without strand separation, which explains the

148 uperhelical DNA to the complete exclusion of linear DNA, indicating that the linker histone's functio

149 To study the fate of linear DNA in Escherichia coli cells, we linearized plas

150 ave been examined by DNase I footprinting of linear DNA with one blunt end, one primer-template junct

151 cluding volume changes, for the formation of linear DNA duplexes and three-arm branched DNA junctions

152 chromosome and the consequent generation of linear DNA branches that provoke recombination and delay

153 replication through multiple generations of linear DNA intermediates, a process we called illegitima

154 Co-injection of linear DNA with the NLS-RecA-Gal4 DNA filaments promotes

155 Due in part to the instability of linear DNA in bacteria, both the initial capture and sub

156 es, but which synthesized elevated levels of linear DNA, could be sustained for several days as the p

157 on and that synthesized normal low levels of linear DNA.

158 he probability of intermolecular ligation of linear DNA molecules in the presence of DNA ligase.

159 cN stimulates the intermolecular ligation of linear DNA molecules in the presence of DNA ligase.

160 erase are facilitated by the large number of linear DNA molecules found in ciliated protozoa, such as

161 chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes,

162 e to support recombination between a pair of linear DNA substrates (linear/linear recombineering) in

163 solated plasmid did not show the presence of linear DNA and demonstrated that none of the constructs

164 dprA is required for efficient processing of linear DNA during cellular transformation in Haemophilus

165 hat can contribute to elevated production of linear DNA in individual cells.

166 ctrophotometric method for quantification of linear DNA is described.

167 major pathway of homologous recombination of linear DNA in Escherichia coli.

168 ly of gene libraries and the regeneration of linear DNA templates between successive screening and se

169 se and RecJ(f), for the selective removal of linear DNA from such mixtures.

170 o examine the binding of SfiI to a series of linear DNA molecules containing two SfiI sites separated

171 ant changes to the B-form Raman signature of linear DNA.

172 rlo simulations to model the supercoiling of linear DNA molecules under tension.

173 ins that attach covalently to the termini of linear DNA replicons.

174 artifactual decrease in molecular weight of linear DNA making accurate determination of the number o

175 ones; mucus did not reduce the diffusion of linear DNAs but retarded the diffusion of supercoiled DN

176 Diffusion of linear DNAs in mucus were better described by the Zimm m

177 in of telomerase as well as the evolution of linear DNAs.

178 difficulty of demonstrating intertwining of linear DNAs.

179 On linear DNA carrying two recognition sites, the majority

180 DNA regions that are 80 base pairs apart on linear DNA are brought into close proximity, resulting i

181 to be defective in a transcription assay on linear DNA.

182 percoiled DNA and dinucleosomes assembled on linear DNA, but Zta-stimulated acetylation was significa

183 oximately one StpA molecule per 60-100 bp on linear DNA for strong inhibition of the nucleases.

184 ns (pKO-FD-NEO) was introduced into cells on linear DNA and selected for NEO gene expression.

185 In contrast, on linear DNA or on supercoiled DNA with sites 1605 bp apar

186 sites on circular DNA but not efficiently on linear DNA.

187 ent repair mechanism is poorly functional on linear DNA in vitro.

188 DNA translocation on circular DNA but not on linear DNA.

189 NA replication is initiated predominantly on linear DNA molecules with one of five possible ends serv

190 rimers synthesized by herpesvirus primase on linear DNA templates, had no effect on the replication o

191 icating that impairment of AP site repair on linear DNA by polbeta-knockout cell extracts is not due

192 had also found that in WT cells chi sites on linear DNA inhibit RecBCD degradation by turning off its

193 The triplex was pre-formed specifically on linear DNA, 4370 bp from an EcoR124I site, and then incu

194 show that the initiation of transcription on linear DNA requires a single intrinsic or induced bend i

195 0-450 fJ fm are obtained from experiments on linear DNAs under tension.

196 When either circular or linear DNA was incubated in an in vitro transcription sy

197 Assembly of relaxed or linear DNA templates into subsaturated chromatin results

198 iption initiation was observed on relaxed or linear DNA templates.

199 ut 30-fold higher than for either relaxed or linear DNA.

200 circular single-stranded, double-stranded or linear DNA.

201 substrates but not positively supercoiled or linear DNA.

202 -labeled packaging anchored 3.7-kb Y-DNAs or linear DNAs, we demonstrate FRET between the dye-labeled

203 aining Cre-circularized DNA is enhanced over linear DNA, as shown in recipient eukaryotic cells.

204 clease activity, but the mutants can package linear DNA.

205 e subunit (gp16) is inhibitory for packaging linear DNAs, but enhances the transcription-replication

206 r intervals of approximately 195 base pairs, linear DNA failed to reconstitute into chromatin contain

207 DNA sequencing demonstrated that pBSSB1 linear DNA was still detectable but that these derivativ

208 erge the fields have been limited to placing linear DNA segments within a polydisperse block copolyme

209 ng primers to amplify the plasmid, producing linear DNA molecules with homologous ends for site-direc

210 packaging resistance and supports a proposed linear "DNA crunching" or torsional compression motor me

211 functions, called Red, efficiently recombine linear DNA with homologies as short as 20-70 bases.

212 This combination of exonucleases can remove linear DNA from a mixture of linear and supercoiled DNA,

213 replicons acquired the ability to replicate linear DNA molecules.

214 deletion strain is an inability to replicate linear DNA.

215 tumor phenotype to predominantly replicating linear DNA and, subsequently, only integrated forms in B

216 The two ends of RSV linear DNA are independently inserted into host DNA by i

217 y, integrase-mediated autointegration of RSV linear DNA in vivo.

218 embly by Xenopus nuclear extracts on a short linear DNA fragment containing a DNA lesion.

219 train whose chromosome recombines with short linear DNA fragments at a greatly elevated rate.

220 n aqueous phases that interacted with short, linear DNA and supercoiled plasmid DNA to form a sandwic

221 ior compared to the enzyme bound to a simple linear DNA duplex.

222 ontacts that would not be possible in simple linear DNA sequences.

223 However, one-site linear DNA is a poor substrate, supporting a mechanism w

224 d on the production of viral double-stranded linear DNA and the expression of I-SceI, and integrated

225 exonuclease, which degrades double-stranded linear DNA and works with RecA in double-strand-break re

226 Both single-stranded and double-stranded linear DNA are substrates, as demonstrated by comparable

227 Herpesviruses have large double-stranded linear DNA genomes that are formed by site-specific clea

228 Double-stranded linear DNA is synthesized as a minor viral DNA species b

229 introduce a novel partially double-stranded linear DNA probe design.

230 le-stranded DNA circle and a double-stranded linear DNA.

231 igin-specific replication of double-stranded linear DNA.

232 reactions using double- and single-stranded linear DNA substrates, so-called targeting constructs, i

233 Bacteriophage with double-stranded, linear DNA genomes package DNA into pre-assembled icosah

234 The MAV1 genome is a double-stranded, linear DNA molecule of about 16 kb.

235 obes with dangling ends and single-stranded, linear DNA probes were immobilized and compared based on

236 the major chromatin subunit that structures linear DNA molecules and regulates access of other prote

237 ds supercoiled DNA with higher affinity than linear DNA and has a preference for DNA with lesions suc

238 Supercoiled plasmids are more reactive than linear DNA; and sequences containing consecutive cytosin

239 ctures which are more rigid in solution than linear DNA.

240 n does not bind forked DNA more tightly than linear DNA.

241 erns, and loop stabilities, we conclude that linear DNA segments of short-to-medium chain length (50-

242 homologous end joining (NHEJ) and found that linear DNA molecules with 5' extensions showed a high fr

243 We further show that linear DNA fragments flanked by loxP repeats can be effi

244 onstrate, using Caenorhabditis elegans, that linear DNAs with short homologies ( approximately 35 bas

245 Here, we report that linear DNAs (single and double stranded) engage in a hig

246 The linear DNA genomes of recombinant adeno-associated virus

247 The linear DNA molecules with homologous ends are joined to

248 The linear DNA was a 4-kb fragment containing the cat gene,

249 The linear DNA was a 4-kb fragment containing the cat gene,

250 eered by chemical synthesis in vitro and the linear DNA is efficiently recombined into place in vivo.

251 ecBCD, a helicase-nuclease that degrades the linear DNA product resulting from Type I cleavage.

252 A gene's location in the linear DNA sequence and its position in the three-dimens

253 g) and an end-closed (i.e., both ends of the linear DNA are covalently closed to prohibit peeling) an

254 The ends of the linear DNA form of the HIV-1 genome are defined by the s

255 ures of covalently linked extremities of the linear DNA genome are found in the African swine fever v

256 not depend upon the mode of delivery of the linear DNA into the cells.

257 ly knotted because of the cyclization of the linear DNA molecule confined in the phage capsid.

258 tulated two steps (i) circularization of the linear DNA molecule that had been injected into the cell

259 rylamide matrix retards the diffusion of the linear DNA molecules so that the amplification products

260 ased by about 1.25-fold, whereas that of the linear DNA remained unchanged.

261 The microheterogeneity of the linear DNA solutions increases with concentration more s

262 Pretreatment of the linear DNA with AP endonuclease did not improve repair,

263 single-strand cleavages, indicating that the linear DNA formed cannot be the result of two random sin

264 The results suggest that the linear DNA produced during DHBV infection initiates cycl

265 Moreover, HMGB1 augmented binding to the linear DNA but not to the microcircle, suggesting that H

266 p53 C terminus inhibited p53 binding to the linear DNA, it was required for the increased affinity o

267 Investigation of this linear DNA stability indicates that a fraction of recA c

268 ired for HMG domain stability in addition to linear DNA binding and bending, which is an important fu

269 We find that DNA-PK can itself bind to linear DNA fragments ranging in size from 18 to 841 bp d

270 d oligonucleotides, the ratio of circular to linear DNA multimers reaches values of 8-9 for circle co

271 of contacts with the minicircle compared to linear DNA.

272 Second, binding of linker histone to linear DNA results in aggregation of histone-DNA complex

273 In contrast, binding of linker histone to linear DNA under the conditions employed here shows no c

274 The binding of this polypeptide to linear DNA fragments and to open circular plasmids has b

275 hich is elevated on circular DNA relative to linear DNA, is important to RA.

276 ates during the conversion of supercoiled to linear DNA, indicating that the enzyme cleaves the two D

277 y of trefoils produced by cyclization of two linear DNAs demonstrates that the two chiral trefoils ar

278 cks or gaps enables the removal of undesired linear DNA when nicked circular DNA has been enzymatical

279 r form often are contaminated with undesired linear DNA fragments arising from shearing/degradation o

280 Using linear DNA for transformation, a double-crossover event

281 tein extracts of the different mutants using linear DNA substrates with different ends reflecting a v

282 eralfold for properly phased circular versus linear DNA templates were predicted.

283 favor suppression of chromosomal lesions via linear DNA degradation at reversed replication forks as

284 nonhomologous end joining between the viral linear DNA ends and the I-SceI-induced break, because sm

285 Analysis of the viral linear DNA genome suggests that its evolution involved d

286 h an alternative experimental model in which linear DNA fragments were generated from phage lambda by

287 nsfection of retrovirus packaging cells with linear DNA from a retroviral vector missing the 3' long

288 us recombination of a native chromosome with linear DNA fragments containing a telomere and a selecta

289 .6 nm in the arrested Y-DNA as compared with linear DNA; the reduction is reversed by resolvase treat

290 served on supercoiled DNA in comparison with linear DNA.

291 antly more salt stable than the complex with linear DNA.

292 or the formation of monomeric complexes with linear DNA.

293 y, in contrast to a much greater effect with linear DNA, or even four-way junctions (another distorte

294 after different incubation times of HU with linear DNA.

295 action of integration host factor (IHF) with linear DNA fragments containing the narG promoter region

296 acile bypass of heterologous insertions with linear DNA substrates is demonstrated, providing evidenc

297 of a chromosomal HMG domain interacting with linear DNA and reveals the molecular basis of non-sequen

298 their non-sequence-specific interaction with linear DNA duplexes were studied using scanning and titr

299 the YAC occurs in yeast by transfection with linear DNA containing YAC-specific, unique, recombinogen

300 kinetic stabilities at internal sites within linear DNA targets after removal of RecA protein from hy