ライフサイエンスコーパス: DNA strand

1 nwinding by engaging and stretching a single DNA strand.

2 formation with distinct positioning of each DNA strand.

3 st of which are purines of the complementary DNA strand.

4 between the nascent RNA and the nontemplate DNA strand.

5 the mismatch was introduced in the invading DNA strand.

6 is hybridized at one end to a complementary DNA strand.

7 vents occurring in the damaged and undamaged DNA strand.

8 backbones of nucleotides in the non-template DNA strand.

9 plisome to bypass blocks on the non-tracking DNA strand.

10 itions or require hybridization with another DNA strand.

11 cles (ONPs) with a single, covalently linked DNA strand.

12 he lesion, the enzyme engages the non-lesion DNA strand.

13 is undamaged or the damage affects only one DNA strand.

14 ytosine) deaminase access to the transcribed DNA strand.

15 as9 HNH domain primed for cutting the target DNA strand.

16 nteractions between the flap and unprocessed DNA strand.

17 rst reported G-Ag(I) -G pair in a short 8mer DNA strand.

18 o RNA, as well as the expelled complementary DNA strand.

19 e supercoiling or breaks in the non-template DNA strand.

20 otein-binding sites on the two complementary DNA strands.

21 olecular association of small, complementary DNA strands.

22 sing additional HMGB1 on their extracellular DNA strands.

23 controlled changes when encoded in synthetic DNA strands.

24 esponsible for concerted cleavage of the two DNA strands.

25 es, is subsequently recruited to degrade two DNA strands.

26 rand promoter (HSP), located in the opposite DNA strands.

27 ncer: mutational asymmetries between the two DNA strands.

28 with a single-strand nick in one of the two DNA strands.

29 roach using single and fourfold Atto-labeled DNA strands.

30 ization of its surface with approximately 25 DNA strands.

31 P use an error-prone method to repair broken DNA strands.

32 lecules, and specific species develop within DNA strands.

33 e functions to methylate only one of the two DNA strands.

34 them to the multiplexed probing of pathogen DNA strands.

35 ing DNAs guide TtAgo to cleave complementary DNA strands.

36 es and drives the unwinding and rewinding of DNA strands.

37 hybridize efficiently with the complementary DNA strands.

38 DRNAs) and their longer precursors from both DNA strands.

39 the challenges involved in using unpurified DNA strands.

40 tructure generated by unwinding the parental DNA strands.

41 nostructures that contain hundreds of unique DNA strands.

42 e complexes in either one DNA strand or both DNA strands.

43 examples containing typically tens of unique DNA strands.

44 , reversible curling in response to stimulus DNA strands added to solution.

45 lities of the DNA glycosylases to incise the DNA strand adjacent to G*, while this base is initially

46 The presence of charged radicals in DNA strands after light absorption may cause reactions--

47 nm in length, are soft and bendable, and the DNA strands allow individual polymers to self-assemble i

48 as the gaps between two rods, with different DNA strands allows one to synthesize nanostructure assem

49 fication enzymes that modify cytosine in one DNA strand and adenine in the opposite strand for host p

50 ssociated with mechanical deformation of the DNA strand and entropy arising from thermal fluctuations

51 exclusion, where the helicase encircles one DNA strand and excludes the other, acting as a wedge wit

52 -coupled damage (TCD) on the non-transcribed DNA strand and provide evidence that APOBEC mutagenesis

53 ntiguous runs of >/=4 RNA nucleotides within DNA strand and the only common substrate between the two

54 Silver clusters develop within DNA strands and become optical chromophores with diverse

55 g from the capsid is capable of binding free DNA strands and DNA-functionalized colloidal particles.

56 They link homologous DNA strands and have to be faithfully removed for proper

57 r describes a methodology to capture labeled-DNA strands and hybrids on paper via the anchoring of an

58 ount for both repulsive interactions between DNA strands and local variability in probe surface densi

59 e simultaneously associated with the growing DNA strands and Mg2 PPi crystals during the rolling circ

60 ) DNA structures, which are formed by G-rich DNA strands and play an important role in the maintenanc

61 semidiscontinuously due to the antiparallel DNA strands and polarity of enzymatic DNA synthesis.

62 sequences in both the target and non-target DNA strands and recognizes the 5'-NNNVRYM-3' as the prot

63 DNA-PKcs, which control the repair of broken DNA strands and relay the damage signal to the tumor sup

64 t exosome-sensitive RNAs that mapped to both DNA strands and resembled RNA:RNA hybrids (dsRNAs), sugg

65 ssumed that the open RNAP separates promoter DNA strands and then closes to establish a tight grip on

66 r initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequ

67 orsional stress by nicking and resealing one DNA strand, and some Top1-dependent mutations are due to

68 helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin.

69 lays a major role in the replication of both DNA strands, and that the paucity of pol3-L612M-generate

70 tive lengths of the brush side chain and the DNA strand are found to play a critical role in the degr

71 tions of all 4.6 million nucleotides of each DNA strand are resolved.

72 and cell biological studies where individual DNA strands are either examined in isolation, or interac

73 lets are initially inert because the grafted DNA strands are pre-hybridized in pairs.

74 majority of intertwines between the parental DNA strands are resolved during DNA replication, there a

75 moves torsional stress that accumulates when DNA strands are separated.

76 w a ring-shaped helicase might trap a single DNA strand as the double helix melts, and before it is u

77 small-angle X-ray scattering that, by using DNA strands as inputs, the structure of a three-dimensio

78 on (LAMP) reaction with an initial number of DNA strands as low as 10 copies.

79 he sliding friction between closely packaged DNA strands, as a result of the repulsive interactions b

80 DNA methylation predominates (plus or minus DNA strands - asymmetric DNA methylation; plus and minus

81 es possess AP lyase activities that nick the DNA strand at the deoxyribose moiety via a beta- or beta

82 ly and inexpensively determine the number of DNA strands attached to AuNPs of different core sizes.

83 DNA strands, attached to the lipid bilayer with choleste

84 The exchange of DNA strands between broken and intact molecules lies at

85 it essential to know the type and number of DNA strands bound to the nanoparticle surface.

86 Moreover it is considered as a polymorphic DNA strand break lesion since it can be borne by any of

87 nd identify PARP1 as a therapeutic target in DNA strand break repair-defective disease.

88 However, cells possess two other DNA strand break-induced PARP enzymes, PARP2 and PARP3,

89 used by mutations in APTX, which encodes the DNA strand-break repair protein aprataxin (APTX).

90 holesterol oxidation and supercoiled plasmid DNA strand breakage inhibition induced by both peroxyl a

91 rt that arf gene transcription is induced by DNA strand breaks (SBs) and that ARF protein accumulates

92 eactive oxygen species, leading to increased DNA strand breaks and apoptosis of normal, but not MF, C

93 ism, overexpression of APE1, accumulation of DNA strand breaks and results in genomic instability.

94 t required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation

95 With increasing LET, less DNA strand breaks are formed per unit dose, but due to t

96 However, leukocyte DNA strand breaks decreased with increased dietary zinc,

97 The repair of DNA strand breaks improves, as do serum protein concentr

98 ion of PARP-1 is the predominant response to DNA strand breaks in cells.

99 Remarkably, we discovered unrepaired DNA strand breaks in SMCs within the human ascending aor

100 We used laser microirradiation to introduce DNA strand breaks into living cells expressing a photoac

101 g mouse fibroblasts, suggesting formation of DNA strand breaks under these treatment conditions.

102 e hamster ovary cells (assesses the level of DNA strand breaks).

103 ssociated with increased mutation frequency, DNA strand breaks, and cytotoxicity.

104 cil (5-FU) by prolonging S phase, generating DNA strand breaks, and inducing DNA damage signaling.

105 displayed increased levels of glycated DNA, DNA strand breaks, and phosphorylated p53.

106 ence for oxidized DNA lesions, double-strand DNA strand breaks, and pronounced susceptibility to sing

107 s during transcription elongation, including DNA strand breaks, DNA lesions, and nucleosomes.

108 DDR-PARPs detect DNA strand breaks, leading to a dramatic increase in the

109 We also found elevated levels of DNA strand breaks, mitochondrial DNA transfer to the nuc

110 possess the appropriate energetics to induce DNA strand breaks, whereas e(-)(aq) in bulk water lies t

111 ate that PhIP induced C8-PhIP-dG adducts and DNA strand breaks.

112 y to DNA damaging agents and accumulation of DNA strand breaks.

113 involved in H2O2 breakdown; and 4) result in DNA strand breaks.

114 omet assays that showed increased numbers of DNA-strand breaks.

115 t even the induction of two SSBs on the same DNA strand can cause genome alterations, albeit at a muc

116 chemical bond between the two complementary DNA strands can be reversibly broken upon light irradiat

117 process, a small and constant set of unique DNA strands can be used to create DNA origami arrays of

118 structure-switching of electrically charged DNA strands can disrupt the charge distribution in the v

119 Guanine-rich DNA strands can fold in vitro into non-canonical DNA str

120 valve, which is made from seven concatenated DNA strands, can bind a specific ligand and, in response

121 es during their incorporation into a growing DNA strand catalyzed by DNA polymerase.

122 The structures reveal that activation of DNA strand cleavage and rejoining involves large conform

123 occupies both PAM-interacting and non-target DNA strand cleavage catalytic pockets.

124 region as an anchor for at least one of the DNA strand cleavage events.

125 e HNH nuclease domain adjacent to the target DNA strand cleavage site in a conformation essential for

126 orable coordination ready for the non-target DNA strand cleavage.

127 To analyse the mechanism and kinetics of DNA strand cleavages catalysed by the serine recombinase

128 based on DNA aptamers that can hybridize to DNA strands conjugated to a near-infrared fluorophore/qu

129 uctures through the incorporation of capping DNA strands conjugated with functional groups.

130 compared to that for an all-DNA strand or a DNA strand containing the corresponding 2'-F-araU nucleo

131 owed Afu Pol-D "in trans", that is, a copied DNA strand could be inhibited by a deaminated base in th

132 re with a predetermined pattern of different DNA strands covalently 'printed' on their exterior, and

133 rmation to the buffer in the form of soluble DNA strands designed to compete with the grafted strands

134 ompare the Ka of hybridization for identical DNA strands differing only by the presence of a fluoresc

135 Proximity-induced intramolecular DNA strand displacement (PiDSD) is one of the key mechan

136 1.3 h) perturbed dynamic processes including DNA strand displacement and primer extension by DNA poly

137 esign that allows the flexible regulation of DNA strand displacement by splitting an input strand int

138 We demonstrate our approach in vitro using DNA strand displacement cascades as well as in vivo usin

139 erimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 dist

140 to successfully design and construct complex DNA strand displacement circuits.

141 DNA strand displacement is a key reaction in DNA homolog

142 Toehold-mediated DNA strand displacement is introduced as a method to pur

143 Toehold-mediated DNA strand displacement is the fundamental basis for the

144 molysin pore was induced by a combination of DNA strand displacement processes and enzyme-catalyzed r

145 eins, is realized through a toehold-mediated DNA strand displacement reaction.

146 udies, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing

147 re previously shown using more sophisticated DNA strand displacement systems, including 1) continuous

148 tics of PiDSD by combining the uses of three DNA strand displacement techniques, including a binding-

149 a useful addition to the current toolbox of DNA strand displacement techniques.

150 parameters for PiDSD, and a toehold-mediated DNA strand displacement to generate fluorescence signals

151 ment techniques, including a binding-induced DNA strand displacement to generate PiDSD, an intermolec

152 have been engineered using toehold-mediated DNA strand displacement, and their programmable applicat

153 combines discrimination by competition with DNA strand displacement-based catalytic amplification.

154 Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field

155 aptamer structure, thus suggesting that the DNA strand-displacement concept can be extended to funct

156 tructures, and motors, many of which rely on DNA strand-displacement reactions.

157 s minimal DNA loading, and non-complementary DNA strands do not get encapsulated within the PEG-CNA-P

158 lso interacts specifically with the excluded DNA strand during unwinding.

159 SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive result

160 ess also generates a bulge in the non-target DNA strand, enabling its handover to Cas3 for cleavage.

161 In vitro, HOP2-MND1 stimulates the DNA strand exchange activities of RAD51 and DMC1.

162 In vitro, RAD52 has ssDNA annealing and DNA strand exchange activities.

163 Although providing an efficient rate of DNA strand exchange between polymorphic alleles, Dmc1 mu

164 ength BRCA2 protein stimulates DMC1-mediated DNA strand exchange between RPA-ssDNA complexes and dupl

165 teins align homologous sequences and promote DNA strand exchange has long been known, as are the crys

166 How DNA mismatches affect Dmc1-mediated DNA strand exchange is not understood.

167 ate common and idiosyncratic features in the DNA strand exchange mechanisms of three RecA-family reco

168 DNA strand exchange plays a central role in genetic reco

169 cD and its cognate RecA led to inhibition of DNA strand exchange promoted by RecA.

170 The DNA strand exchange protein RAD51 facilitates the centra

171 The meiosis-specific DNA strand exchange protein, DMC1, promotes the formatio

172 combined biochemical reconstitutions of the DNA strand exchange reactions with total internal reflec

173 ort shape changing films that are powered by DNA strand exchange reactions with two different domains

174 All three variants are proficient in DNA strand exchange, but G151D is slightly more sensitiv

175 red for DNA repair, including RAD51 mediated DNA strand exchange, but is dispensable for DNA replicat

176 ion results in stimulation of RAD51-promoted DNA strand exchange.

177 ding specificity in a manner that stimulates DNA strand exchange.

178 acement to generate PiDSD, an intermolecular DNA strand-exchange strategy to measure a set of key kin

179 naptic complex and orchestrates the order of DNA strand exchanges.

180 of this R-loop structure in positioning each DNA strand for cleavage by the two Cas9 nuclease domains

181 lating the structure of chromatin by binding DNA strands for defining the boundary between active and

182 ads attached via single-immune complexes and DNA strands form tethers, and tether formation in the ab

183 cation forks, which in turn protects nascent DNA strands from extensive degradation.

184 such as a protein, when bound to a signaling DNA strand generates steric hindrance effects, which lim

185 hat is able to cut preferentially the coding DNA strand, generating a nicked DNA target.

186 The number, orientation and sequence of DNA strands grafted onto the polymeric core can be contr

187 Mismatches near the 3' end of the initiating DNA strand have a small effect, whereas most mismatches

188 ol of the orientation of fluorophore-labeled DNA strands immobilized on an electrode surface has been

189 Ssl2 tracks along one DNA strand in the 5' --> 3' direction, implying it uses

190 of the A ring, which are next to the cleaved DNA strand in the drug-DNA-Top1 ternary cleavage complex

191 larly versatile in this context because each DNA strand in the origami nanostructure occupies a uniqu

192 e, the psbN gene, is located on the opposite DNA strand in the psbT/psbH intergenic region.

193 th increased processing of newly synthesized DNA strands in hydroxyurea-stalled forks.

194 eotides inside cells, and the degradation of DNA strands in serum was significantly slowed.

195 he RNA oligonucleotides and the paths of the DNA strands in the complete initiation complexes provide

196 DNA duplexes with a nick, NEIL3 targets both DNA strands in the ICL without generating single-strand

197 s of AacC2c1 with both target and non-target DNA strands independently positioned within a single Ruv

198 ng to form an RNA-DNA hybrid and a displaced DNA strand inside the protein.

199 cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amp

200 orylated HP1alpha induce rapid compaction of DNA strands into puncta, although with different charact

201 The displacement loop (D loop) is a DNA strand invasion product formed during homologous rec

202 nge protein, DMC1, promotes the formation of DNA strand invasion products (joint molecules) between h

203 51/RecA family of recombinases catalyzes the DNA strand invasion reaction that takes place during hom

204 vidence that the RecN protein stimulates the DNA strand invasion step of RecA-mediated recombinationa

205 e functions to mediate repair via homologous DNA strand invasion to form D-loops.

206 uplex DNA by steric exclusion (SE) where one DNA strand is encircled by the hexamer and the other is

207 replication errors by keeping track of which DNA strand is new and which is the template.

208 trophoretic washing, the fluorophore-labeled DNA strand is then thermally released for hybridization

209 rcular (RC) DNA, in which neither of the two DNA strands is covalently closed.

210 Accurate pairing of DNA strands is essential for repair of DNA double-strand

211 ion between delocalized G blocks on opposite DNA strands is known to support partially coherent long-

212 s including two simultaneously bound, looped DNA strands is not involved here.

213 ophoretic processing of unfragmented genomic DNA strands is time-consuming, because of the length.

214 For nucleotides and short DNA strands, it has been shown that a high degree of acc

215 nbound, partially bound, or fully bound to a DNA strand, leaving opportunities for other molecules in

216 he combined absence of UNG and MSH2 and that DNA strand lesions arise in an UNG-dependent manner but

217 ely and efficiently generate genome edits at DNA strand lesions made by DNA double strand break reage

218 mismatch repair (MMR) to yield mutations and DNA strand lesions.

219 pyogenes Cas9 R-loop that show the displaced DNA strand located near the RuvC nuclease domain active

220 , AgNP concentration, PNA concentration, and DNA strand mismatches.

221 oduction of different types of reprogramming DNA strands modifies the DNA shells of the nanoparticles

222 t LacI can move between cages when hindering DNA strands move out of the way.

223 sertion of 2',4'-diF-araU nucleotides in the DNA strand of a DNA-RNA hybrid decreases the rate of bot

224 x structures without using a large number of DNA strands of different sequences.

225 er ITR restores each of these functions, but DNA strands of only single polarity are encapsidated in

226 dence that a DDE/D active site can hydrolyze DNA strands of opposite polarity, a mechanism that has r

227 to the chromosome, which comprises parental DNA strands of opposite polarity, has been unknown.

228 trast, cut-and-paste transposases cleave two DNA strands of opposite polarity, which is usually achie

229 rors to achieve accurate replication of both DNA strands of the nuclear genome.

230 .0001) detect the origin (sense vs antisense DNA strands) of DNA methylation at splice site junctions

231 The DNA strand on AuNPs is shown to preserve its functions.

232 r, coupled incisions are made in the damaged DNA strand on both sides of the adduct.

233 esting the dye-tagged sequence-matched probe DNA strand only, so that the amount of free dye removed

234 d a significant influence on the assembly of DNA strands onto the AuNPs.

235 ement RNA strand compared to that for an all-DNA strand or a DNA strand containing the corresponding

236 ediated DNA-cleavage complexes in either one DNA strand or both DNA strands.

237 the BRC5-8 region potentiates RAD51-mediated DNA strand pairing and provides complementation function

238 ting methods used to determine the number of DNA strands per gold nanoparticle (AuNP) require that th

239 MMR is bidirectional at the level of DNA strand polarity as it operates equally well in the 5

240 s helicases, as apparent from their distinct DNA strand preferences, which can be rationalized from t

241 ions; whereas, the denatured single-stranded DNA strands readily reform duplexes at neutral pH.

242 Metnase-induced enhancement of Exo1-mediated DNA strand resection required the presence of these over

243 nucleotides downstream on the top and bottom DNA strands, respectively, in an NTP-hydrolysis dependen

244 on usually occurs at pairs of Ts on opposite DNA strands, separated by 12 nucleotides.

245 ng to a promoter, the sigma factor initiates DNA strand separation and captures the melted nontemplat

246 t that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion.

247 inged-helix domain, the latter implicated in DNA strand separation and oligomer formation.

248 Competition assays provide evidence that DNA strand separation and RNA-DNA heteroduplex formation

249 Foremost, DNA strand separation by transcription or increased tors

250 The issue hinges on whether DNA strand separation is the basis for the chromosomal i

251 (SIDD) method, which analyzes stress-driven DNA strand separation.

252 k replication fork progression by inhibiting DNA strand separation.

253 Nanopore DNA strand sequencing has emerged as a competitive, port

254 sing an oxidative coupling strategy, and the DNA strands served as easily tunable and reversible chem

255 an average ratio of 29.2% by targeting both DNA strands simultaneously with an over 98.6% coverage.

256 namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbl

257 Additionally, a CpG sequence of the template DNA strand spanning the active site of RNAP inhibits elo

258 e nuclease active site sufficient to cut one DNA strand suggesting that two complexes are required to

259 curs at methylated cytosines on the template DNA strand, suggesting a co-transcriptional feedback to

260 hemselves been used to make viral capsids of DNA strands, supramolecular nanotapes and pH-responsive

261 By scanning this tip along a single DNA strand suspended between surface-bound micron-scale

262 ure approach using RNA probes targeting both DNA strands, termed DEEPER-Capture.

263 Hybridization to a target DNA strand tethers the beads together, inducing bead agg

264 etrically releases the 3' end of the cleaved DNA strand that is not complementary to the sgRNA (nonta

265 nerates closely spaced incisions on opposite DNA strands that are permissive for TNR expansion.

266 rlattices, with dye molecules coupled to the DNA strands that link the particles together, in the for

267 t region of homology between the recombining DNA strands that promote joint molecule formation to ini

268 We show that for shorter DNA strands the interaction distance affects the transit

269 t considers the role of ions surrounding the DNA strands, the distance dependence of the applied pote

270 DCPs prevent reassociation of denatured DNA strands: they make one of the two strands of a dsDNA

271 The structure reveals the route of an intact DNA strand through the transposase active site before se

272 o is to stabilize DnaA filaments on a single DNA strand, thus providing essential precision to this b

273 that it is regulated by the 5'-flaps in the DNA strand to be displaced.

274 tivity, which is responsible for nicking the DNA strand to be transferred and for covalent attachment

275 ith its DNA template exposes the nontemplate DNA strand to mutagens and primes unscheduled error-pron

276 site-selectively attached the complementary DNA strand to the N-terminus of a protein.

277 TR, allowing viral genes encoded on opposite DNA strands to be simultaneously transcribed.

278 ase to promote somatic hypermutation on both DNA strands to generate double-strand DNA breaks for eff

279 een a number of labeled and unlabeled target DNA strands to measure the impact of fluorescent labelin

280 that uses the hybridization of complementary DNA strands to model the formation of the SNARE four-hel

281 reted pectinases are expressed from the same DNA strand (transcriptional co-orientation).

282 ransposition: DNA binding, DNA cleavage, and DNA strand transfer.

283 dge insertion, initiating directional target DNA strand unwinding to allow segmented base-pairing wit

284 l transferase reaction during extension of a DNA strand using the complementary strand as a template.

285 g replication of the leading and the lagging DNA strands were reported in yeast and in human cancers,

286 DR2-dependent transcripts correspond to both DNA strands, whereas the RNA polymerase II (Pol II)-depe

287 us competitive exchange with a complementary DNA strand which breaks PSA-aptamer interactions is stud

288 This sensing system involves only four DNA strands which is quite simple.

289 misincorporated nucleotides from the nascent DNA strand, which carries by definition the erroneous ge

290 r complementary base-pairing with the target DNA strand while displacing the non-target strand, formi

291 te DNA synthesis directly at the 3' end of a DNA strand while simultaneously attaching a DNA-seq adap

292 ing of the target triggered a release of the DNA strand with the quencher and thus relief of the cont

293 III, were used in combination to degrade all DNA strands with a free 3' end, which would nevertheless

294 were used to detect complementary, labelled DNA strands with different lengths and sequences by hybr

295 The brush architecture provides embedded DNA strands with enhanced nuclease stability and improve

296 oncentrations of the oxidizing agent O2, and DNA strands with greater, similar20 nucleotides.

297 veloped to analyse the markers in individual DNA strands with the potential to identify multiple lesi

298 on nucleosome by combining HRF data for both DNA strands with the pseudo-symmetry constraints.

299 Although interactions of the encircled DNA strand within the central channel provide an accepte

300 strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the mot