ライフサイエンスコーパス: minicircle

1 A and oriB) located 180 degrees apart on the minicircle.

2 This is the first report of a three-gene minicircle.

3 d inevitably to only one functional gRNA per minicircle.

4 bound DNA, and the linking number Lk of the minicircle.

5 d fluctuations when bound to the supercoiled minicircle.

6 180 degrees apart along the periphery of the minicircle.

7 oflagellates, where genes are located on DNA minicircles.

8 of the replication process of DNA maxi- and minicircles.

9 cient method to obtain covalently closed DNA minicircles.

10 4-65-bp minicircles, but not in the 85-86-bp minicircles.

11 network containing thousands of interlocked minicircles.

12 nucleus, with a few remaining genes found on minicircles.

13 exhibit preferred binding to constrained DNA minicircles.

14 n, although they can extensively unwind free minicircles.

15 veral thousand topologically interlocked DNA minicircles.

16 aining the DNA within the closed loop of the minicircles.

17 lanking the kDNA disk along with nascent DNA minicircles.

18 the repair of gaps in the newly synthesized minicircles.

19 network containing thousands of interlocked minicircles.

20 heir HMG-box domains, to 88 bp and 75 bp DNA minicircles.

21 k containing 5,000 topologically interlocked minicircles.

22 le gRNAs are encoded by both maxicircles and minicircles.

23 are encoded in circular DNA molecules called minicircles.

24 gh free energy cost of substantial writhe in minicircles.

25 s and the repair of gaps in newly replicated minicircles.

26 g several thousand topologically interlocked minicircles.

27 into the endogenous gaps of newly replicated minicircles.

28 DBD to the prebent ERE in covalently closed minicircles.

29 ls transfected by electroporation with HPV18 minicircles.

30 es retained similar numbers of kDNA maxi- or minicircles.

31 ced kinks in DNA on the overall shape of DNA minicircles.

32 tes, had no effect on the replication of the minicircles.

33 In contrast, Trypanosoma brucei progeny minicircles accumulate on opposite ends of the kDNA disk

34 Although the same dose of the minicircle amplicon vector in normal human fibroblasts r

35 hose template was both a small synthetic DNA minicircle and a larger DNA substrate.

36 The evolutionary rate of minicircle and plastid-transferred genes in the dinoflag

37 of trypanosomatids, consists of thousands of minicircles and 20 to 30 maxicircles catenated into a si

38 l DNA consisting of thousands of interlocked minicircles and 20-30 maxicircles.

39 rlocked DNA rings including several thousand minicircles and a few dozen maxicircles.

40 rlocked DNA rings including several thousand minicircles and a few dozen maxicircles.

41 ome mitochondrial DNA, contains thousands of minicircles and dozens of maxicircles interlocked in a g

42 inetoplast DNA (kDNA), contains thousands of minicircles and dozens of maxicircles topologically inte

43 mitochondrial DNA consisting of thousands of minicircles and dozens of maxicircles topologically inte

44 locked DNA rings, including several thousand minicircles and dozens of maxicircles.

45 alysis in U2OS cells carrying episomal HPV18 minicircles and HeLa cells.

46 and at particular sites along simulated DNA minicircles and loops.

47 re, silencing of TbPOLIC caused loss of both minicircles and maxicircles and accumulation of minicirc

48 NA of trypanosomes is a catenated network of minicircles and maxicircles called kinetoplast DNA (kDNA

49 iculata has an unusual structure composed of minicircles and maxicircles topologically interlocked in

50 anosomatid Crithidia fasciculata consists of minicircles and maxicircles topologically interlocked in

51 TbHslVU dramatically increased abundance of minicircles and maxicircles, presumably because a positi

52 es from the network, replication of the free minicircles and reattachment of progeny at two sites on

53 es from the network, replication of the free minicircles and reattachment of the progeny.

54 ficient bending stress, which appears in DNA minicircles and small DNA loops, the double helix experi

55 ure-eight molecules are the precursor to IS2 minicircles and that the formation of these two products

56 lently bound to a negatively supercoiled DNA minicircle, and its behavior compared to the enzyme boun

57 es from the network, replication of the free minicircles, and reattachment of the progeny back onto t

58 Fluorescence in situ hybridization with minicircle- and maxicircle-specific probes showed that m

59 f TBP-induced topoisomers suggests that this minicircle approach is able to distinguish TBP-induced u

60 Three minicircles are full-length, one of 2.6 kb encoding the

61 During kinetoplast DNA synthesis, minicircles are released from the network for replicatio

62 tion revealed that before their replication, minicircles are released vectorially from the network fa

63 Fraction S minicircles are so underwound that on isolation they bec

64 We find that minicircles are transcribed polycistronically and that t

65 ain that stably expresses a set of inducible minicircle-assembly enzymes, PhiC31 integrase and I-SceI

66 DNA length-dependent ATPase assays, and DNA-minicircle ATPase assays to establish that RSC, as well

67 We propose that the minicircle binding assay may be intrinsically insensitiv

68 crocircles contain the core region common to minicircles, but are missing a coding region, providing

69 upted by bending deformation in the 64-65-bp minicircles, but not in the 85-86-bp minicircles.

70 They appear to be formed from full-length minicircles by homologous recombination and internal del

71 rough efficient formation of 170-bp-long DNA minicircles by means of dimerization of two bent DNA fra

72 There are some 250 different types of minicircle, called classes, with each encoding several g

73 croRNA-210 precursor group compared with the minicircle carrying microRNA-scramble control.

74 rcle vector carrying microRNA-210 precursor, minicircle carrying microRNA-scramble, or sham surgery.

75 Minicircles carrying a SB transposon cassette containing

76 h minicircle is highly conserved within each minicircle class but highly divergent between classes.

77 uenced and found to be derived from only one minicircle class.

78 his process leads to an increasing number of minicircle classes and inevitably to only one functional

79 both redundancy, where gRNAs from different minicircle classes edit exactly the same part of an mRNA

80 at minicircles from only a limited number of minicircle classes had acted as template in the reaction

81 eover, we show that the genome contains more minicircle classes than is actually necessary for cell s

82 he population via drift and replaced by more minicircle classes that contain fewer functional gRNA ge

83 Minicircle classes that contain several functional gRNA

84 e variation was determined by the particular minicircle classes that had been represented in the temp

85 ng the product of PCR on a limited subset of minicircle classes, and consequently, it was thought tha

86 Since the primers amplify all minicircle classes, this indicated that as little as 1/1

87 unequally distributed among approximately 10 minicircle classes.

88 0-bp conserved region which is common to all minicircle classes; the remaining approximately 600 bp o

89 ays an increased number of contacts with the minicircle compared to linear DNA.

90 a significantly longer residence time on DNA minicircles compared with linear duplex DNA.

91 We demonstrate the use of a DNA minicircle competition binding assay, together with DNA

92 to validate independently our results with a minicircle competition binding assay.

93 The more abundant product is a minicircle composed of the complete IS2 with just a sing

94 ptions used in our Monte Carlo simulation of minicircle conformations specifies these conformations b

95 8 degrees) were observed in axially strained minicircles consisting of tandemly repeated d(A)5 and d(

96 nscriptional cleavage from the mitochondrial minicircle constructs in a mitochondrial environment and

97 Minicircles containing a new L strand have a single nick

98 dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we co

99 Recent studies by our lab, using minicircles containing only one nucleosome, indicated th

100 We have studied DNA minicircles containing the ATF/CREB binding site for GCN

101 tive PCR strategy, we have found that 2-4 kb minicircles containing the origin of heavy-strand replic

102 ndant minicircle replication intermediate as minicircle copy number declines.

103 Maxicircle and minicircle copy numbers differed up to 6-fold between Le

104 least the first Okazaki fragment in network minicircles, demonstrating that this enzyme in fact func

105 Moreover, the uptake of protein on small minicircles depends on chain length, taking advantage of

106 We observed directed nucleosome movement on minicircles derived from the human SWI/SNF-regulated c-m

107 n of multiply interlocked, covalently closed minicircle dimers (fraction U).

108 that is composed mainly of covalently closed minicircle dimers.

109 Minicircle DNA (mcDNA) is recently becoming an exciting

110 state induced by exposure to non-integrative minicircle DNA (MCDNA)-based reprogramming factors, foll

111 iferase activity persisting for 2 weeks from minicircle DNA compared to plasmid formulations.

112 vation by transfection of a simple, nonviral minicircle DNA construct into human adipose stromal cell

113 , which has important implications for using minicircle DNA for gene therapy.

114 Minicircle DNA give enhanced and more persistent transge

115 dult mice via hydrodynamic delivery of IL-23 minicircle DNA in vivo and in mice genetically deficient

116 The screening primers recognize kinetoplast minicircle DNA of all Leishmania species.

117 Using a minicircle DNA primer-template, the wild-type catalytic

118 We also show that an 80-mer minicircle DNA using the same TG-motifs faithfully repro

119 Minicircle DNA vectors allow sustained transgene express

120 Minicircle DNA vectors are free of bacterial DNA and thu

121 When the ERE in minicircle DNA was prebent toward the major groove, whic

122 In this study we compared minicircle DNA with plasmid DNA in transfections of airw

123 f cells transfected was 2-4-fold higher with minicircle DNA.

124 ion origins located 180 degrees apart on the minicircle DNA.

125 ind preferentially to a specific fragment of minicircle DNA.

126 We report the use of 'minicircle' DNA, a vector type that is free of bacterial

127 nucleic acid binding domain and plasmid-DNA, minicircle-DNA or small interfering RNA (siRNA).

128 enome, with genes located on multiple small 'minicircle' elements, and a number of idiosyncratic feat

129 We propose that the minicircle-encoded antisense transcripts, which are stab

130 Here we identify 48 of the non-minicircle-encoded photosynthetic genes in the nuclear g

131 nome in these taxa is reduced to single-gene minicircles encoding an incomplete (until now 15) set of

132 MSCs were transfected with recombinant minicircles encoding etanercept (trade name, Enbrel), wh

133 hesis in a computer simulation of a model of minicircle evolution.

134 We confirmed minicircle expression in MSCs in vitro based on GFP.

135 st in vitro and in vivo applications whereas minicircle expression in vitro is significantly increase

136 We further describe the generation of minicircle expression vectors for mammalian mitochondria

137 The minicircles fell into distinct categories based on lengt

138 tructs to create supercoiled gene expression minicircles for gene therapy.

139 Seven new minicircles, forming part of the fragmented plastid geno

140 ns from the highest dilutions suggested that minicircles from only a limited number of minicircle cla

141 inetoplast DNA synthesis involves release of minicircles from the network, replication of the free mi

142 DNA synthesis involves release of individual minicircles from the network, replication of the free mi

143 inetoplast DNA synthesis involves release of minicircles from the network, replication of the free mi

144 Minicircle-functionalized magnetic nanoparticle (MNP)-me

145 ed for rate of sequence evolution, including minicircle genes (presumably plastid-encoded), genes pro

146 le but, in most cases, not as extreme as the minicircle genes.

147 gth, with the same codon bias found in other minicircle genes.

148 more complex topology of the supercoiled DNA minicircle gives rise to a secondary DNA binding site in

149 Sequencing of gRNAs and minicircles has revealed a surprising amount of both red

150 We engineered a minicircle HBV cccDNA with a Gaussia Luciferase reporter

151 ation that minimizes the elastic energy of a minicircle in a mononucleosome with specified values of

152 ent sites results in distribution of progeny minicircles in a ring around the network periphery.

153 This bacterial strain produces purified minicircles in a time frame and quantity similar to thos

154 d DNA preparation, making it feasible to use minicircles in place of plasmids in mammalian transgene

155 elective DNA-binding of the HMG boxes to DNA minicircles in the presence of equimolar linear DNA, and

156 ar, putative transposition intermediate (the minicircle) in the first step.

157 d monocistronic transcripts from A. carterae minicircles, including several regions containing ORFs p

158 The frequency of kinks in identical minicircles increased 4-fold in the presence of 1 mM Zn2

159 er stages of replication, the number of free minicircles increases, accumulating transiently in the K

160 plication involving vectorial export of free minicircles into the KFZ.

161 These data confirm that the minicircle is an essential intermediate in the two-step

162 ; the remaining approximately 600 bp of each minicircle is highly conserved within each minicircle cl

163 random distribution and segregation model of minicircles is assumed.

164 we show that IS2 possesses a highly reactive minicircle junction at which a strong promoter is assemb

165 The second is the assembly at the minicircle junction of a strong hybrid promoter which ge

166 optimize expression of transposase from the minicircle junction promoter, Pjunc.

167 ges also impose a characteristic size on the minicircle junction spacer.

168 At the resulting minicircle junction, the two abutted ends are separated

169 er contains a single-stranded version of the minicircle junction--the precise 3' end of IRR has been

170 is retained by the IRL in the context of the minicircle junction.

171 thod specifically amplified whole linearized minicircle kinetoplast DNA (kDNA) of the Leishmania subg

172 Initiation of minicircle leading-strand synthesis involves the synthes

173 dings we highlight the clinical potential of minicircle/magnetofection technology for therapeutic del

174 Two aspects of the minicircle may involve its proposed role in the second s

175 overcome these hurdles, we successfully used minicircle (MC) naked-DNA vectors devoid of any viral or

176 METHODS AND We first created minicircles (MC) carrying double-fusion reporter gene co

177 plicon vector devoid of bacterial sequences (minicircle [MC] amplicon).

178 RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic

179 rcle DNA is stretched out between segregated minicircle networks, indicating that maxicircle segregat

180 ce-specific information about individual DNA minicircles observed by cryo-electron tomography (cryo-E

181 plify the variable region of the kinetoplast minicircles of all Leishmania species which infect mamma

182 One empty minicircle, of 1.7 kb, and three 'microcircles', between

183 DNA minicircles offer a robust model system to study stress-

184 Using DNA minicircles on the order of 100 bp in size, we have been

185 population of replicated, network-associated minicircles only becomes repaired to the point of having

186 In contrast, for DNA minicircles, optimal stability may arise from either the

187 oping of both linear DNA and supercoiled DNA minicircles over a broad range of DNA interoperator leng

188 diac progenitor cells (CPCs) with a nonviral minicircle plasmid carrying HIF1 (MC-HIF1) into the isch

189 Compared to non-HBV minicircle plasmids, mcHBV-GLuc cccDNA showed persistent

190 To improve minicircle production, we genetically modified Escherich

191 DNA cyclization of loops gave minicircle products with altered topologies.

192 ation as theta-structures, and then the free minicircle progeny reattach to the network.

193 Leading and lagging strand minicircle progeny similarly declined during POLIB silen

194 Although traditionally thought to reattach minicircle progeny to the network, here we show that it

195 with topoisomerase II, in the segregation of minicircle progeny.

196 transient DNA transfection using plasmids or minicircles, protein transduction, or RNA transfection.

197 of the non-coding region of the plastid psbA minicircle (psbA(ncr)) were used to independently examin

198 We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to t

199 nce-specific cryo-ET tomogram fitting of DNA minicircles, registering the sequence within the geometr

200 t also mends holes in the network created by minicircle release.

201 Here, we employ a minicircle remodeling approach to provide the first evid

202 tages of recovery, there were changes in the minicircle repertoire.

203 Minicircles replicate after release from the network, an

204 The minicircles replicate free of the kDNA network but nicks

205 Individual minicircles replicate unidirectionally from either of tw

206 idence that the core region is necessary for minicircle replication and maintenance.

207 y closed precursors become the most abundant minicircle replication intermediate as minicircle copy n

208 Minicircle replication intermediates decrease during RNA

209 icircles and maxicircles and accumulation of minicircle replication intermediates, consistent with a

210 the network and accumulation of gapped free minicircle replication intermediates.

211 KFZ with DNA provides support for models of minicircle replication involving vectorial export of fre

212 erforms an essential role at the core of the minicircle replication machinery.

213 ce-binding protein, which normally binds the minicircle replication origin and triggers replication.

214 dia fasciculata, has been proposed to remove minicircle replication primers.

215 ith RNAi-induced loss of p38 cannot initiate minicircle replication, although they can extensively un

216 may be involved in RNA primer removal during minicircle replication.

217 otational movement of the kinetoplast during minicircle replication.

218 rt that one of the six, TbPIF1, functions in minicircle replication.

219 stulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs

220 arge plasticity in the relative abundance of minicircle sequence classes has been observed during cel

221 We also analyse the available minicircle sequence data and conclude that T. brucei is

222 oxin, also caused oxidation of the universal minicircle sequence-binding protein and kDNA loss.

223 s of maxicircles suggests that the universal minicircle sequence-binding protein might also control m

224 rols the oxidization status of the universal minicircle sequence-binding protein via tryparedoxin, a

225 s by oxidation/inactivation of the universal minicircle sequence-binding protein, which normally bind

226 p38 binds to minicircle sequences within the replication origin.

227 Primer/templates were composed of a minicircle single-stranded DNA template annealed to prim

228 mononucleosome with specified values of the minicircle size N in base pairs, the extent w of wrappin

229 We demonstrate for the first time that DNA minicircles (small DNA vectors encoding essential gene e

230 toplast DNA and accumulation of a novel free minicircle species named fraction S.

231 chanical treatment of the disruptions in DNA minicircles, studied experimentally by Du et al.

232 We show here that the minicircle substrate supports coordinated leading and la

233 T4 has been assembled as a single unit on a minicircle substrate with a replication fork that permit

234 ion system was studied on a synthetic 70-mer minicircle substrate.

235 ome can be simultaneously assembled onto the minicircle substrate.

236 esults on the characterization of the 70-mer minicircle substrate.

237 mes and in U2OS cells transfected with HPV18 minicircles, suggesting that it is not cell type specifi

238 MNP functionality as gene delivery vectors, minicircle technology provides key benefits from safety/

239 absence of a primase recognition site on the minicircle template no lagging strand synthesis occurs.

240 Depending on the nature of the minicircle template, the replication complex synthesized

241 by herpes simplex virus type 1 and a 70-base minicircle template, we obtained robust DNA synthesis wi

242 ates a functional replisome assembled on the minicircle template.

243 ed leading and lagging strand synthesis on a minicircle template.

244 nclude that the bending mechanics within the minicircle templates dominate the observed repression.

245 Further, we show that minicircle templates sustaining variable levels of twist

246 e accumulation of a novel population of free minicircles that is composed mainly of covalently closed

247 etwork containing several thousand catenated minicircles that is condensed into a disk-shaped structu

248 systemic administration of tumor-activatable minicircles that use the pan-tumor-specific Survivin pro

249 We demonstrate that on the minicircle the synthesis of the leading and lagging stra

250 f IS2 transposition, the formation of an IS2 minicircle, the roles of the two IS ends differ.

251 The replicating minicircles then move to two antipodal sites that flank

252 iated release and reattachment mechanism for minicircle theta structure replication.

253 ed the reattachment of newly replicated free minicircles to the network and caused a delay in kinetop

254 n of this topoisomerase II is to attach free minicircles to the network periphery following their rep

255 of the gaps, and reattachment of the progeny minicircles to the network periphery, are thought to tak

256 We found that DNA minicircle topoisomers can have multiple bend locations

257 tigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoil

258 We have investigated minicircle transcription and the processing of gRNAs in

259 hat dictate the 3D structure of a 336 bp DNA minicircle under torsional stress.

260 cate that the conformational distribution of minicircles under torsional stress can be designed, whic

261 distal recognition sites on supercoiled DNA minicircles using MD simulations.

262 eft ventricular fractional shortening in the minicircle vector carrying microRNA-210 precursor group

263 ce underwent intramyocardial injections with minicircle vector carrying microRNA-210 precursor, minic

264 Here we use a single minicircle vector to generate transgene-free iPSCs from

265 y specific overexpression of IL-22 through a minicircle vector-based technology.

266 To confirm in vitro data, shRNA minicircle vectors were injected intramyocardially after

267 and FIH were inserted into novel, nonviral, minicircle vectors.

268 le of inducing DeltaTw between 0 and -0.3 in minicircles, via loss of out-of-plane bending upon retra

269 In vitro, luciferase gene expression from minicircles was 5-10-fold higher than with plasmid DNA.

270 Binding of the ER DBD to ERE-containing minicircles was rapid when the EREs were prebent toward

271 To detect structural disruptions in the minicircles we treated them by single-strand-specific en

272 ce-dependence of DNA denaturation within DNA minicircles, we have observed that whenever the ends of

273 DNA minicircles, where the length of DNA is below the persis

274 vast majority of gRNAs are transcribed from minicircles, which are approximately one kilobase in siz

275 ontains approximately 10,000 kinetoplast DNA minicircles, which are unequally distributed among appro

276 esults indicate that strongly underwound DNA minicircles, which mimic the physical behavior of small

277 We have constructed a minicircle with a replication fork that permits an asses

278 perturbation of lagging strand elongation on minicircles with a highly asymmetric G:C distribution wi

279 s with transposase (positions 1-7) result in minicircles with longer, and inappropriate, spacers.

280 for the first time the feasibility of using minicircles with magnetofection technology to safely eng

281 hermodynamics of a canonical ensemble of DNA minicircles with specified linking number difference del

282 of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers be

283 Minicircle yields using standard culture volumes are suf