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

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

9 cient method to obtain covalently closed DNA minicircles.

10 of other eukaryotes) and thousands of ~1-kb minicircles.

11 4-65-bp minicircles, but not in the 85-86-bp minicircles.

12 network containing thousands of interlocked minicircles.

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

14 exhibit preferred binding to constrained DNA minicircles.

15 n, although they can extensively unwind free minicircles.

16 veral thousand topologically interlocked DNA 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 oflagellates, where genes are located on DNA minicircles.

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

22 k containing 5,000 topologically interlocked minicircles.

23 le gRNAs are encoded by both maxicircles and minicircles.

24 are encoded in circular DNA molecules called minicircles.

25 gh free energy cost of substantial writhe in minicircles.

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

27 g several thousand topologically interlocked minicircles.

28 into the endogenous gaps of newly replicated minicircles.

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

30 NA, composed of mutually catenated maxi- and minicircles.

31 ls transfected by electroporation with HPV18 minicircles.

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

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

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

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

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

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

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

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

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

45 The unprecedented organization of minicircles and gRNAs in T. lewisi broadens our knowledg

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

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

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

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

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

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

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

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

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

55 ta, a cell-free workflow using synthetic DNA minicircles and rolling circle amplification enables com

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

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

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

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

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

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

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

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

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

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

66 We find that minicircles are transcribed polycistronically and that t

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

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

69 ding ribosomal RNAs (rRNAs) and proteins and minicircles bearing guide RNAs (gRNAs) for mRNA editing.

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

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

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

73 We further show that mitochondrial minicircles-but not maxicircles-show a similar evolution

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

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

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

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

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

79 Minicircles carrying a SB transposon cassette containing

80 g) RNA genes, with two differently organized minicircle categories both encoding essential gRNAs.

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

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

83 uide RNAs (gRNAs), but the precise number of minicircle classes and gRNA genes was unknown.

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

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

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

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

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

89 Minicircle classes that contain several functional gRNA

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

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

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

93 By assembling a total of 58 minicircle classes, which fall into two distinct categor

94 unequally distributed among approximately 10 minicircle classes.

95 0-bp conserved region which is common to all minicircle classes; the remaining approximately 600 bp o

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

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

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

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

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

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

102 8 degrees) were observed in axially strained minicircles consisting of tandemly repeated d(A)5 and d(

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

104 Minicircles containing a new L strand have a single nick

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

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

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

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

109 ndant minicircle replication intermediate as minicircle copy number declines.

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

111 icircle structure and to explore dynamics of minicircle copy numbers.

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

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

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

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

116 that is composed mainly of covalently closed minicircle dimers.

117 Minicircle DNA (mcDNA) is recently becoming an exciting

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

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

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

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

122 Minicircle DNA give enhanced and more persistent transge

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

124 We herein hydrodynamically delivered IL-23 minicircle DNA into wild-type and CCR6-deficient (CCR6-k

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

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

127 The optimized polymers are used to deliver minicircle DNA to multipotent adipose derived stem cells

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

129 Minicircle DNA vectors allow sustained transgene express

130 Minicircle DNA vectors are free of bacterial DNA and thu

131 gineered using magnetofection technology and minicircle DNA vectors- a promising cell engineering app

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

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

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

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

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

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

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

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

140 ween nuclear-encoded mitochondrial genes and minicircle-encoded guide RNA genes is essential to maint

141 rocess is mediated by hundreds of species of minicircle-encoded guide RNAs (gRNAs), but the precise n

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

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

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

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

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

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

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

149 The minicircles fell into distinct categories based on lengt

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

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

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

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

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

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

156 Minicircle-functionalized magnetic nanoparticle (MNP)-me

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

175 random distribution and segregation model of minicircles is assumed.

176 ally, a scenario describing the evolution of minicircles is presented.

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

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

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

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

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

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

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

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

185 Initiation of minicircle leading-strand synthesis involves the synthes

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

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

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

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

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

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

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

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

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

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

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

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

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

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

200 of homogeneous uniparental maxicircles, but minicircles originated from both parental species.

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

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

203 nicircle plasmids, termed SyMPL (SyngenicDNA Minicircle Plasmid) tools, before transformation.

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

205 SyngenicDNA" tool, and propagate the tool as minicircle plasmids, termed SyMPL (SyngenicDNA Minicircl

206 To improve minicircle production, we genetically modified Escherich

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

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

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

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

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

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

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

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

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

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

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

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

219 Minicircles replicate after release from the network, an

220 The minicircles replicate free of the kDNA network but nicks

221 Individual minicircles replicate unidirectionally from either of tw

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

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

224 Minicircle replication intermediates decrease during RNA

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

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

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

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

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

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

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

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

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

234 otational movement of the kinetoplast during minicircle replication.

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

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

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

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

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

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

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

242 p38 binds to minicircle sequences within the replication origin.

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

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

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

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

247 used our data set to refine definitions for minicircle structure and to explore dynamics of minicirc

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

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

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

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

252 ome can be simultaneously assembled onto the minicircle substrate.

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

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

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

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

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

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

259 ates a functional replisome assembled on the minicircle template.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

300 Minicircle yields using standard culture volumes are suf