ライフサイエンスコーパス: single base

1 ucleic acids with design precision down to a single base.

2 le, which are not observable in a mixture of single bases.

3 These DinB polymerases also generate single-base (-1) deletions at high frequencies with most

4 ggest that perhaps nature has selected for a single-base addition to control folding to the functiona

5 firmed 15 off-target sites, each harboring a single-base bulge and one to three mismatches to the gui

6 By contrast, single-base bulges 6'U7' and 6'A7' on the target strand

7 Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand

8 gonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed seg

9 1 patient 3 years apart did not accumulate a single base change across the genome.

10 igo contained multiple nucleotide changes: a single base change allowing recombinant selection, and s

11 st-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an

12 Genome sequencing identified a single base change resulting in a threonine-to-methionin

13 ntaining complex variation (i.e. more than a single base change), thus making identification of such

14 lar localization analyses strongly suggest a single-base change at the coding region of ClVST1(97) as

15 onfirmed by DNA analysis, which identified a single-base change of cytosine to guanine at the second

16 single nucleotide polymorphisms (nsSNPs) are single base changes leading to a change to the amino aci

17 t the chromosome and structural level, while single base changes occur at very low rates.

18 Nevertheless, subtle edits such as single base changes or small deletions may be difficult

19 sses modifications ranging from thousands of single base changes to megabase-scale path reorganizatio

20 s chromosomal rearrangements, deletions, and single base changes.

21 ferences in hybridization energy provided by single-base changes makes identification of these mutati

22 Our patient carries a single base deletion at -225, significantly decreasing i

23 s laxa, we engineered a cutis laxa mutation (single base deletion) into the human elastin gene contai

24 that the interdomain linker also affects the single-base deletion frequency and the mispair extension

25 e spectrum of transitions, transversions and single base deletions are observed.

26 opose two distinct mechanisms for generating single base deletions in vivo.

27 Remarkably, the rate of single base deletions is preferentially increased in cod

28 le base than large deletions, and that these single base deletions were possibly caused by replicatio

29 ral Old World monkeys and apes by frameshift single-base deletions forming premature stop codons.

30 tter property explains how hPolkappa creates single-base deletions in non-repetitive sequences, but d

31 Thus, the tumor-dependent introduction of a single base difference in the miR-376a* sequence dramati

32 of miR at a very low concentration and with single-base discrimination without the need for sophisti

33 y we devised a novel approach for homozygous single base editing based on utilising simultaneously tw

34 rters for quantification and optimization of single base editing by APOBEC-Cas9 editosomes.

35 of APOBEC3B and APOBEC3H display the highest single base editing efficiencies.

36 /Cas9 allows gene knock-outs, knock-ins, and single-base editing at chromosomal loci.

37 Here the authors show high efficient single-base editing in zebrafish using modified Cas9 and

38 al deletion, indel, CRISPR interference, and single-base editing), we modified rs2076295 and measured

39 er optimization is required to generate true single base editors and the eGFP reporters described her

40 Compared to single base editors, A&C-BEmax's activity on adenines is

41 quencing technologies that are less prone to single-base errors should confirm these results by apply

42 single and metagenomic assemblies, including single-base errors, insertions/deletions, genome rearran

43 ide datasets, multiplex-PCR and detection by single-base extension and MALDI-TOF mass spectrometry, i

44 racterization of DNMT-mutant ESCs, including single-base genome-wide maps of the targets of these enz

45 L1, and NEBL, with mutational hot spots at a single base in 3 of 12 tumors sequenced.

46 re capable of distinguishing variations of a single base in a stretch of target DNA.

47 nthesis in which a nucleotide specified by a single base in the DNA template is repetitively added to

48 ase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to

49 , which allow selective UV excitation of one single base in the strand.

50 evelopment of a novel molecular tool to edit single bases in the mtDNA (Mok et al., 2020).

51 rtion in polymerase active sites could allow single base insertion or deletion mutations to occur, an

52 The second carries a single base insertion with respect to the wild type.

53 eletions, 3 siblings harbored a heterozygous single-base insertion, and 2 subjects had a balanced tra

54 ozygous single-nucleotide variants (SNVs) or single-base insertions/deletions, 3 siblings harbored a

55 substantial differential methylation at the single base level.

56 Not only can maNCB identify m(6)A at the single-base level but it also can quantify the extent of

57 At the single-base level with Illumina data, ALE recovers 215 o

58 explicitly models positive selection at the single-base level, as well as highly heterogeneous backg

59 er analysis using expressed region-level and single base-level approaches provides a compromise betwe

60 Using single-base methylation maps and transcriptome analyses

61 sequencing has become the primary choice for single-base methylation quantification of multiple targe

62 This contribution provides the first single-base methylome profiles of haploid gametophytes a

63 been considered to monitor hybridization of single base mismatch (SBM) in synthetic oligonucleotides

64 calibration curve of the chMB for detecting single base mismatch and ultraviolet (UV)-induced DNA da

65 rmore, the HpSGN system was sensitive to the single base mismatch at the position next to the hairpin

66 Generating a single base mismatch in the growing primer duplex, which

67 ly challenging due to the presence of only a single base mismatch in the middle of the 251 base long

68 s quantitation platform can also distinguish single base mismatch of DNA hybridization and observe th

69 he probe and was found that the system has a single base mismatch selectivity.

70 non-complementary target (un-hybridized) and single base mismatch target (named as SMM) hybridized su

71 ed (non-complementary target hybridized) and single base mismatch target hybridized surfaces sensitiv

72 significantly lower binding with DNA having single base mismatch.

73 proves to have a better distinction against single-base mismatch oligonucleotide sequences compared

74 enables direct 100-aM limit of detection and single-base mismatch selectivity in a 2-h kinetic discri

75 ard the complementary DNA target, as well as single-base mismatch selectivity.

76 Moreover, it has high selectivity against single-base mismatch sequences and can be used directly

77 RNA detection with attomolar sensitivity and single-base mismatch specificity.

78 sensor to study the type and location of the single-base mismatch, as well as the influence of the le

79 the target analyte over full complementary, single-base mismatch, three base-mismatch and non-comple

80 gets that are perfectly matched or contain a single-base mismatch.

81 en incorporating a correct nucleotide over a single-base mismatch.

82 es can be reliably quantified with excellent single-base-mismatch differentiation capability by this

83 for the complementary oligonucleotides over single-base-mismatch, two-base-mismatch, and noncompleme

84 n fully complementary, non-complementary and single base mismatched targets, and even between the com

85 excellent discrimination efficiency toward a single-base mismatched target.

86 ynamic difference between the target and the single-base-mismatched DNA, resulting in a differential

87 intensity of the complex with DNA containing single base mismatches correlates with the thermodynamic

88 move all non-target nucleic acids, including single base mismatches flanked by adenines or uracils.

89 ) serves as a luminescent "light switch" for single base mismatches in DNA.

90 perturbations and capable of distinguishing single base mismatches in the target miRNA.

91 to program Cpf1 nucleases are insensitive to single base mismatches, but that many of the other bases

92 ions, including DNA melting and detection of single base mismatches.

93 sults, such as the greater Cas9 tolerance to single-base mismatches in PAM-distal region than to PAM-

94 he enzymes facilitated the discrimination of single-base mismatches within the recognition or ligatio

95 roduplex structures and is even able to nick single-base mismatches.

96 DNA with the capability of discriminating a single-base mutant of DNA.

97 C.I. 1.82 x 10(-10) to 5.23 x 10(-10)) and a single base mutation rate of 2.08 x 10(-10)/site/generat

98 Our data document the power of a single base mutation, inducing an extensive remodeling o

99 RNA comprising either a terminal or a middle single base mutation.

100 A single-base mutation at codon 6 leads to formation of Hb

101 t mismatch is also demonstrated by detecting single-base mutation in target nucleic acids.

102 ical assays of BsRppH on RNA substrates with single-base-mutation changes in the first four nucleotid

103 litate, for the first time, the detection of single base mutations in a gene segment and, specificall

104 Recently, the landscape of single base mutations in diffuse large B-cell lymphoma (

105 c diversity of HsDhn3 alleles and effects of single base mutations on the intrinsically disordered st

106 sed to detect and phase up to 82% of de novo single base mutations with a false-positive rate of abou

107 ding deletions at the LdMT transporter gene, single-base mutations and changes in somy.

108 to Cas9 nickase, up to 28% of site-specific single-base mutations are achieved in multiple gene loci

109 of dense combinatorial barcode libraries and single-base mutations produced by CRISPR base editors wi

110 is used to directly measure the kinetics of single-base nucleotide incorporation into primed DNA tem

111 at captures the genome-wide homology through single-base-offset tiling windows of 100 continual nucle

112 We found that single-base omissions (i.e., gaps) occurred at significa

113 Using optical tweezers with single base pair (bp) resolution, we analyzed DNA unwind

114 s significantly slower than the fraying of a single base pair and (ii) initiating branch migration in

115 rties by the snake proteins, but rather to a single base pair change in a Hox/Paired box (Pax)-respon

116 In the diminuendo mouse, which carries a single base pair change in the seed region of miR-96, th

117 h-M74a strain (GhV-F) is likely incorrect: a single base pair deletion near the N terminus results in

118 strating the ability of our method to detect single base pair differences in DNA specificity of two s

119 namic switch-based on the rearrangement of a single base pair in the miRNA-mRNA duplex-that elongates

120 a limit of detection of 1nM and can detect a single base pair mismatch between probe and complementar

121 Our data indicate that a single base pair mismatch in the invader stalls branch m

122 lly relevant concentration levels as well as single base pair mismatch, without requiring complex and

123 d we track the effects of incorporating a CA single base pair mismatch.

124 nsor was optimized to allow the detection of single base pair mismatched sequences, able to detect as

125 d the influence of the cooperative effect on single base pair mismatches.

126 from circulating clades require as few as a single base pair mutation to quantitatively switch their

127 lds seamless mutations that are precise to a single base pair of DNA.

128 nthesis products, and from DNA duplexes with single base pair overhangs.

129 determine distribution of 5-mC and 5-hmC at single base pair resolution at MspI restriction sites.

130 evelopment in mammals and can be captured at single base pair resolution by whole genome bisulfite se

131 ths of inherited microsatellite alleles with single base pair resolution from short sequence reads is

132 nome-wide measurements of DNA methylation at single base pair resolution.

133 nscription factor (TF)-DNA interactions with single base pair resolution.

134 a single-molecule fluorescence assay with a single base pair resolution.

135 ssible the rapid identification of CGRs with single base pair resolution.

136 Here, we report that a homozygous single base pair substitution in POLE1 (polymerase epsil

137 ls to engineer mouse strains with reciprocal single base pair substitutions (B6-Cdh23(c.753A>G) and 1

138 ndergo ion-induced folding is conferred by a single base pair that follows the conserved A.G pairs, t

139 The genomic impact ranged from a single base pair to 5.4 Mb.

140 a purine and often primed transcription on a single base pair to either the terminal or penultimate r

141 on mutations in TTDN1 ranging in size from a single base pair to over 120 kb.

142 ile most indels at non-coding regions were a single base pair, 3 base pair indels were observed when

143 criminate between DNA ligands differing by a single base pair.

144 mains using targeted mutations as small as a single base pair.

145 inguish between two alleles that differ by a single base pair.

146 f distinguishing alleles differing by even a single base pair.

147 pair and unwinds DNA with the step size of a single base pair.

148 differs from the wild-type allele at only a single base pair.

149 ing low expression of these putative piRNAs, single-base pair CpG methylation analyses across the gen

150 described, which allows for the presence of single-base pair mismatches arising from sequencing erro

151 By profiling genome-wide DNA methylation at single-base pair resolution in thirteen DLBCL diagnosis-

152 most direct evidence thus far that forward, single-base pair stepping of a helicase utilizes the spo

153 at is accessible from the current state by a single base-pair addition/deletion following the Gillesp

154 We show that the position of a single base-pair mismatch in the -ssDNA/microRNA duplex

155 ich could effectively distinguish and reject single base-pair mismatches.

156 thermore, we extend this approach to perform single base-pair modifications in the TERT promoter; rev

157 Patterns of single base-pair mutations (SNPs) in aligned pairs disti

158 discriminate between alleles differing by a single base-pair regardless of the position in the guide

159 d for transcriptome analysis that provides a single base-pair resolution map of transcription start s

160 ryngeal swab samples, and presented superior single base-pair resolution of this assay.

161 tprints, high-resolution X-ChIP-seq achieves single base-pair resolution of transcription factor bind

162 the kinetics of much longer RNA sequences at single base-pair resolution while also allowing for the

163 enabling precise chromosome modifications at single base-pair resolution with an efficiency of >40%,

164 cations within Hi-C data with breakpoints at single base-pair resolution.

165 cing data and pinpoints their breakpoints at single base-pair resolution.

166 while operating at room temperature and with single base-pair resolution.

167 estigation of genome-wide RBP-RNA binding at single base-pair resolution.

168 e the folding kinetics of an RNA molecule at single base-pair resolution.

169 rteen of the most widely used BCG strains at single base-pair resolution.

170 breakpoints in 35 parasite clones with near single base-pair resolution.

171 ure into smaller substructures composed of a single base-pair stack, which allows us to leverage exis

172 e, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular mo

173 he impact of both large-scale structural and single base-pair variations.

174 ing nucleosomes do not provide the necessary single-base-pair accuracy to determine these positions.

175 s of transcription through a nucleosome with single-base-pair accuracy.

176 sed to make modifications from as small as a single-base-pair change to insertion of DNA fragments.

177 This patient carries a homozygous, germline, single-base-pair deletion in FASLG exon 1, leading to a

178 The densely sampled alignment provides a single-base-pair map of selection, has more than doubled

179 e presence of an excess of a sequence with a single-base-pair mismatch.

180 etection, with the capabilty to discriminate single-base-pair mismatched DNA mutation (single nucleot

181 and the donor carries different densities of single-base-pair mismatches.

182 Notably, we demonstrate that this single-base-pair mutation abrogates the ability of the e

183 These results suggest how a single-base-pair mutation can cause a dramatic epigeneti

184 ng tool for genome-editing DNA in cells with single-base-pair precision, which allows novel in vitro

185 cis-regulatory binding sites (footprints) at single-base-pair resolution to compare binding sites and

186 made it possible to decode DNA methylomes at single-base-pair resolution under various physiological

187 modification of the ssODNs enabled effective single-base-pair substitution.

188 of selected novel dinB alleles, generated by single-base-pair substitutions in the dnaE915 strain, in

189 the toxT promoter, promoter derivatives with single-base-pair transversions spanning the ToxR-footpri

190 toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains,

191 class of DNA mutation (ranging in scale from single base pairs to multiple chromosomes), (c) developm

192 ence and structure across length scales from single base pairs to whole organisms.

193 resistance alleles, including alteration of single base pairs.

194 al steps that correspond to the unwinding of single base pairs.

195 let-7 microRNA family that differ in only a single base position.

196 technology to define TOP2 cleavage sites at single-base precision, and use the technology to charact

197 developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC.

198 Applications that do not require single base resolution are completed with faster separat

199 quantify expression of nearly 10,000 TSS at single base resolution by Capp-Switch sequencing, which

200 ability to detect DNA modification sites at single base resolution could significantly advance studi

201 across flowering plant species, we compared single base resolution DNA methylomes of 34 diverse angi

202 of AmpSeq-SSR were nearly 100 and 94% with a single base resolution for homozygous and heterozygous s

203 Nearly single base resolution of short tandem repeats relevant

204 pecific m6A sites from MeRIP-Seq data with a single base resolution using deep learning and Hot-m6A,

205 mC levels can be computationally inferred at single base resolution using sequencing or array data fr

206 me showing differential expression signal at single base resolution without relying on existing annot

207 nsive methylomes of two H. pylori strains at single base resolution, using Single Molecule Real-Time

208 for visual bacterial pathogen detection with single base resolution.

209 e determination of charged tRNA fractions at single-base resolution (Charged DM-tRNA-seq).

210 Last, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) map

211 Using ME-Class2 we analyze whole-genome single-base resolution 5mCG and 5hmCG datasets from 20 p

212 to determine cytosine methylation states at single-base resolution across entire genomes and populat

213 hese cells, we profile the DNAm landscape at single-base resolution across the first two decades of h

214 tical resolution to quantify rare lesions at single-base resolution across the genome.

215 s the most promising approaches due to their single-base resolution and genome-wide coverage.

216 termination of the nick site and strand with single-base resolution at penetrance as low as one stran

217 fy a comprehensive, experimentally obtained, single-base resolution CGI catalog.

218 alyses of human and mouse methylomic data at single-base resolution confirm that sloping shores are u

219 efore, knowing cellular RNA modifications at single-base resolution could provide important informati

220 le stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide.

221 rack, an efficient mechanism for visualizing single-base resolution DNA methylation data on a genome

222 Single-base resolution DNA methylation measurements were

223 We describe large-scale single-base resolution DNA methylation profiling on a di

224 nce genome assemblies and methods to profile single-base resolution DNA methylation states, DNA methy

225 pproaches for locating alkylation adducts at single-base resolution in DNA could enable new technolog

226 quencing (CAB-Seq) that can detect 5caC with single-base resolution in DNA.

227 quantitatively locate 5mC and 5hmC marks at single-base resolution in genomic DNA.

228 cificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex

229 A methylation and hydroxymethylation maps at single-base resolution in human normal liver and lung as

230 equencing to evaluate the mutational load at single-base resolution in individual gene-corrected huma

231 ytosine (5hmC) and 5-formylcytosine (5fC) at single-base resolution is important to understand their

232 This study provides the first single-base resolution map of the mammalian cardiac DNA

233 ylation (gbM) within exons, we have gathered single-base resolution methylome data that span the phyl

234 Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptom

235 Herein, we obtained the DNA methylomes at single-base resolution of Madin-Darby canine kidney cell

236 n electrophoresis ("micelle-ELFSE") provides single-base resolution of Sanger sequencing products up

237 However, genome-wide detection of 5fC at single-base resolution remains challenging.

238 how a much-conserved synteny, whereas at the single-base resolution there are considerable species di

239 7 DNAP at the replication fork junction with single-base resolution to create a structural model that

240 aneous detection of m(5)C, Psi, and m(1)A at single-base resolution transcriptome-wide.

241 molecule electronic DNA sequencing data with single-base resolution were obtained.

242 epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed

243 By generating single-base resolution, allele-specific DNA methylomes f

244 quantitative method to decode 5fC in DNA at single-base resolution, based on a selective chemical re

245 rate methylome maps for four sample types at single-base resolution, identify a link between DNA meth

246 To interrogate 6mA sites at single-base resolution, we report DA-6mA-seq (DpnI-Assis

247 traploids and their diploid-progenitors at a single-base resolution.

248 can discriminate between viral strains with single-base resolution.

249 is method generated a genome-wide 5fC map at single-base resolution.

250 cation of cytosine DNA methylation states at single-base resolution.

251 eq), a method that directly maps 5fC/5caC at single-base resolution.

252 ze the methylomes of Dnmt2-only organisms at single-base resolution.

253 o measure the methylation of whole genome at single-base resolution.

254 criptional system of yeast mitochondria with single-base resolution.

255 ns simultaneously, transcriptome-wide and at single-base resolution.

256 lecular nature of Cas activity in cells with single-base resolution.

257 ntaining multiple different modifications at single-base resolution.

258 ylation (DmM) sites from MeRIP-Seq data at a single-base resolution.

259 he unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this

260 Here we show that the single base-resolution DNA methylome from adult mouse de

261 and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-speci

262 , and primordial germ cell (PGC), as well as single-base-resolution maps of oxidized cytosine bases f

263 Here, we report single-base-resolution whole-genome DNA methylomes, mRNA

264 Speed, single-base sensitivity and long read lengths make nanop

265 Clear identification of DNA with single-base sensitivity and the observation of a hybridi

266 C) methylation events at localized sites and single-base sensitivity.

267 ual specificity of the T-box is allowed by a single base shift on the SL from one overlapping codon t

268 h as the uplink from many mobile phones to a single base station.

269 mology tool and provides a means to identify single base structural changes in dsDNA.

270 Whole genome sequencing revealed a single base substitution in Dde_2265, the sulfate adenyl

271 k clusters in two counties were defined by a single base substitution in the viral genome.

272 Each mutational lesion (single base substitution or deletion) extended the fabK

273 Single base substitution signatures SBS85, SBS37, and SB

274 is and candidate genes for causing the major single-base substitution in cancer-associated DNA mutati

275 Family 1 had a single-base substitution that led to the replacement of

276 m the remains and one living relative, and a single-base substitution when compared with a second rel

277 which codons are mutually exchangeable by a single-base substitution.

278 We identified 49 single-base-substitution, 11 doublet-base-substitution,

279 Single base substitutions (SBSs) and insertions/deletion

280 mparison, we characterized 54 signatures for single base substitutions (SBSs), 11 for doublet base su

281 se substitutions are not due to two adjacent single base substitutions but likely occur as single gen

282 Single base substitutions predominated including frequen

283 ted diseases have been found to be caused by single base substitutions, small insertions or deletions

284 kely to be due to both inherited and somatic single base substitutions.

285 ancers, where each signature is a pattern of single base substitutions.

286 g acute infection is predominantly fueled by single-base substitutions and is limited by treatment in

287 facilitate the high-fidelity introduction of single-base substitutions via HDR following co-delivery

288 nts, enabling isolation of mutant lines with single-base substitutions without antibiotic selection.

289 eosarcomas exhibit a specific combination of single-base substitutions, LOH, or large-scale genome in

290 f these were derived from GGX for glycine by single-base substitutions.

291 rtiary interactions in a group I ribozyme by single-base substitutions.

292 In addition, we found that FNs induced more single base than large deletions, and that these single

293 ation data may be viewed at any scale from a single base to an entire chromosome.

294 us to dissect the contribution of different single bases to the excited state.

295 comW bypass mutations and mapped them to 10 single-base transitions, all within rpoD, encoding the p

296 omain motions of NS3 helicase and reproduced single-base translocation of NS3 helicase along ssDNA in

297 contains high-quality 3'-UTR data mapped at single-base ultraresolution for 23,084 3'-UTR isoform va

298 We further fine-mapped and validated a single-base variant that modulates YY1 binding and the a

299 nomics to predict the impact of all possible single-base variants and deletions.

300 ysis is highly suitable for the detection of single-base variants and small insertions or deletions.