ライフサイエンスコーパス: base substitution

1 codons are mutually exchangeable by a single-base substitution.

2 rganisms, primarily because of a low rate of base substitution.

3 h compound through trinucleotide patterns of base substitution.

4 te-directed mutagenesis, usually by a single-base substitution.

5 with the promoter is weakened by a promoter base substitution.

6 is explored by temperature jump kinetics and base-substitution.

7 effect on deletions, simple frameshifts, or base substitutions.

8 ing frameshifts, deletions, duplications and base substitutions.

9 were derived from GGX for glycine by single-base substitutions.

10 gnificance of the G runs, we altered them by base substitutions.

11 f previously reported capreomycin resistance base substitutions.

12 ns, whereas 10.0% showed semitargeted single-base substitutions.

13 e greater than nucleotide-specific rates for base substitutions.

14 2-11 of the p53 gene where we identified 19 base substitutions.

15 where each signature is a pattern of single base substitutions.

16 as the potential to detect very rare de novo base substitutions.

17 be due to both inherited and somatic single base substitutions.

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

19 We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clust

20 (4.6%) (mostly small deletions) and multiple-base substitutions (2.7%) also were detected.

21 nome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 re

22 fied 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17

23 Also, the level of semitargeted single-base substitutions 5' to the lesion was increased and 3'

24 directional sequencing identified the single-base substitution +57C>T in miR-184.

25 ectrum of mutations was predominantly G to T base substitutions, a result that is consistent with pre

26 Two base substitutions, A1913U and mU1915G, and a single bas

27 Here, the pathogenesis-associated base substitutions A3243G, T3250C, T3271C, A3302G and C3

28 None of these species-based substitutions affected the ability of alphaIIbbeta

29 In the present study, we used base substitution analyses to assess the importance of i

30 Base substitution analysis showed that [4Fe-4S]-NsrR rec

31 deletion of this region and a site-specific base substitution and a 3-base deletion in the CrfA comp

32 m in which T-->C is the most frequent single-base substitution and differs significantly from the clo

33 by high-fidelity polymerases and induce both base substitution and frame-shift mutations.

34 This dNTP-stabilized misalignment reduced base substitution and frameshift deletion fidelities.

35 and the gyrB gene leading to Nal(r) and for base substitution and frameshift mutations that occur in

36 eading and mismatch repair (MMR) can lead to base substitution and frameshift mutations.

37 thesis polymerases leads to large numbers of base substitution and frameshift mutations.

38 is shown here to limit reverse transcriptase base substitution and indel 'errors' in the run of A's i

39 to genome rearrangements and revealed twelve base substitution and six rearrangement signatures.

40 Base substitutions and abasic replacements at the LTR te

41 characterized by enhancement of transversion base substitutions and certain (-1) frameshift mutations

42 induced psoralen-pcPNA mutations were single-base substitutions and deletions at the predicted pcPNA-

43 We also present evidence for base substitutions and deletions introduced to minisatel

44 reas semitargeted mutations included several base substitutions and deletions near the DpC lesion.

45 Quantitative analysis of base substitutions and deletions occurring at the lesion

46 enesis of the targeted crosslinks results in base substitutions and deletions.

47 olished, leading to a great decrease in both base substitutions and deletions/insertions of 1-3 nucle

48 rameshift that is accompanied by one or more base substitutions and depends completely on the activit

49 DNA mismatch repair (MMR) genes elevate both base substitutions and insertions/deletions in simple se

50 infection is predominantly fueled by single-base substitutions and is limited by treatment initiatio

51 ude nucleoside insertions and deletions, and base substitutions and modifications.

52 using a mutation model with a wide range of base substitutions and rearrangements.

53 sease-associated mutations constitute single-base substitutions and short deletions and/or insertions

54 The performance of OpEx for high-quality base substitutions and short indels in both small and la

55 ro for L612M pol delta are elevated for both base substitutions and single base deletions but in a hi

56 s in single-stranded DNA to uracils, causing base substitutions and strand breaks.

57 els is approximately 1/12th of the number of base substitutions and the average length of the indels

58 ajority of mutations that fixed (82.4%) were base substitutions and we failed to find any signatures

59 h the gene copy number increases followed by base substitutions and, finally, contraction of the gene

60 n, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion si

61 were hypermutated, with a high frequency of base substitutions, and an especially large relative exc

62 Finally, we show that while regenerant base substitutions are a likely major genetic cause of t

63 with the modified nucleotides, and specific base substitutions are dramatically reduced or eliminate

64 In both germline and somatic mutations, base substitutions are more abundant in regions of close

65 enced cancers reveals: (i) that most doublet base substitutions are not due to two adjacent single ba

66 tant DNA fragments, each containing a single base substitution, are achieved using both single- and 1

67 We also observed that low level base substitution artifacts could be introduced when pre

68 from the susceptible isolate revealed a one-base substitution at nucleotide position 1449 which resu

69 ncrease in the frequency of C to G or G to C base substitutions at a specific site within the cII tar

70 tain sequence contexts, and generates single base substitutions at an average rate of 2.4 x 10(-3), c

71 our analyses of human DM1 alleles containing base substitutions at CTCF-binding motifs indicate that

72 DNA from these tumors contained T>G base substitutions at GTG trinucleotides.

73 Pol also generates certain base substitutions at high rates within sequence context

74 It appeared that the majority of the base substitutions at or near the cross-links resulted f

75 nd ihfA by examining the effects of multiple base substitutions at sbyA and ihfA on binding and plasm

76 (2)t(3)T(4)G(5)G(6)G(7)G(8) repeat show that base substitutions at some sites do not substantially de

77 of property-conserving and property-altering base substitutions at the codon level by means of finite

78 ssociated with all individual amino acid and base substitutions at the interface.

79 e we examine the effect of single and double base substitutions at these positions on plasmid mobiliz

80 biotechnology tool emerged when a structure-based substitution at Asp-207 was shown to be an infrare

81 titutions are not due to two adjacent single base substitutions but likely occur as single genomic ev

82 sis causes the majority of genotoxin-induced base substitutions, but averts larger deletions.

83 A in the context of BIR without formation of base substitutions, but instead this pathway frequently

84 del8bp) in exon 6, as well as a heterozygous base substitution (c.1208G-->A) in exon 11 that causes a

85 The results support the original idea that a base substitution can originate from a mismatch having W

86 In the low-transcription strain base substitutions comprised the majority (64%) of mutat

87 atic analysis of mutant proteins showed that base substitutions conferred increased enzymatic activit

88 rrow down the possibilities, 7-deaza adenine base substitutions (dA-->7) were engineered into homo-(d

89 le base substitutions (SBSs), 11 for doublet base substitutions (DBSs) and 16 for small insertions an

90 stem that we developed in E. coli to monitor base substitutions, defining 33 base change substitution

91 We observed divergent spectra of single base substitutions derived from general and inducible hy

92 C base pairs in the supF gene were the major base substitution detected in all cell lines.

93 spectrum of fast-neutron (FN)-induced single base substitutions differed substantially from those of

94 flaA, and atpA) revealed a approximately 2% base substitution difference, on average, between the tw

95 Probes complementary to two base substitutions displayed the highest average specifi

96 ority of both spontaneous and damage-induced base substitutions during BIR.

97 Furthermore, the base substitution error frequency of the exonuclease-def

98 ntrinsic to four human DNA polymerases whose base substitution error rate during gap-filling DNA synt

99 type Pol epsilon proofreads at least 92% of base substitution errors and at least 99% of frameshift

100 fact, combined with the high rate of single base substitution errors and complex mutations observed

101 h high-fidelity polymerases that rarely make base substitution errors.

102 -crRNA) sequence with specific stem-loop G-C base substitutions exhibit increased editing efficiencie

103 Together, the simulation and base substitution experiments predict that the coralyne-

104 The polymerase activity of hPol has a high base substitution fidelity (10(-4)-10(-7)) resulting fro

105 hree-subunit Pol delta does indeed have high base substitution fidelity for the 12 possible base-base

106 NA polymerase beta-DNA complex, although the base substitution fidelity of both polymerases is 10(-)(

107 proteins in the BER reaction may enhance the base substitution fidelity of DNA polymerase beta during

108 The extremely low base substitution fidelity of human Rev1 (10(0) to 10(-5

109 However, the average base substitution fidelity of pol zeta is substantially

110 Under these conditions, the base substitution fidelity of polymerase beta-dependent

111 ther indicate that proofreading enhances the base substitution fidelity of the wild type enzyme by at

112 The base substitution fidelity of this mutant was kineticall

113 ype Pol delta and Pol epsilon both have high base substitution fidelity, Pol delta is much less accur

114 s increased the DNA binding affinity and the base substitution fidelity.

115 ity, implies that Pol delta should have high base substitution fidelity.

116 ajor determinant of polymerase conformation, base-substitution fidelity, and abasic-site translesion

117 This base substitution forms a valine-glutamic acid-glycine a

118 ion bypass was accompanied by an increase in base substitution frequency for the base preceding the l

119 ination of the ATG initiation codon by a one-base substitution (G > A) did not result in a complete l

120 t is, newly arisen and not inherited) single-base substitution, G608G(GGC > GGT), within exon 11.

121 A C to A base substitution has been identified at -571 bp in the

122 nucleotides previously described, but a 100% base substitution has never been observed to have been m

123 overproducing Smu10A displays one prominent base substitution hotspot in the rpoB gene, which coinci

124 t in the rpoB gene, which coincides with the base substitution hotspot we have observed in cells that

125 There are prominent base substitution hotspots in rpoB in both D. radioduran

126 The base substitution in agaF, which encodes EIIA(Aga/Gam) o

127 candidate genes for causing the major single-base substitution in cancer-associated DNA mutations.

128 Whole genome sequencing revealed a single base substitution in Dde_2265, the sulfate adenylyltrans

129 Deep sequencing identified a single-base substitution in guanylate cyclase 2D, membrane (ret

130 olster evidence for a relatively low rate of base substitution in modern humans and highlight a centr

131 A single base substitution in SMN2, c.859G>C,, was identified in

132 d infectivity of CM972 and detected a single base substitution in TC_0236 in CM3.1 that may be respon

133 Bacterial one-hybrid experiments showed that base substitution in the expanded motif either increase

134 ers in two counties were defined by a single base substitution in the viral genome.

135 ry DNA strands to account for any particular base substitution in vivo (e.g. T-dGMP or A-dCMP for T t

136 nerates -1 frameshifts in "long" repeats and base substitutions in "short" repeats.

137 sequences of 518 kinase genes, revealing 90 base substitutions in 71 genes.

138 lonA was weakly mutagenic inducing all three base substitutions in approximately equal frequency, whe

139 Viral RNA with base substitutions in both S1 and S2 failed to produce i

140 mina RNA-seq method that can assess noncoded base substitutions in mRNA at 10(-4)-10(-5) per base fre

141 t studies indicate that cumulative levels of base substitutions in mtDNA can be very low even in old

142 wever, there was a decrease in tandem double-base substitutions in Polzeta(+/-) Poleta(-/-) cells com

143 The rate of base substitutions in recent evolutionary history shows

144 ) but not Msh3 is involved in generating A/T base substitutions in somatic hypermutation.

145 We have accumulated over 20 single-base substitutions in T. thermophilus 16S and 23S rRNA,

146 The impact of specific base substitutions in the A-site RNA constructs on bindi

147 olzeta can simultaneously introduce multiple base substitutions in the absence of an accompanying fra

148 ase substitutions within the microsatellite, base substitutions in the flanking regions, indels in th

149 Single-base substitutions in the fnr and resA promoters were pe

150 Most of the R2 base substitutions in the forward mutation assay were ca

151 Notably, the increase of base substitutions in the homologous recombination-defic

152 Base substitutions in the major eEF1A binding site or ad

153 vivo transcription termination of systematic base substitutions in the T/U-tract of the pyrBI attenua

154 Most of the base substitutions in these regions caused large decreas

155 Base substitutions in these regions were almost exclusiv

156 e Ser codon boxes, differing by at least two-base substitutions, in contrast to Leu and Arg, of which

157 red a low frequency of deletions relative to base substitutions, indicating that removal of retrotran

158 mage and DNA repair processes that result in base substitutions, insertions and deletions or structur

159 ing thousands of somatic mutations including base substitutions, insertions and deletions, rearrangem

160 r how the primordial mutational processes of base substitutions, insertions, and deletions influence

161 comprise a distinctive molecular spectrum of base substitutions, insertions, and deletions that proba

162 re DNA sequences that are 100% identical (no base substitutions, insertions, or deletions) and locate

163 can result in the Rif(r) phenotype by single-base substitution is more limited than in certain other

164 In contrast, the frequency of base substitutions is dependent on the activity of ERCC1

165 eriod, the ratio of nonsynonymous/synonymous base substitutions is unusually high, suggesting a rapid

166 as an ethyl-methane sulfonate derived single base substitutions, is limited by array coverage and sen

167 mas exhibit a specific combination of single-base substitutions, LOH, or large-scale genome instabili

168 d out using the BLOSUM matrices or structure-based substitution matrices SDM and HSDM when validated

169 HMMSUM (HMMSTR-based substitution matrices) is a new model for structur

170 However, maximum likelihood codon-based substitution models did not detect any site under

171 in bacterial and mammalian cells, leading to base substitutions (mostly M(1)dG to dT and M(1)dG to dA

172 roximately 70% of mutations comprised single-base substitutions, mostly at G.C base-pairs, with the r

173 The high rate of base substitution mutagenesis demonstrated by our experi

174 Through deletion and base substitution mutagenesis we identify GCAATTA elemen

175 esults in a large increase in frameshift and base substitution mutagenesis.

176 is of the narK2/X promoter region revealed a base substitution mutation in all tested BCG strains and

177 Spontaneous base substitution mutation rates increased sevenfold upo

178 y elevated frameshift mutation rates but not base substitution mutation rates.

179 h, fully half of spontaneous frame-shift and base-substitution mutation during starvation also requir

180 While base-substitution mutation rates are similar to those in

181 Established base-substitution mutation rates in eukaryotes range bet

182 de more rapid than the rate of Y-chromosomal base-substitution mutation, and given assumptions about

183 Strand realignment results in a base-substitution mutation, minimizing generation of mor

184 ted by structural studies possibly to permit base substitution, mutation of this U to C greatly inhib

185 melanomas with mutations had 1 to 4 UV type base substitution mutations (occurring at adjacent pyrim

186 cer genome contains more than 17,000 somatic base substitution mutations and bears the imprint of a d

187 ants did not show an increase in the rate of base substitution mutations by the CAN1 forward mutation

188 Base substitution mutations identified in the current st

189 (MMS), and showed that MMS also induces more base substitution mutations in BRCA1/2-deficient cells.

190 Single base substitution mutations in codons 248 and 273 of TP5

191 oxidative stress conditions the majority of base substitution mutations in ssDNA are caused by erron

192 to rifampicin-resistance assay that detects base substitution mutations in the essential rpoB gene,

193 s of variants of EBV strain B95.8 containing base substitution mutations in this ZIIR element.

194 All APOBEC3G-induced base substitution mutations mapped to the nuclear CAN1 g

195 We estimate that approximately three base substitution mutations occur per cell per cell-doub

196 rived a good direct estimate for the rate of base substitution mutations on the human Y chromosome.

197 This is true for base substitution mutations that occur in the rpoB gene

198 Reverse transcriptase (RT) derived base substitution mutations were commonly found at sites

199 anti-[BP]-N(2)-dG adduct can cause all three base substitution mutations, and the SOS response in Esc

200 microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast funct

201 ild type but did show an altered spectrum of base substitution mutations, including an increased accu

202 f small insertion/deletion, duplication, and base substitution mutations, including G:C>T:A, G:C>A:T,

203 h together constitute over one-fourth of all base substitution mutations, show genomic distributions

204 xtent of the immunogenicity of nonsynonymous base substitution mutations.

205 ivation of Pol epsilon proofreading elevates base-substitution mutations and accelerates a unique spe

206 aracterize hundreds of spontaneously arising base-substitution mutations in 10 Caenorhabditis elegans

207 which directed the creation of deletant and base-substitution mutations of MuRF1 promoter constructs

208 significant effect on frame shifts and most base-substitution mutations.

209 The accumulation of base substitutions (mutations) not subject to natural se

210 Base substitution occurs at a high rate at CpG dinucleot

211 ge this is the first example where a general base substitution of an Asp for His preserves both the s

212 C>T in exon 3 of CPT1C, which determined the base substitution of an evolutionarily conserved Cys res

213 measure directly one mutation rate, that of base substitutions on the human Y chromosome.

214 e entire 2.2-Mb interval identified 2 single-base substitutions, one in an intergenic region and a se

215 ll as all mismatches, including three single-base substitutions, one microdeletion, one microinsertio

216 Motility-specific mutants resulted from base substitutions only in the fliC-coding region.

217 Mutation of the bulge by base substitution or deletion showed that the size of th

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

219 y distinct mutational routes that resolve to base substitutions or deletions.

220 mer extension is also observed, resulting in base substitutions or even +1 frameshifts.

221 reengineered reporters that detect specific base substitutions or frameshifts in lacZ with the rever

222 complex mutations comprising multiple nearby base substitutions or insertion-deletions.

223 anscription conditions, AID can cause single-base substitutions or MCMs.

224 ut the contribution of COSMIC signature 3 to base substitutions, or a combined measure of different f

225 We found that base substitutions outnumber frameshift mutations, as se

226 ssociated with a mutation rate of 7 x 10(-9) base substitutions per site per generation, growth at st

227 l mutation burdens that increase at about 29 base substitutions per year and that are many-fold lower

228 , have indicated that, in addition to single-base substitutions, Polkappa generates single-base delet

229 Second, specific tandem base substitutions (predominantly GC>TT/AA) occur in spe

230 Single base substitutions predominated including frequent A:A (

231 We assess the similarity of base substitution processes, described by empirically de

232 We examined the neutral base substitution rate by measuring the sequence diverge

233 The neutral mutation rate is equal to the base substitution rate when the latter is not affected b

234 Using base substitution rates in intronic regions as a calibra

235 Analysis of synonymous base substitution rates indicated that the triplicated B

236 Analysis of synonymous base substitution rates within modeled genes revealed a

237 from plants and among the lowest spontaneous base-substitution rates known in eukaryotes.

238 Mechanisms of base substitution, rates of accumulation, and the amount

239 most changes in repeat number occur through base substitutions rather than slippage, and the relativ

240 us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE

241 igins establish a strand bias in the rate of base substitutions resulting from replication of unrepai

242 aled a remarkable diversity of deletions and base substitutions resulting in at least 34 different re

243 Overall, we introduced 133,313 base substitutions, resulting in the rewriting of 123,56

244 Single base substitutions (SBSs) and insertions/deletions are c

245 n, we characterized 54 signatures for single base substitutions (SBSs), 11 for doublet base substitut

246 imized CSCE protocol detected 93 of 95 known base substitution sequence variants.

247 vely parallel DNA sequencing to characterize base substitutions, short insertions and deletions (inde

248 , we find a universal HR deficiency-specific base substitution signature that is similar to COSMIC si

249 Single base substitution signatures SBS85, SBS37, and SBS39 wer

250 ty followed by those complementary to single base substitutions, single base deletions and single bas

251 Attenuation of age-dependent increases in base substitutions, small DNA insertions/deletions, and

252 eases have been found to be caused by single base substitutions, small insertions or deletions (<1Kb)

253 tational landscapes, differently composed of base substitutions, small insertions/deletions (InDels),

254 alian translesion DNA polymerase eta: tandem base substitutions, strand slippage, and small insertion

255 entify loci containing elevated densities of base substitutions suggestive of horizontal sequence tra

256 n is known to increase in older mothers, and base substitutions tend to go up with paternal reproduct

257 wever, we found a higher frequency of single base substitution than deletion mutations.

258 ion segment of the kinase domain as a single-base substitution that converts a valine to glutamic aci

259 Family 1 had a single-base substitution that led to the replacement of one gly

260 de polymorphism of the NTH1 gene is a G-to-T base substitution that results in the NTH1 D239Y variant

261 Base substitutions that decreased the downstream adenine

262 f 3HT and 5HT complexes is blocked by single-base substitutions that disrupt individual intermolecula

263 e a high-affinity hnRNP A1 binding site, and base substitutions that disrupt it restore exon 7 inclus

264 Base substitutions that disrupt the base triples reduce

265 However, base substitutions that prevent formation of the antiter

266 ssense mutations, one frameshift, one single base substitution to a stop codon and one dinucleotide t

267 Comparison of the effects of nonpolar base substitution to the effects of abasic lesions repor

268 (23F)-1) multidrug-resistant lineage enabled base substitutions to be distinguished from polymorphism

269 We have shown that in cell culture, base substitutions to mimic editing at different combina

270 On average, <1 coding base substitution/tumor is lost through negative selecti

271 of point mutation and skewed distribution of base-substitution types in the mitochondrion, a very hig

272 ate the high-fidelity introduction of single-base substitutions via HDR following co-delivery with a

273 A single base substitution was detected in spl11, which results i

274 GENETIC STUDIES: A unique homozygous T to C base substitution was found in exon 6 in the vitamin D r

275 Surprisingly, when an additional G to A base substitution was introduced at position 3 of NHEIII

276 reover, a clear strand bias among UV-induced base substitutions was observed in wild-type cells that

277 on-gain alleles with that for derived single-base substitutions, we also provide evidence that newly

278 und no significant effect of parental age on base substitutions, we found that frameshift mutations a

279 '- and/or 3'-ends and by making compensatory base substitutions, we found that two elements interfere

280 Using somatic base substitutions, we reconstructed the early cell divi

281 DNA could lead to in vivo mutations, if this base substitution were efficiently elongated.

282 caused by poly-C tract variability; however, base substitutions were also prevalent, as follows: 14.7

283 Arachidonic acid-induced base substitutions were consistent with the presence of

284 All but one base substitutions were G:C to A:T, their distribution b

285 nternal or DNA 3'-end-directed cleavage, and base substitutions were tested at specific nucleotide po

286 However, we report that two-thirds of single base substitutions were tolerated without loss of activi

287 emains and one living relative, and a single-base substitution when compared with a second relative.

288 3T cells, 5.8% of progeny contained targeted base substitutions, whereas 10.0% showed semitargeted si

289 ain mutations that we identified were single-base substitutions, whereas all of the PEST domain mutat

290 on (Zdhhc13luc) was identified as a nonsense base substitution, which results in a premature stop cod

291 cyclophosphamide and etoposide induce extra base substitutions with distinct spectra.

292 in mutagenesis, (+/-)-anti-BPDE induced 85% base substitutions with predominant G --> C followed by

293 Single and double base substitutions within adenine tracts modulate CPC de

294 s at least 2-fold more rapid than synonymous base substitutions within genes.

295 erator mutants, we found that several single base substitutions within the 14 bp recA operator sequen

296 interactions are absent within the loop, and base substitutions within the loop that favor such inter

297 Size homoplasy was apparent, caused by base substitutions within the microsatellite, base subst

298 ns and deletions, we assume HIV-1 evolves by base substitution without selection pressure during the

299 abling isolation of mutant lines with single-base substitutions without antibiotic selection.

300 cur at rates orders of magnitude higher than base substitutions, yet our understanding of the mechani