ライフサイエンスコーパス: base pair

1 base pair is favored over the non-mutagenic base pair.

2 the major groove as in a normal Watson-Crick base pair.

3 s from the wild-type allele at only a single base pair.

4 te between DNA ligands differing by a single base pair.

5 backbone and hydrogen bonding of an adjacent base pair.

6 itional letters that form a third, unnatural base pair.

7 onical Watson-Crick base pair or a nonplanar base pair.

8 f in canonical nucleic acid structure is the base pair.

9 of substrates containing even one mismatched base pair.

10 ectively cleaving the A base from the A:oxoG base pair.

11 base pair, the oxidation product of the C:G base pair.

12 (I) is more flexible in pairing with natural base pairs.

13 resulting from the association of G:C or G:T base pairs.

14 ochondrial DNA (kDNA), comprising of >70% AT base pairs.

15 hin a total genomic load of more than 15,000 base pairs.

16 s, which describe only the Watson-Crick (WC) base pairs.

17 f helices rather than counting and combining base pairs.

18 ecies form hydrogen-bonded Watson-Crick-like base pairs.

19 A:T base pairs than for those with only G:C base pairs.

20 when compared to MORFs composed of 20 and 25 base pairs.

21 agated and retrieved by the formation of two base pairs.

22 s with hundreds of taxa and thousands of DNA base pairs.

23 et of 349 primates taxa with over 60,000 DNA base pairs.

24 as the ligand threads between disrupted DNA base pairs.

25 the latter rapidly localize on two adjacent base pairs.

26 g miniduplex containing two out-of-phase G.C base pairs.

27 ular genetic map, a distance of >/=2 million base pairs.

28 6 putative lncRNAs with a mean length of 695 base pairs.

29 loops and a core built of an even number of base pairs.

30 ly connected linear sequence of nucleic acid base pairs.

31 n-pairing and re-ordering of its central A:T base pairs.

32 an 8-bp target site consisting solely of A:T base pairs.

33 ring a 50%-GC segment to have no adjacent GC base pairs.

34 phyla, averaging one site every 2,000-4,000 base pairs.

35 trands form any significant amount of native base pairs.

36 e-pairs and maximum lengths reaching 100,000 base- pairs.

37 ability to participate in Watson-Crick (W-C) base pairing.

38 fully determined by underlying Watson-Crick base pairing.

39 nalogue that can participate in Watson-Crick base pairing.

40 an extended triangle strand by Watson-Crick base pairing.

41 ements, do not participate in intermolecular base pairing.

42 is the alignment of the two strands prior to base pairing.

43 ping the sequences involved in inter-segment base-pairing.

44 Furthermore, the two ZRE elements differ at base pair 6 (C:G versus G:C), forming a pseudo-symmetric

45 quartile, with an average difference of 170 base pairs (95% confidence interval: 4, 340).

46 crimination between two structurally similar base pairs: A:oxoG and A:T.

47 urring within fragile zones of less than 200 base pairs account for the formation of the most common

48 e minor groove tetrads and the nearby C:C(+) base pairs affords a strong stabilization, which results

49 separation of a few PAM-proximal protospacer base pairs allowing initial target interrogation by guid

50 egments that are strung out over millions of base pairs along the chromatin fiber to find each other

51 scribe an algorithm for performing frequency-based pairing (alphabetr) that accommodates CDR3alpha- a

52 identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longe

53 nd A6 bases form an intramolecular Hoogsteen base pair and directly contact WDR33.

54 inct DNA shape features, including six intra-base pair and six inter-base pair parameters and minor g

55 MR) pathway recognizes and repairs errors in base pairing and acts to maintain genome stability.

56 In RACER, base pairing and stacking interactions each provide an a

57 re by maximizing the number of complementary base pairs and minimizing the energy.

58 ude DNAzymes, G-quadruplexes, and mismatched base pairs and nanomaterials cover gold nanoparticles (G

59 We focus our analysis on the non-WC base pairs and on RNA modules.

60 Software to predict non-canonical base pairs and pairing probabilities is now provided as

61 A motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge.

62 display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T base

63 with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pa

64 Mismatched base-pairs and other factors that would perturb the geom

65 toward the mismatch compared to well-matched base pairs, and (ii) the excited state emission lifetime

66 eractions between adjacent codons and wobble base pairing are key.

67 Data obtained with handles of 370 and 70 base pairs are indistinguishable, but at low forces shor

68 c DNA miniduplexes, each containing just two base pairs, are investigated using time-resolved infrare

69 carbonyl symmetric and N1-carbonyl, N7-amino base-pairing arrangements.

70 structure by treating hydrogen bonds between base pairs as constraints.

71 ng RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interact

72 eal that G:C base pairs form faster than A:T base pairs because of faster conformational diffusion, p

73 ich recognizes a specific DNA target through base pairing between a synthetic guide RNA and DNA, outp

74 perone Hfq is an Sm protein that facilitates base pairing between bacterial small RNAs (sRNAs) and mR

75 ith homology to FinO, a factor that promotes base pairing between the FinP antisense sRNA and the tra

76 strand scission are driven by complementary base pairing between the guide RNA and target DNA, Cas9-

77 th high 3'-5' regioselectivity, Watson-Crick base pairing between the RNA monomers and the template i

78 She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer t

79 sses the expression of target mRNAs and that base-pairing between HSUR2 and miR-142-3p and miR-16 is

80 cats confirmed that cats homozygous for a 2 base pair (bp) deletion within IQ calmodulin-binding mot

81 We oxidized a 32 base pair (bp) double-stranded (ds) oligonucleotide repr

82 endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5-ATTTAAAT-3, and cle

83 ompass the majority of the approximately 270 base pairs (bp) of vector space required for shRNA expre

84 ocol generates short paired-end tags (2 x 20 base pairs (bp)) to detect two genomic loci that are far

85 fter 1 year of intervention (difference -163 base pairs (bp), p=0.001).

86 quencing for oligonucleotides longer than 20 base pairs (bp).

87 anonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with spars

88 pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor

89 a C:G base pair (G-Arg interaction) to a G:C base pair (C-Asp interaction).

90 that the catalytic cooperativity of the acid-base pair can be affected by two factors: (1) the compet

91 genomic rearrangements of up to one million base pairs can be generated by direct injection of CRISP

92 Human GROW1 contains a common base-pair change that decreases enhancer activity and co

93 We designed and de novo synthesized 536,024-base pair chromosome synV in the "Build-A-Genome China"

94 lly inherited and in humans contain a 16,569-base-pair circular genome (mtDNA) encoding 37 genes requ

95 ting transposable elements (TEs) through the base-pair complementarity.

96 is discovers novel modes of U2snRNA:pre-mRNA base-pairing conserved in yeast and provides insight int

97 pins with the same helix length but with G:C base-pair content varying from 0 to 100%, we determined

98 Molecular studies showed a 42-base pair deletion in exon 11 of the KIT gene that would

99 a conserved structural signature of the 180-base pair DNA fragment comprising the homeobox.

100 replicate a plasmid containing the unnatural base pair dNaM-dTPT3.

101 raphics tools lack built-in support even for base pairs, double helices, or hairpin loops.

102 tion in the MHC to a region of about 50 kilo base pairs, down from 1 mega base pairs in the previous

103 is-regulatory site located approximately 600 base pairs downstream of UAS1) through a loop structure

104 OBEC3H molecules at opposite ends of a seven-base-pair duplex interact extensively with both RNA stra

105 his has been attributed to a semi-dominant 7-base-pair duplication in the first exon of the forkhead

106 rt, the preferred use of certain nonstandard base pairs, e.g., U-G.

107 th-generation ABEs that convert targeted A*T base pairs efficiently to G*C (approximately 50% efficie

108 roove, the relative orientations of adjacent base pairs, etc.

109 e is stabilized by two hemiprotonated C:C(+) base pairs, flanked by two minor groove tetrads resultin

110 ucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the

111 uence is split into overlapping pentamers (5 base pairs) for calculating transcription factor-pentame

112 These results reveal that G:C base pairs form faster than A:T base pairs because of fa

113 Predicting the base pairs formed between two interacting sequences rema

114 The modifications conserve the coding and base-pairing functions of DNA, but add regulatory and pr

115 ermits adaptability to variations from a C:G base pair (G-Arg interaction) to a G:C base pair (C-Asp

116 We synthesize the 335 base-pair gene that encodes the green fluorescent protei

117 sequence pattern, a 3-nt bulge and G-A, A-G base-pairs, generates an angle of approximately 50 degre

118 gh kinetic stabilities of T-Hg(II)-T metallo-base pairs (half-lives = 0.3-1.3 h) perturbed dynamic pr

119 DNA base pairing has been used for many years to direct the

120 vices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past

121 Metal-mediated base pairs have been extensively utilized in many resear

122 d methods for experimentally determining RNA base pairs have remained inaccurate.

123 uctures displaying noncanonical Watson-Crick base pairing, have recently emerged as key controllers o

124 g DSB end and its donor template share a 108-base-pair homology region and the donor carries differen

125 inding to DNA structures stabilized by inter-base-pair hydrogen bonding was observed.

126 The predictable chemistry of Watson-Crick base-pairing imparts a unique structural programmability

127 and efficient participation of the unnatural base pair in decoding at the ribosome.

128 l human AlaRS-mischarged tRNAs have a G4:U69 base pair in the acceptor stem.

129 DB2277, specifically recognizes a single G*C base pair in the minor groove of mixed base pair sequenc

130 nates from pivoting at stacked non-canonical base pairs in a Family A three-way junction and bending

131 ce 'excited states' that form by reshuffling base pairs in and around non-canonical motifs.

132 fferent types of analysis across millions of base pairs in hundreds or thousands of isolates.

133 e corresponding duplex structures having G-C base pairs in place of the G-tetrads.

134 ce rapid making and breaking of miRNA:target base pairs in the 3' half of the seed region.

135 f about 50 kilo base pairs, down from 1 mega base pairs in the previous study.

136 Once the base pairs in these lesioned systems are broken, disloca

137 Conservation of RNA base pairing induces pairwise covariations in sequence a

138 the older individuals with the homozygous 18 base pair insertion.

139 In many cases, the base-pairing interaction is facilitated by the RNA chape

140 volved in monitoring the U2 BSRR-branch site base-pairing interaction.

141 g single-stranded RNA (ssRNA) free of strong base pairing interactions can be created either by confi

142 A components, establishing that Watson-Crick base-pairing interactions alone suffice for complex chem

143 erent means to assemble DNA-NPs-Watson-Crick base-pairing interactions and depletion interactions-and

144 Random base-pairing interactions between messenger RNAs and non

145 t specifically disrupt critical noncanonical base-pairing interactions in the crystal lattice leads t

146 of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structur

147 lative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted reg

148 t enables the programmable conversion of one base pair into another without double-stranded DNA cleav

149 uires in vivo transcription of the unnatural base pair into mRNA and tRNA, aminoacylation of the tRNA

150 MutM and MutY, DNA glycosylases that process base pairs involving 8-oxo-dGTP.

151 Notably, extension from the mutagenic base pair is favored over the non-mutagenic base pair.

152 The highly mutagenic A:8-oxoguanine (oxoG) base pair is generated mainly by misreplication of the C

153 This Lewis acid-base pair is initiated and preserved by disrupting the d

154 The A:oxoG base pair is particularly insidious because neither base

155 This observation of reverse Watson-Crick base pairing is further supported by thermal melting ana

156 extension from both 8-oxoG:dC and 8-oxoG:dA base pairs is 18- to 580-fold less efficient compared to

157 DNA base-pairing is the central interaction in DNA assembly.

158 density (i.e., the selection coefficient per base pair) is a key parameter underlying this relationsh

159 first appears to possess a low capacity for base pairing, it forms a thermodynamically stable struct

160 With these main-group element Lewis acid base pairs, it is not only possible to polymerize steric

161 This pattern of base pairing, known as RNA secondary structure, is criti

162 Most RNA molecules form internal base pairs, leading to a folded secondary structure.

163 Repeated sequences with >100 base pair lengths occupy more than 1% of bacterial genom

164 k to develop a method to locate deletions at base pair level using next-generation sequencing data.

165 ially indicating convergent evolution at the base pair level.

166 We designed and synthesized a 976,067-base pair linear chromosome, synXII, based on native chr

167 Molecular conductances of 10 base pair long homoduplexes of DNA, aeg-PNA, gamma-PNA,

168 equence readout of a polymerase-bound 20,000-base-pair-long DNA template within seconds from a sub-na

169 ion of ZF11 allows PRDM9c to recognize three-base-pair-longer sequences.

170 of Pgt virulent to Sr50 contained a 2.5 mega-base pair loss-of-heterozygosity event.

171 backbone chimeric duplexes that would impede base-pair mediated interactions (and functions).

172 he detection system could discriminate a one base pair mismatch (1BPM) target and was functional with

173 of detection of 1nM and can detect a single base pair mismatch between probe and complementary DNA.

174 Our data indicate that a single base pair mismatch in the invader stalls branch migratio

175 cyclization of DNA sequences that contain a base pair mismatch.

176 With every eighth base pair mismatched, repair was about 14% of that of co

177 With every sixth base pair mismatched, repair was still more than 5%.

178 nfluence of the cooperative effect on single base pair mismatches.

179 donor carries different densities of single-base-pair mismatches.

180 dyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA antico

181 s consistent with their 0.00065-Mbp (million base pair) mitochondrial barcodes and their ecological d

182 lariat reads are refined by U2snRNP/pre-mRNA base-pairing models to return the largest current data s

183 of apoptotic activity was observed for a 28 base pair MORF sequence when compared to MORFs composed

184 Most of the variable base pairs (N) also engage in H bonds with the protein.

185 4 (SL4) and interacts with both unpaired and base-paired nucleotides.

186 re, we compile folding information for every base pair of the genome that may be transcribed: coding,

187 PTC suppression is mediated by the base pairing of a near-cognate aminoacyl-tRNA with a PTC

188 to store and encode information arises from base pairing of the four-letter nucleobase code to form

189 thereby affecting only particular regions or base pairs of a gene.

190 olymerase II therefore navigates hundreds of base pairs of altered chromatin in the sense direction b

191 ome-wide dataset of more than half a million base pairs of DNA to test for a glacially induced burst

192 sign 60 circuits forEscherichia coli(880,000 base pairs of DNA), for which each DNA sequence was buil

193 in extant organisms we analyzed 6.4 trillion base pairs of metagenomic sequences and 24 903 microbial

194 her derivatives of MmeI and delineates which base pairs of the recognition sequence are more amenable

195 n complex during early elongation within 500 base pairs of the transcription start site and akin to i

196 , Hfq acts in a canonical pathway, promoting base-pairing of ArcZ sRNA with the mutS leader to inhibi

197 Base-pairing of U4 and U6 snRNAs during di-snRNP assembl

198 extra 201 deletions genome-wide, sized 1-100 base pairs often with microhomology at the junction.

199 dual conformational parameters revealed that base-pair opening - known to be important in strand sepa

200 ciation of the EF-G by providing alternative base-pairing options.

201 s bound in either the canonical Watson-Crick base pair or a nonplanar base pair.

202 t in the generation of short fragments (<150 base pairs) or highly branched long DNA products.

203 stance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA

204 including six intra-base pair and six inter-base pair parameters and minor groove width, is availabl

205 detailed insight into these Ag(I) -mediated base-pairing patterns in DNA, but also represents the fi

206 mutation rate of 1.45 +/- 0.05 x 10(-8) per base pair per generation in autosomal coding sequence, w

207 Our estimate for the mutation rate per base pair per generation is 1.05 x 10(-8), well within t

208 onversion rate of 8.75 +/- 0.05 x 10(-6) per base pair per generation.

209 ance of >/=10 kilobases at a velocity of 60 base pairs per second.

210 that the homeobox DNA has a characteristic 3-base-pair periodicity in the hydroxyl radical cleavage p

211 for genome-editing DNA in cells with single-base-pair precision, which allows novel in vitro models

212 from 36.8% to 57.8% in mean sensitivity for base pair prediction.

213 Cas1-Cas2 selectively binds to a splayed 30-base-pair prespacer bearing 4-nucleotide 3' overhangs.

214 is introduced that allows the estimation of base pairing probabilities for both canonical and non-ca

215 ach individual parameter change on predicted base-pair probabilities and secondary structures as comp

216 rgonaute (AGO) protein to target mRNAs via a base-pairing process (1) .

217 d to the methylation-elicited alterations in base pairing properties of the nucleobases, and the mech

218 frequently-occurring set of x seeds in an L-base-pair read in [Formula: see text] operations on aver

219 minate between alleles differing by a single base-pair regardless of the position in the guide is dem

220 The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a

221 However, structural basis underlying these base pairs remains poorly understood.

222 hort-patch base excision repair of 8-oxoG:dA base pairs requires human DNA polymerase beta (hPolbeta)

223 Furthermore, base pair resolution analysis of cytosine methylation an

224 the rapid identification of CGRs with single base pair resolution.

225 r small drugs and large proteins with nearly base-pair resolution in an unbiased fashion.

226 Chromatin profiling at base-pair resolution in neuronal nucleosomes extracted f

227 Together, our results provide the first base-pair resolution map of transcription elongation in

228 g precise chromosome modifications at single base-pair resolution with an efficiency of >40%, without

229 disequilibrium in Drosophila, we obtain near base-pair resolution, resolving causal mutations in deve

230 d 1 cell line to detect and characterize, at base-pair resolution, SRs of the PDL locus (9p24.1; harb

231 e-wide variants in single mammalian cells at base-pair resolution.

232 phenotypic consequences of mutations at the base-pair resolution.

233 his study, we provide the first genome-wide, base pair-resolution map of 6mA in Tetrahymena by applyi

234 s associated with isoguanine and isocytosine base pairing, respectively, over the canonical nucleobas

235 athways to generate mutations at G-C and A-T base pairs, respectively.

236 n factor that recognizes two versions of a 7-base pair response element, either 5- GAG CA-3 or 5- GAG

237 related to function, yet methods to identify base-paired RNA strands in a transcriptome-wide manner i

238 e, nucleic acid probes based on Watson-Crick base-pairing rules are also being widely applied in bios

239 d operate through predictable and designable base-pairing rules, allowing the effective in silico des

240 engages in extensive interactions with a 15-base pair segment of the distorted nucleosomal DNA doubl

241 e further show that a highly conserved eight-base-pair segment of SL3 is not only necessary for Pxr t

242 the Cas1-Cas2 protein complex captures 30-40 base pair segments of foreign DNA and catalyzes their in

243 e G*C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT.

244 gidity of the poly(rA/dT) tract and leads to base-pair slippage of this sequence upon deformation int

245 half-sites separated by a variable number of base pairs (spacers).

246 introduce a new strategy to characterize the base-pair-specific thermal dissociation mechanism of DNA

247 GA loop, together with particular first stem base pairs, specifies their hydrolysis without involving

248 We were able to recover base-paired sRNA-mRNA duplexes in association with RNase

249 owever, not all bacteria encode Hfq and some base-pairing sRNAs do not require Hfq raising the possib

250 o smaller substructures composed of a single base-pair stack, which allows us to leverage existing ap

251 ry structure motifs composed of specific two base-pair stacks, we identified significantly enriched o

252 ngineer mouse strains with reciprocal single base pair substitutions (B6-Cdh23(c.753A>G) and 129S1-Cd

253 , the ligase must efficiently join correctly base-paired substrates, while discriminating against the

254 TPs) into DNA approximately once every 2,000 base pairs synthesized.

255 Increasing the number of base pairs targeted by synthetic molecules strengthens t

256 entary strand DNA hybridization of 9- and 10-base pair targets, where the tracer assay predicts the s

257 being 50% longer for hairpins with only A:T base pairs than for those with only G:C base pairs.

258 tructure, which is stabilized by dynamic G:G base pairs that transit between N1-carbonyl symmetric an

259 rated mainly by misreplication of the C:oxoG base pair, the oxidation product of the C:G base pair.

260 omposed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk

261 low-abundance species form Watson-Crick-like base pairs, their conformation could not be directly ded

262 ary ends, and thus instead of assembling via base-pairing, they can interact by pi-stacking of their

263 e OrzO sRNA can inhibit zorO translation via base pairing to the of the EAP region.

264 ral optimization and extension of the target base pairs to allow more specific stain-ing of telomeres

265 etry of canonical G.C and A.T/U Watson-Crick base pairs to discriminate against DNA and RNA mismatche

266 From DNA base pairs to drug-receptor binding, hydrogen (H-)bondin

267 -assembles via Crick-Watson and noncanonical base pairs to form crystals.

268 ability to efficiently convert targeted A*T base pairs to G*C could therefore advance the study and

269 ment, at scales ranging from several hundred base pairs to many kilobases.

270 -orzO type I system where the OrzO antitoxin base pairs to the 174-nucleotide zorO 5 UTR.

271 association of U2 snRNPs and the U2 snRNA is base-paired to the pre-mRNA.

272 We have developed an unnatural base pair (UBP) and a semisynthetic organism (SSO) that

273 information, we have developed the unnatural base pairs (UBPs) dNaM and d5SICS or dTPT3 (dNaM-d5SICS

274 sociations and enrichment of variants 0-5000 base pairs upstream of genes, hypothetically due to cont

275 Through systematic base pair variations, we observed the influence of the c

276 ks and about 20,000 uniquely addressable, 13-base-pair 'voxels' that serves as a molecular canvas for

277 study of DNA films containing metal-mediated base pairs was performed to investigate the charge trans

278 tic chromosome X (synX), designed as 707,459 base pairs, was synthesized chemically.

279 -small-molecules to include both A.T and G.C base pairs, we recently discovered that the heterocyclic

280 a sterically frustrated Lewis acid/Bronsted base pair, which is proposed to operate cooperatively: W

281 major source of transitions from C*G to T*A base pairs, which account for half of known pathogenic p

282 expansions create templates for multivalent base-pairing, which causes purified RNA to undergo a sol

283 snR13 snoRNA the unusual C/D motif and extra base-pairing, which stimulates rRNA 2-O-methylation, are

284 by hundreds of small guide RNAs (gRNAs) that base pair with mRNA.

285 These two sRNAs base pair with the 5' UTR of oprD leading to increase in

286 s, whereas dTTP partakes in stable Hoogsteen base pairing with 1-MeA, dCTP fails to gain a "foothold"

287 PR-Cas nucleoproteins target foreign DNA via base pairing with a crRNA.

288 thiazine, tCfTP) that maintains Watson-Crick base pairing with guanine.

289 NAs), particularly those that act by limited base pairing with mRNAs, are part of most regulatory net

290 s mainly recognized through non-Watson-Crick base pairing with the 5' ss and branch point.

291 olling target genes posttranscriptionally by base pairing with their mRNAs.

292 with deoxycytidine (8-oxoG:dC) and Hoogsteen base pairs with deoxyadenosine (8-oxoG:dA).

293 bility of 8-oxoG to form stable Watson-Crick base pairs with deoxycytidine (8-oxoG:dC) and Hoogsteen

294 incapable of forming contiguous Watson-Crick base pairs with each other-has enforced a "homochiral" p

295 These uracil lesions base-pair with adenines during the completion of reverse

296 mponent (snoRNA) contains guide regions that base-pair with the target site to select the single nucl

297 Here we show that HSUR2 also base-pairs with mRNAs in infected cells.

298 One of these HSURs (HSUR2) base-pairs with two host cellular microRNAs (miR-142-3p

299 Non-canonical base pairing within guanine-rich DNA and RNA sequences c

300 Most of the variable base pairs within the core sequence also engage in inter