ライフサイエンスコーパス: base pairing

1 cterized by the iconical Watson-Crick nucleo-base pairing.

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

3 based on overall 3' UTR structure formed by base pairing.

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

5 fully determined by underlying Watson-Crick base pairing.

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

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

8 ements, do not participate in intermolecular base pairing.

9 to disrupt base stacking, while maintaining base pairing.

10 ary structures as a result of intramolecular base pairing.

11 miRNA base pairing or by creation of wobble base pairing.

12 al detection can be achieved by Watson-Crick base pairing.

13 o their target nucleic acids by Watson-Crick base pairing.

14 both stacking interactions and Watson-Crick base pairing.

15 nates the need for conventional Watson-Crick base pairing.

16 due to the competition from the Watson-Crick base pairing.

17 ization via intermolecular kissing loop (KL) base pairing.

18 interact with native d-RNA via Watson-Crick base pairing.

19 n as target sites for the 18S rRNA by direct base pairing.

20 logs designed to bind to RNA by Watson-Crick base pairing.

21 partially lack intramolecular complementary base pairing.

22 e at position -1, which is not recognized by base pairing.

23 tering RNA structure mainly by destabilizing base pairing.

24 modular specificity similar to Watson-Crick base pairing.

25 to errors that are reminiscent of dA:8-oxodG base pairing.

26 nd programmable self-assembly through mainly base pairing.

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

28 pology is not easily accessed through native base-pairing.

29 y an artificial tRNA not dependent on wobble base-pairing.

30 The core of twister is stabilized by base pairing, a large network of stacking interactions,

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

32 s9 genome editing relies on sgRNA-target DNA base pairing and a short downstream PAM sequence to reco

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

34 dified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three n

35 The 1-MeA lesion impairs Watson-Crick base pairing and blocks normal DNA replication.

36 itiation sites are sequestered by long-range base pairing and guanosines essential for both packaging

37 le system primarily due to their predictable base pairing and highly regulated conformations, which g

38 f the cell and as a result of intermolecular base pairing and interactions with RNA-binding proteins.

39 Base pairing and ionization can be coupled via global co

40 aling ability relies solely on interterminal base pairing and is an independent cis-acting signaling

41 ctural complexity, but they lack the precise base pairing and molecular recognition available with nu

42 e nucleotide opposite epsilondA by Hoogsteen base pairing and of Polzeta to extend synthesis.

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

44 ical structure of DNA results from canonical base pairing and stacking interactions.

45 varied tendencies of modifications to alter base pairing and their interactions with DNA repair enzy

46 he structure of the rpoS mRNA to enable sRNA base pairing and translational control.

47 techniques to show that the kinetics of DNA base pairing and unpairing, which are fundamental to bot

48 ble chain of events that lead to alternative base-pairing and altered expression output.

49 dxGMP, dxTMP, dxAMP) which exhibit canonical base-pairing and enhanced base stacking.

50 lization of experimental information such as base-pairing and hydroxyl-radical probing.

51 ock multiple functional DNAs through DNA-RNA base pairing, and the resulting RNA/DNA hybrids self-ass

52 ent on a fundamental biological process, DNA base pairing, and to illustrate the benefits of single-m

53 These sRNAs recognize transcripts through base-pairing, and sRNA-mRNA annealing consequently alter

54 wnregulates the synthesis of Fis and AcpP by base-pairing, and this regulation requires the RNA chape

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

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

57 as evolved to undergo large-scale changes in base pairing as part of ribosome function.

58 ow that native transcripts are recognized by base pairing at positions -2 to -5 of the PFS and by a g

59 ssify modifications that affect Watson-Crick base pairing at three different levels of the Arabidopsi

60 ension (SHAPE) to investigate intramolecular base-pairing at single-nucleotide resolution.

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

62 Such dichotomous base-pairing behavior of the 5-azauracil moiety, in orga

63 anded nucleic-acid substrates, Ago relies on base pairing between a small nucleic-acid guide and its

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

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

66 mer of dimers of PC4, which is stabilized by base pairing between homologous regions of the ASOs boun

67 e-telomerase scanning interactions, and then base pairing between hTR and telomere ssDNA promotes lon

68 In many bacteria, the base pairing between most small regulatory RNAs (sRNAs)

69 is results from disruption of the continuous base pairing between SD and rRNA.

70 efficiency of translation repression is the base pairing between the 'seed' region of the miRNA and

71 protospacer adjacent motif and complementary base pairing between the crRNA spacer and the DNA target

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

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

74 in cell-free translation using Watson-Crick base pairing between the mRNA and a complementary gamma-

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

76 d kissing-loop motif, involving Watson-Crick base pairing between the single-stranded regions of a bu

77 which an arginine patch on the rim promotes base pairing between their complementary sequences.

78 ocking of mRNP and gRNP modules via specific base pairing between their respective mRNA and gRNA carg

79 A interactions are built up by complementary base pairings between interacting RNAs and high level of

80 ent of the EBER2-PAX5 complex is mediated by base-pairing between EBER2 and nascent transcripts from

81 o what has been observed in humans and mice, base-pairing between highly complementary transposable e

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

83 he activating RNAs identifies intramolecular base-pairing between positions +1 and +7 and a pseudotem

84 microorganisms, based on complementarity of base-pairing between probe and target molecules.

85 by multiple factors, including the extent of base-pairing between transcription-regulating sequences

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

87 hia coli Hfq is not needed to accelerate RNA base pairing but is required for the release of dsRNA.

88 erence by TtCsm does not proceed via initial base pairing by a seed sequence.

89 eaved prior to A2 and both cleavages require base-pairing by the U3 snoRNA to the central pseudoknot

90 nation mechanism, induced by nontemplate DNA base-pairing, channels transcripts to the associated RNA

91 "(DMA)C" exhibits the same pKa and base pairing characteristics as native cytosine residues

92 e we show that Aub-loaded piRNAs use partial base-pairing characteristics of Argonaute RNPs to bind m

93 The programmability of Watson-Crick base pairing, combined with a decrease in the cost of sy

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

95 MEJ, independent of microhomology length and base-pairing continuity.

96 DNA polymerase delta (Poldelta) to incorrect base pairing contributes to its extremely high accuracy

97 ct alignment methods that capture nested RNA base-pairing correlations (stochastic context-free gramm

98 e binder (netropsin) and ligands binding DNA base-pairing defects (naphthalenophanes).

99 DNA as a model ligand instead of the typical base-pairing design for programmability, long-range 2D D

100 -methylated m42C also results in the loss of base pairing discrimination between C:G and other mismat

101 By using non-base-pairing DNA as a model ligand instead of the typica

102 We show here that with base pairing-driven target recognition it is possible to

103 g(2+)-reinforced DNA binding to validate DNA base pairing during the adenylyl transfer and nick-seali

104 an R-loop includes four terms-junctional and base-pairing energies and energies associated with super

105 own-6 polyether with protonated peptides and base-pairing energies of nucleobases.

106 First, base-pairing energy can favor RNA:DNA over DNA:DNA duple

107 comparison to other approaches, such as the base-pairing entropy and energy landscapes dynamics.

108 attractive for screening for metal-mediated base pairing events.

109 eam of cleavage site must not form canonical base pairing for the optimal catalysis, and this nucleob

110 e DIS stem nucleotides in the intermolecular base pairing, forming an extended dimer (ED).

111 ation probability varying in accord with DNA base-pairing free energies at the crossover site.

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

113 ibility to undergo self-organization through base pairing has been conceptualized and accomplished.

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

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

116 The predictable base pairing, high programmability, and superior new che

117 ovalent interactions, including Watson-Crick base pairing, Hoogsteen H-bonding, and pai-pai stacking,

118 cleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a

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

120 interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as inte

121 with reporter assays, we establish that weak base pairing in both seed and 3' regions is required to

122 cificity to RNA processing reactions through base pairing in diverse settings.

123 owires through non-canonical, Ag(+)-mediated base pairing in duplexes containing cytosine-cytosine mi

124 first functional demonstration of mRNA-rRNA base pairing in mammalian cells.

125 udies have evaluated the effects of s(2)U on base pairing in RNA, where it has been shown to stabiliz

126 Mismatch dependent instability in the base pairing in the heteroduplex strand exchange product

127 NAs (mRNAs) and can involve non-Watson-Crick base pairing in the miRNA seed region.

128 e genetic code by facilitating non-canonical base pairing in the ribosome decoding centre.

129 d structural remodeling demonstrate that the base pairings in the stem of these DRs control sfRNA for

130 their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained

131 ts confirm previous reports that strength of base-pairing in the siRNA seed region is the primary fac

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

133 terminal repeats, showing their alignment or base-pairing information.

134 ension, and we identify a previously unknown base-pairing interaction between the 5' end and the 3' e

135 ere that a single additional trans-Hoogsteen base-pairing interaction in the minimal hammerhead riboz

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

137 Formation of this additional base-pairing interaction requires only that the substrat

138 stability than an additional adenine-thymine base-pairing interaction, 2.7 kJmol(-1).

139 guously demonstrates that a single Hoogsteen base-pairing interaction, in full-length hammerheads pos

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

141 een the OrzO sRNA and the zorO mRNA, not all base pairing interactions are needed for repression; how

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

143 As, which bind to targeted mRNAs via limited base pairing interactions, act to reduce protein product

144 hods rely on both backbone conformations and base pairing interactions, none of them consider the ent

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

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

147 -rich molecule with predictable and reliable base-pairing interactions and well-studied kinetics, and

148 Random base-pairing interactions between messenger RNAs and non

149 Base-pairing interactions between nucleic acids mediate

150 Base-pairing interactions between sequences in the intro

151 rrelated chemical probing to directly detect base-pairing interactions in cells.

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

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

154 Such action requires specific base-pairing interactions of piRNAs with target mRNAs in

155 PARIS determines base-pairing interactions on an individual-molecule leve

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

157 Mutagenesis studies designed to probe for base-pairing interactions suggest that the additional gu

158 ormation of complex and intricate long-range base-pairing interactions which make the direct detectio

159 Qrr3 forms different base-pairing interactions with each mRNA target, and the

160 By forming base-pairing interactions with the 3' end of 16S rRNA, m

161 er-specific microRNA miR-122 forms extensive base-pairing interactions with the 5' noncoding region o

162 secondary structures and form intermolecular base-pairing interactions, as in other organisms.

163 We identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA inte

164 sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects th

165 ltiple target messenger RNAs (mRNAs) through base-pairing interactions.

166 ibosome then scans mRNA in search of optimal base-pairing interactions.

167 mable intra- and intermolecular Watson-Crick base-pairing interactions.

168 s that use reversible covalent bonds to form base-pairing interactions.

169 y the concomitant Watson-Crick and Hoogsteen base pairings involved in target recognition, our sensor

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

171 Understanding HG base pairing is important because the underlying "breath

172 ognized that the thermodynamics of mRNA-tRNA base pairing is insufficient to explain the high fidelit

173 nding our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in

174 Base pairing is observed at the interacting regions betw

175 he existence of evolutionary conservation in base pairing is strong evidence for functional elements

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

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

178 A long-range, 5-nucleotide, base-pairing kissing loop interaction between the 3'BTE

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

180 elity checks on newly adopted codon position base pairings lead to either resumed translation or earl

181 This binding disrupts base pairing leading to ejection of the central AT bases

182 icity and predictability of the Watson-Crick base pairing make DNA an excellent building material for

183 need to forward-design specific Watson-Crick base pairing manually for any given target structure.

184 rm that enabled the in vivo determination of base pairing-mediated target recognition kinetics.

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

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

187 architectures through specific Watson-Crick base-pairing, molecular plasticity, and intermolecular c

188 two programmable barcoding methods based on base-pairing, namely forming a gap in dsDNA and creating

189 for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutua

190 ine (epsilondA), which disrupts Watson-Crick base pairing, occurs via Poliota/Polzeta-, Rev1-, and Po

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

192 Notably, base pairing of A with OG uniquely positions the 2-amino

193 recognizes the vRNA panhandle, formed by the base pairing of complementary nucleotides at the 5' and

194 ated racemic PNA monomers reveal interesting base pairing of enantiomers and packing arrangements dir

195 e excision leads to the disruption of wobble base pairing of SsrA due to site-specific recombination,

196 e dominated by hydrophobic interactions, not base pairing of the DNA arms.

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

198 Canonically, miRNA targeting is reliant on base pairing of the seed region, nucleotides 2-7, of the

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

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

201 sRNA:mRNA base-pairing often results in altered mRNA stability and

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

203 e to the miRNA either by disruption of miRNA base pairing or by creation of wobble base pairing.

204 re of the transcript by blocking the RNA-RNA base-pairing or protein-RNA binding interactions that oc

205 es the enzyme to favor faithful Watson-Crick base pairing over mutagenic configurations.

206 t presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimate

207 demonstrated that m4C retains a regular C:G base pairing pattern in RNA duplex and has a relatively

208 and suggest that N7 alkylation may alter the base pairing patterns of guanine by promoting the format

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

210 equire RNA sequences that fold into specific base-pairing patterns, but computational algorithms gene

211 utes using reversible covalent chemistry for base-pairing pose unique synthetic challenges.

212 screte two-dimensional space of Watson-Crick base pairing possibilities.

213 en for candidate structured regions based on base pairing potential and provides a readily interpreta

214 enhanced target repression independently of base pairing potential to the miRNA.

215 interactions identified by CLASH have strong base-pairing potential and are highly enriched for compl

216 the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a re

217 tructure) have overall better performance if base pairing probabilities are considered rather than mi

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

219 More interestingly, the resulting base-pairing probabilities are even better correlated wi

220 n, to approximate the partition function and base-pairing probabilities, which is shown to be orders

221 l edges and structural edges weighted by the base-pairing probabilities.

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

223 In vitro base pairing properties between each modified and canoni

224 hesis and a preliminary investigation of the base pairing properties of (6' --> 4')-linked 1',5'-anhy

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

226 pool of nucleotides with various sugars and base pairing properties, which is critically important f

227 hensive investigation of their structure and base pairing properties.

228 ucleoside modification and correlate them to base pairing properties.

229 rchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utili

230 alpha-dNs could be attributed to the unique base-pairing properties of the nucleobases elicited by t

231 on of nucleobases are known to disrupt their base-pairing properties within RNA.

232 The enzymatic synthesis, base-pairing properties, structure, and stability of oli

233 s versatile mode of interaction via variable base-pairing provides HSUR2 with a mechanism for differe

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

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

236 r system, mutagenesis to disrupt and restore base pairing revealed that the MTE interacts with the 5'

237 Base pairing RNAs modulate gene expression in all studie

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 RNA structure and the number and position of base pairing sites relative to the start of translation

241 tidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficienc

242 In this paper, we studied the base pairing specificity of f(5)C in different RNA duple

243 this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA olig

244 ncrease duplex thermal stability and enhance base pairing specificity.

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

246 lex and has a relatively small effect on its base pairing stability and specificity.

247 ly the joint modeling approach for inferring base pairing states on simulated data sets and RNase-seq

248 to the requirement for only short regions of base-pairing that can accommodate mismatches.

249 adjacent motif (PAM) recognition and RNA-DNA base-pairing that serves as a final specificity checkpoi

250 ins or ribosomes or coaxial small RNA (sRNA) base pairing-that disrupt the path from the 5' end to th

251 lthough m(6)A does not preclude Watson-Crick base pairing, the N(6)-methyl group alters the stability

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

253 n, a preference for maintaining or improving base pairing throughout the remainder of the stem, and a

254 gulators of gene expression acting by direct base pairing to 3'-UTR target sites in messenger RNAs.

255 y, Hfq interaction, stem-loop formation, and base pairing to both luxR and luxO, to luxR only, and to

256 teen DNA base pairs (bps) are an alternative base pairing to canonical Watson-Crick bps and are thoug

257 e-cell technique that harnesses nucleic acid base pairing to detect the abundance and positioning of

258 ogy has harnessed the programmability of DNA base pairing to direct single-stranded DNAs (ssDNAs) to

259 2 to the transcriptionally active TE loci by base pairing to nascent transcripts, however the downstr

260 We find that NarS acts by Hfq-dependent base pairing to repress the synthesis of the nitrite tra

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

262 ns are defined by noncanonical mechanisms of base pairing to U1 small nuclear RNA.

263 ion initiation site (DIS) is sequestered via base pairing to upstream sequences.

264 quences that could mediate robust long-range base-pairing to bring exons into proximity for splicing,

265 intrinsically to regulate gene expression by base-pairing to complementary mRNA targets while in asso

266 more unpaired bases, and (iii) long distance base pairing transfers this complex to the 5'-end of the

267 ation speed including mRNA structure, wobble base pairing, tripeptide motifs, positively charged upst

268 irs being disrupted whereas no disruption of base pairing was observed with the ss/ds junction.

269 This base pairing was shown to prevent the action of Rho over

270 i-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained th

271 ures due to the primacy of a net increase in base pairing, whereas rebinding of 'recovery' strands is

272 Telescripting requires U1:pre-mRNA base-pairing, which can be disrupted by U1 antisense oli

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

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

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

276 rate by directing ribosome targeting through base pairing with 18S rRNA.

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

278 ion of DNA polymerases by adopting Hoogsteen base pairing with adenine in a Watson-Crick-like geometr

279 nol tautomeric form of N7mdG involves in its base pairing with dT.

280 e, is how U34 base pairs with A without also base pairing with G.

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

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

283 t bacterial small non-coding RNAs (sRNAs) is base pairing with partially complementary sequences of t

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

285 effect through reestablishment of canonical base pairing with the altered region.

286 ze edA in the syn conformation for Hoogsteen base pairing with the correct nucleotide.

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

288 of the keto tautomeric form of N7mdG in the base pairings with dC and dG.

289 rget DNA strand unwinding to allow segmented base-pairing with crRNA.

290 Using base-pairing with nascent RNA to guide an interacting tr

291 ession and propose that it does this through base-pairing with nascent viral transcripts.

292 rect post-transcriptional gene silencing via base-pairing with target transcripts.

293 ion of double-stranded DNA for complementary base-pairing with the target DNA strand while displacing

294 oxylate oxygen, two phosphonate oxygens, and base-pairing with the template.

295 tion is to stabilize sRNAs and to facilitate base-pairing with trans-encoded target mRNAs.

296 U1 small nuclear RNP (snRNP) through strong base-pairing with U1 snRNA.

297 Most interactions combine seed-based pairing with distinct, miRNA-specific patterns of

298 grammability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensi

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

300 Mutations that stabilize base pairing within this element eliminate NC binding to