ライフサイエンスコーパス: base pairing

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

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

3 both stacking interactions and Watson-Crick base pairing.

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

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

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

7 omplex to the viral genomic RNA, directed by base pairing.

8 ts into the effects of 2-thio-uridine on RNA base pairing.

9 to produce parental molecules with restored base pairing.

10 ding of the stability and specificity of RNA base pairing.

11 cked by an E. coli aptamer via complementary base pairing.

12 bility and increase affinity in Watson-Crick base pairing.

13 uptake by a mechanism that is independent of base pairing.

14 A-guided targeting of RNAs via complementary base pairing.

15 ion does not exclusively involve A:U and G:C base pairing.

16 e generally accompanied by specific, nonseed base pairing.

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

18 fully determined by underlying Watson-Crick base pairing.

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

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

21 ements, do not participate in intermolecular base pairing.

22 to disrupt base stacking, while maintaining base pairing.

23 ary structures as a result of intramolecular base pairing.

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

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

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

27 cle-QD assemblies programmed by Watson-Crick base-pairing.

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

29 case at a step that does not require correct base-pairing.

30 The destabilization of a highly conserved base-pairing (5A-68U) by the m.12201T>C mutation alters

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

32 While SgrS base-pairing activity has been characterized in detail,

33 ated sgrT translation had minimal effects on base-pairing activity.

34 cale through the specificity of Watson-Crick base pairing, allowing both complex self-assembled struc

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

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

37 all RNAs regulate gene expression by RNA-RNA base pairing and also code for small proteins.

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

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

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

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

42 Base pairing and ionization can be coupled via global co

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

44 ty of scAAV vectors might arise from partial base pairing and optimal organization of packaged scDNA.

45 e third stem-loop plays an accessory role in base pairing and stability.

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

47 rge type VI secretion system cluster through base pairing and they repress HapR, the activator of the

48 terized in detail, little is known about how base pairing and translation of sgrT are coordinated.

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

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

51 s positive effect requires specific miR:mRNA base-pairing and Ago2, but not its functional partner GW

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

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

54 In the absence of base-pairing and tertiary structure, ribonucleic acid (R

55 er small-RNAs, miRNAs do not require perfect base pairing, and thus, can regulate a network of broad,

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

57 that recognises specific transcripts through base-pairing, and its activities are facilitated by the

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

59 is different, and chemical shift markers of base pairing are different.

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

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

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

63 ant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of p

64 ed PIWI domain contributes to recognition of base pairing at the 15th nucleotide of a duplex, while t

65 Base pairing at the 15th nucleotide of a miRNA duplex is

66 ion kinetics, assists proper codon-anticodon base pairing at the ribosome A-site, and prevents frames

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

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

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

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

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

72 The former is most likely due to wobble base pairing between ClU and G, which may be more common

73 Our structures suggest that Hoogsteen-type base pairing between G and C8-modified G could be accomm

74 all RNAs (sRNAs) in bacteria and facilitates base pairing between sRNAs and their mRNA targets.

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

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

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

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

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

80 in the P site of the 40 S subunit driven by base pairing between the start codon in the mRNA and the

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

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

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

84 Human SBSs can form by intermolecular base-pairing between a 3' UTR Alu element and an Alu ele

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

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

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

88 displaced from the P decoding site to permit base-pairing between Met-tRNAi and the AUG codon, as wel

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

90 e fourU element (U5C, U7C) that strengthened base-pairing between the anti-SD and SD sequences preven

91 cting the inhibitory effect of long distance base-pairing between the uvrY mRNA leader and coding reg

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

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

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

95 he selection of correct dNTP by Watson-Crick base pairing, but it cannot explain how low-fidelity DNA

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

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

98 These results show that base-pairing can measurably affect nonradiative decay pa

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

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

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

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

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

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

105 anslation of sgrT affected the efficiency of base pairing-dependent regulation and vice versa.

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

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

108 ereas in the presence of DNA and a correctly base-pairing dNTP, it re-equilibrates to a closed state.

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

110 ions such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elus

111 luence of methylation or halogenation on the base-pairing energies (BPEs) of proton-bound dimers of c

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

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

114 g that RNA polymerization and other critical base pairing events in the virus life cycle require RNP

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

116 with stabilization by tertiary Watson-Crick base pairing found in the folded Diels-Alderase structur

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

118 To investigate how Hfq promotes sRNA-mRNA base pairing from a distance, we deleted the natural AAN

119 ell growth under stress conditions, the SgrS base-pairing function alone was indispensable for growth

120 The base-pairing function of SgrS regulates a number of mRNA

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

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

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

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

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

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

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

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

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

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

131 Intramolecular hydrogen bonded base pairing in the absence of a cation was indicated fo

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

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

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

135 appears to facilitate the destabilization of base pairing in the secondary structure of RNA.

136 ee-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic co

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

138 ation codon] phenotype), whereas eliminating base pairing increases accuracy (the Ssu(-) [suppressor

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

140 ure analysis provides significantly more RNA base pairing information than a single minimum free ener

141 V IRES activity requires a 3-nt Watson-Crick base-pairing interaction between the apical loop of subd

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

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

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

145 -distance ( approximately 530-nt separation) base-pairing interaction to regulate alternative splicin

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

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

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

149 These data are consistent with long-range base pairing interactions and a three-domain genome arch

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

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

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

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

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

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

156 Random base-pairing interactions between messenger RNAs and non

157 Base-pairing interactions between nucleic acids mediate

158 Base-pairing interactions between sequences in the intro

159 expression from target mRNAs through limited base-pairing interactions between the 5' 'seed' region o

160 We created a 'molecular vise' in which base-pairing interactions generated a compressive force

161 The stronger base-pairing interactions in C(+)*C proton-bound dimers

162 Base-pairing interactions in proton-bound dimers of cyto

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

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

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

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

167 Conversely, mutations that impaired base-pairing interactions resulted in increased SgrT pro

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

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

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

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

172 binding events initiated by a few metastable base-pairing interactions, followed by zippering of the

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

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

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

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

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

178 Hoogsteen (HG) base pairing involves a 180 degrees rotation of the puri

179 y (or promiscuity) of the metal-ion-mediated base pairing is discussed in terms of the ability of the

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

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

182 Base pairing is observed at the interacting regions betw

183 nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in

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

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

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

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

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

189 guide RISC to target RNAs via complementary base pairing, leading to posttranscriptional gene silenc

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

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

192 messenger RNA (mRNA) target through perfect base pairing, microRNAs (miRNAs) are endogenous small RN

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

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

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

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

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

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

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

200 Targets are determined by imperfect base pairing of the microRNA to the 3'-UTR of the mRNA.

201 We show biochemically that base pairing of the PAM region is unnecessary for target

202 -assembly of these oligomers by Watson-Crick base pairing of the recognition sequences creates linear

203 A subtle non-coding mutation, extending base pairing of this accessory helix, confers significan

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

205 ed to target loci by AGO4-siRNA and involves base-pairing of associated siRNAs with nascent RNA trans

206 at SMD occurs in mouse cells via mRNA-lncRNA base-pairing of partially complementary elements and tha

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

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

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

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

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

212 Both miR-122 binding sites involve extensive base pairing outside of the seed sequence; yet, they hav

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

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

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

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

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

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

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

222 hensive investigation of their structure and base pairing properties.

223 ucleoside modification and correlate them to base pairing properties.

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

225 ncluding this dA nucleoside analogue possess base-pairing properties similar to those of the parent o

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

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

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

229 The well-understood base pairing rules have enabled nucleic acids to be asse

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

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

232 onserved signals of two aligned columns with base-pairing rules.

233 Further, our data suggest that a base-pairing secondary structure forms between these two

234 tinguishing two base-pair mismatches in a 22-base pairing segment of microRNAs associated with oral c

235 Analyses of miRNA:mRNA base pairing showed that miRNA species systematically di

236 Watson-Crick base-pairing slows the rate of vibrational cooling compa

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

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

239 ncrease duplex thermal stability and enhance base pairing specificity.

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

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

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

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

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

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

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

247 quence (i.e., the ribosome binding site) via base-pairing, thus preventing translation initiation.

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

249 olecular transport based on its non-covalent base pairing to assemble both stationary and mobile elem

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

251 delity DNA polymerases overcome Watson-Crick base pairing to catalyze non-Watson-Crick dNTP incorpora

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

253 s are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity.

254 though not all, ncRNAs exploit the power of base pairing to selectively bind and act on other nuclei

255 orms well at guide strand position 12, where base pairing to target was expected to be important.

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

257 The sRNA represses toxin gene expression by base pairing to the toxin mRNA.

258 MicA has an inhibitory function, base pairing to the translation initiation region of tar

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

260 an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria.

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

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

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

264 tion of the kissing complex was dominated by base pairing, whereas its dissociation was significantly

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

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

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

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

269 em-loops: the first stem-loop is crucial for base pairing with a subset of targets.

270 Base pairing with AUG is thought to promote isomerizatio

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

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

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

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

275 ng RNAs that regulate protein production via base pairing with mRNAs.

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

277 epression of sugar transporter synthesis via base pairing with sugar transporter mRNAs is the first p

278 ect posttranscriptional gene suppression via base pairing with target transcripts.

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

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

281 pts anti conformation and forms Watson-Crick base pairing with the incoming dCTP analog.

282 adopts syn conformation and forms Hoogsteen base pairing with the incoming dGTP analog.

283 op contains conserved sequences required for base pairing with the majority of the target mRNAs.

284 anines of the Pt-GG lesion form Watson-Crick base pairing with the primer terminus dC and the incomin

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

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

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

288 ion hot-spot sequence studied, non-canonical base-pairing with exposed DNA groove atoms of a neighbor

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

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

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

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

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

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

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

296 pyrazol-1-yl)adenine, for metal-ion-mediated base pairing within an oligonucleotide environment has b

297 he purine base relative to Watson-Crick (WC) base pairing within DNA duplexes, creating alternative D

298 ity of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new SAR dat

299 ity of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new structu

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