ライフサイエンスコーパス: pseudoknot

1 t-forming A48 is looped out at the apex of a pseudoknot.

2 correct folding of the platform and central pseudoknot.

3 and functionally important template-adjacent pseudoknot.

4 e and function of the third stem of the SARS pseudoknot.

5 timulatory RNA structure, a stem-loop or RNA pseudoknot.

6 direct evidence for base triples in the tTER pseudoknot.

7 stribution of forces required to unfold each pseudoknot.

8 avirus, and a nonframeshifting bacteriophage pseudoknot.

9 sequence into an alternative intra-molecular pseudoknot.

10 h the tTERT active site and formation of the pseudoknot.

11 tructure that has been proposed to be an RNA pseudoknot.

12 ng that SL9266 forms the core of an extended pseudoknot.

13 tivity and that the region could fold into a pseudoknot.

14 ated pseudoknot sequence stably folds into a pseudoknot.

15 tural rearrangement and folds into an H-type pseudoknot.

16 rts of the RNA prevents the formation of the pseudoknot.

17 is bound as part of a triplex formed with a pseudoknot.

18 ary interactions, namely kissing loops and a pseudoknot.

19 ulated an NMR-based model of the full-length pseudoknot.

20 structures are identified, including a novel pseudoknot.

21 he aptamer domain is an integral part of the pseudoknot.

22 ranges around the melting temperature for a pseudoknot.

23 a solution NMR structure of the Tetrahymena pseudoknot.

24 the same tertiary interactions as the human pseudoknot.

25 irs and tertiary interactions in the minimal pseudoknot.

26 e that the central domain is stabilized by a pseudoknot.

27 n, followed by 2) formation of a 3'-terminal pseudoknot.

28 tant of the 26 nt potato leaf roll virus RNA pseudoknot.

29 s on the conformational dynamics of the SARS pseudoknot.

30 tationally predicted structures that include pseudoknots.

31 cted shape to structure prediction including pseudoknots.

32 been predicted to form in diverse fungi TER pseudoknots.

33 sfactory, especially on sequences containing pseudoknots.

34 n RNA:RNA and RNA:DNA duplexes, hairpins and pseudoknots.

35 e more potent than the previously identified pseudoknots.

36 rammar (CFG), which cannot effectively model pseudoknots.

37 limited to RNA secondary structures without pseudoknots.

38 luyveromyces lactis and human telomerase RNA pseudoknots.

39 netic control of the biological functions of pseudoknots.

40 structure profiles or are not able to detect pseudoknots.

41 ences for RNA secondary structures including pseudoknots.

42 y searching, formatting and visualization of pseudoknots.

43 of the search of complex motifs that include pseudoknots.

44 ncluding stem-loop structures and long-range pseudoknots.

45 secting the vectorial unfolding mechanism of pseudoknots.

46 ge network of stacking interactions, and two pseudoknots.

47 elements, including experimentally validated pseudoknots.

48 on between a purine-purine mismatch near the pseudoknot (A-A/G) and the loop sequence of domain IIIe

49 The pseudoknot, a DNA structure containing two stem-loops in

50 t be removed to allow folding of the central pseudoknot, a key feature of the small subunit.

51 tructure of the primer-binding site, a novel pseudoknot adjacent to the primer-binding sites, three r

52 ficiency is related to the resistance of the pseudoknot against mechanical unfolding.

53 vitro The TCV RSE also contains an internal pseudoknot along with the long-distance interaction, and

54 psed state (preorganization) by coordinating pseudoknot and 5'-P1 fluctuations.

55 at only the junction nucleotides between the pseudoknot and CEH are essential.

56 arly identical in secondary structure to the pseudoknot and CR4/5 within vertebrate TERs.

57 tructural elements in the vertebrate TR, the pseudoknot and CR4/5, bind TERT independently and are es

58 Therefore, we also model a short RNA pseudoknot and find good agreement between the MD result

59 ddition, we observe two alternative pathways-pseudoknot and inchworm internal displacement-through wh

60 tigated the structures of the full-length TR pseudoknot and isolated subdomains in Oryzias latipes (J

61 s to elucidate how mechanical stability of a pseudoknot and its frameshifting efficiency are regulate

62 higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoog

63 s characterized by a conserved nested double-pseudoknot and minimal sequence conservation.

64 Mechanical unfolding of a model pseudoknot and mutants designed to dissect specific inte

65 Average unfolding forces of the pseudoknot and mutants ranging from 50 to 22 picoNewtons

66 strong nonadditivity of chain entropy in RNA pseudoknot and other tertiary folds.

67 vide the first observation of a fast-folding pseudoknot and present a benchmark against which computa

68 ary interactions can significantly stabilize pseudoknots and extending the length of stem 2 may alter

69 evious work introduced a graph model for RNA pseudoknots and proposed to solve the structure-sequence

70 ctures reveals that whereas both form H-type pseudoknots and recognize preQ1 using one A, C, or U nuc

71 ity, such as a yeast-like template boundary, pseudoknot, and a vertebrate-like three-way junction.

72 mRNA-mediated -1 PRF is directed by an mRNA pseudoknot, and is stimulated by at least two microRNAs.

73 icked P9 tetraloop, reorganization of the P3 pseudoknot, and refolding of nonnative conformers, respe

74 ory action of a "slippery" sequence, an mRNA pseudoknot, and the CopA nascent chain.

75 Viruses inhibited by pseudoknot aptamers were rendered insensitive by a natur

76 e RNP complexes containing a properly folded pseudoknot are catalytically active.

77 Pseudoknots are a fundamental RNA tertiary structure wit

78 RNA pseudoknots are examples of minimal structural motifs in

79 Pseudoknots are found with half or better of the false-p

80 Pseudoknots are motifs in RNA secondary structures that

81 the 3D shape of the human and K. lactis TER pseudoknots are remarkably similar.

82 of sequences that do not contain the native pseudoknots are reported by these tools.

83 Pseudoknots are usually excluded from RNA structure pred

84 rough basepair-exchange pathways and through pseudoknot-assisted pathways, respectively.

85 rtiary interactions including a K-turn and a pseudoknot at a four-way junction.

86 lled by a DNA leader that is attached to the pseudoknot at the 5' or 3' ends.

87 es have the propensity to form two potential pseudoknots between identical five-nucleotide terminal l

88 We tested whether pseudoknots bound with an anti-frameshifting ligand exhi

89 s, which are the template region, downstream pseudoknot, boundary element, core-closing stem and trip

90 demonstrate the functional importance of the pseudoknot but also reveal the critical role played by t

91 hat the RSV stimulatory RNA is indeed an RNA pseudoknot but that the pseudoknot per se is not absolut

92 n for small RNA systems such as hairpins and pseudoknots, (c) the intraloop interactions and sequence

93 Our results show how a processed RNA pseudoknot can inhibit a deleterious protein with exquis

94 or tertiary structure in an mRNA, such as a pseudoknot, can create a physical barrier that requires

95 re is no algorithmic restriction in terms of pseudoknot complexity and a test is made for steric feas

96 rediction that is not restricted in terms of pseudoknot complexity.

97 , one of which is consistent with a proposed pseudoknot conformation, and another of which we have id

98 at high -1 PRF efficiency was linked to high pseudoknot conformational plasticity via the formation o

99 tructure based tool can conduct genome-scale pseudoknot-containing ncRNA search effectively and effic

100 lease sensitivities for nucleotides near the pseudoknot core were altered in the presence of GTPgamma

101 tually exclusive with folding of the central pseudoknot (CPK), a universally conserved rRNA structure

102 SL9266 forms the core of an extended pseudoknot, designated SL9266/PK, involving long distanc

103 th weakly and strongly bound ligands promote pseudoknot docking through an induced-fit mechanism.

104 ty in vitro NMR studies also reveal that the pseudoknot does not form in the context of full-length T

105 An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, fo

106 ctly upstream of the TYMV TLS is an upstream pseudoknot domain (UPD) that has been considered to be s

107 y conserved, functionally essential template/pseudoknot domain of human telomerase RNA and that inhib

108 The pseudoknot domain positions the AUG start codon near the

109 ion, contained within the conserved template/pseudoknot domain, and a conserved regions 4 and 5 (CR4/

110 C virus internal ribosome entry site (IRES) pseudoknot domain.

111 red region that encompasses the template and pseudoknot domains.

112 ed ncRNA identification tools usually ignore pseudoknots during search.

113 that the extra stem-loop strongly influences pseudoknot dynamics in a manner that decreases its prope

114 SMD), we found that the unusual stability of pseudoknotted element H4a/Psi3 required five upstream ad

115 base-pairing by the U3 snoRNA to the central pseudoknot elements of the 18S rRNA.

116 epeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1.

117 The 'h18' pseudoknot encompassing residues 500-545 of the small ri

118 gy landscape for mechanical unfolding of the pseudoknot (energy barrier height and distance to the tr

119 iring with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3' from t

120 The solution structure is an unusual H-type pseudoknot featuring a P4 hairpin embedded in loop 3, wh

121 These pseudoknot fluctuations disrupt the binding site by faci

122 eQ(1) class I riboswitch preorganizes into a pseudoknot fold in a temperature- and Mg(2+)-dependent m

123 are not presently understood, the classical pseudoknot fold of this system harbors an extra stem-loo

124 ) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for

125 he cleaved 3'-fragment retains its compacted pseudoknot fold, despite the absence of the phylogenetic

126 ture of an extended A-twist motif within the pseudoknot fold.

127 al studies facilitates the identification of pseudoknot folding intermediates.

128 their inter-conversions, and derive the RNA pseudoknot folding pathway.

129 hermoanaerobacter tengcongensis) relative to pseudoknot folding, leading to the proposal that the pri

130 dictor of the order of stem formation during pseudoknot folding.

131 itical role played by telomerase proteins in pseudoknot folding.

132 ed ground state structures tend to have more pseudoknotted folding intermediates than RNAs with pseud

133 n predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known st

134 ld stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions

135 crucial and unexpected roles in controlling pseudoknot formation and, in turn, sequestering the Shin

136 Pseudoknot formation in the core region of the telomeras

137 g(2+)-dependent tertiary structure involving pseudoknot formation within the central domain.

138 tions are important for tertiary folding and pseudoknot formation, whereas in a bimolecular context,

139 energy model for the entropic cost of single pseudoknot formation.

140 of the aptamer competes with intramolecular pseudoknot formation.

141 helicase Dhr1 supposedly involved in central pseudoknot formation; this suggests that Bud23-Trm112 mi

142 A pseudoknot forms in an RNA when nucleotides in a loop pa

143 me template core domain lacks the ubiquitous pseudoknot found in all known TRs, suggesting later evol

144 lar simulations of coarse-grained model of a pseudoknot found in the conserved core domain of the hum

145 Here, we report RNA pseudoknot free energy changes at 37 degrees C measured

146 knotted folding intermediates than RNAs with pseudoknot-free ground state structures.

147 g methods have been mostly restricted to the pseudoknot-free secondary structures.

148 ediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of co

149 MTV and SRV-1 from viral genomes and the hTR pseudoknot from human telomerase) using coarse-grained m

150 reviously described an unusual three-stemmed pseudoknot from the severe acute respiratory syndrome (S

151 ng efficiencies ranging from 2% to 30%: four pseudoknots from retroviruses, two from luteoviruses, on

152 We observe that RNAs with pseudoknotted ground state structures tend to have more

153 P2ab than predicted, and the medaka minimal pseudoknot has the same tertiary interactions as the hum

154 Two hairpins and two pseudoknots have been confirmed as important for satC re

155 Pseudoknots have been recognized to be an important type

156 RNA pseudoknots have important functions, and thermodynamic

157 Studies in vitro suggest that pseudoknot I (PKI) immediately preceding the initiation

158 residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a

159 ip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center.

160 Pseudoknot I of the IRES occupies the ribosomal decoding

161 ccharomyces cerevisiae telomerase RNA (TLC1) pseudoknot identified tertiary structural interactions t

162 are consistent with the formation of an RNA pseudoknot in active human telomerase.

163 PseudoBase++ links each pseudoknot in PseudoBase to the GenBank record of the co

164 The method reveals a probable pseudoknot in the part of the coding region of the R2 re

165 A ends can be moved between the template and pseudoknot in vitro and in vivo.

166 P1-P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdo

167 ermodynamic stability is a key to predicting pseudoknots in RNA sequences and to understanding their

168 tagenesis identified four hairpins and three pseudoknots in this TCV region that participate in repli

169 of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

170 H), template-boundary element, template, and pseudoknot, in this order along the RNA.

171 All vertebrate pseudoknots include two subdomains: P2ab (helices P2a an

172 Naturally occurring, pseudoknot-insensitive viruses were rendered sensitive b

173 s into two short stem-loops, with a possible pseudoknot interaction between a C-rich bulge at the bra

174 um serves an important role in stabilizing a pseudoknot interaction between the P2 and P4 helices, ev

175 tly, a defined base pair mutation within the pseudoknot interaction stipulates whether, in the absenc

176 h the involvement in a functionally relevant pseudoknot interaction, extensive mutagenesis of nucleot

177 prediction approaches differ by the way RNA pseudoknot interactions are handled.

178 ost approaches only allow a limited class of pseudoknot interactions or are not considering them at a

179 the riboswitch stems for long-range tertiary pseudoknot interactions that contribute to the organizat

180 The occurrence and influence of pseudoknotted intermediates on the folding pathway, howe

181 ng a more complex picture of the role of the pseudoknot involving the conformational dynamics.

182 pseudoknot (PK) regions, predicted an H-type pseudoknot involving TL1 of the 5' DB and the complement

183 for S4 binding, while the conserved helix 18 pseudoknot is dispensable.

184 with the long-distance interaction, and the pseudoknot is not compatible with the phylogenetically c

185 s of characterized ncRNA families containing pseudoknots is an important component of genome-scale nc

186 e thermodynamics and folding pathways of RNA pseudoknots is an important problem in biology, both for

187 previously attenuated DENV replication, this pseudoknot may participate in regulation of RNA synthesi

188 hat targeting the conformational dynamics of pseudoknots may be an effective strategy for anti-viral

189 The detailed molecular determinants of pseudoknot mechanical stability and frameshifting effici

190 single-molecule force spectroscopy to unfold pseudoknots mechanically, we found that the ligand bindi

191 lar level, we performed simulations of three pseudoknots (MMTV and SRV-1 from viral genomes and the h

192 Whether the pseudoknot motif is formed in the active telomerase RNP

193 he complex folding mechanism inherent to the pseudoknot motif.

194 and 2 (TL1 and TL2) and their complementary pseudoknot motifs, PK2 and PK1.

195 econd, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the

196 folding/unfolding kinetics of a hairpin-type pseudoknot obtained with microsecond time-resolution in

197 -to-closed conformational transitions of the pseudoknot occur, akin to breathing.

198 Pseudoknots occur relatively rarely in RNA but are highl

199 nd tertiary structural elements, including a pseudoknot, occur to sequester the putative Shine-Dalgar

200 e homodimeric RNA complex formed by the SARS pseudoknot occurs in the cellular environment and that l

201 encode protein toxins that are inhibited by pseudoknots of antitoxic RNA, encoded by short tandem re

202 in, bulge, internal, and junction loops) and pseudoknots of arbitrary complexity.

203 The pseudoknot only forms in the presence of preQ(1), and th

204 rameshifting, whether promoted by stem-loop, pseudoknot or antisense oligonucleotide stimulator.

205 both -1 and -2 frameshifting with stem-loop, pseudoknot or antisense oligonucleotide stimulators.

206 cated hexanucleotide CAUAGC to form either a pseudoknot or terminator stem.

207 solated pairs and the ends of stems, whether pseudoknotted or not, to define junction loops.

208 with a 5/6-nt internal loop) and the minimal pseudoknot (P2b-P3 and associated loops).

209 anking helices), the conserved region of the pseudoknot (P2b/P3, previously determined) and the remai

210 redicting the secondary structure, including pseudoknotted pairs, conserved across multiple sequences

211 RNA is indeed an RNA pseudoknot but that the pseudoknot per se is not absolutely required for virus v

212 Formation of a pseudoknot (PK) in the conserved RNA core domain in the

213 their proposed interactions with downstream pseudoknot (PK) regions, predicted an H-type pseudoknot

214 ed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single-molecul

215 e 3' domain and the formation of the central pseudoknot (PK) structure depends on the presence of the

216 ance of the Beet Western Yellow Virus (BWYV) pseudoknot (PK) to unfolding.

217 In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA inter

218 ) are typically two-stemmed hairpin (H)-type pseudoknots (pks).

219 t Utp24 UV-crosslinked in vivo to U3 and the pseudoknot, placing Utp24 close to cleavage at site A1.

220 ates gene expression in many viruses, making pseudoknots potential targets for anti-viral drugs.

221 higher positive predictive value than other pseudoknot prediction tools.

222 m expected accuracy structure prediction and pseudoknot prediction.

223 estigated the folding mechanism of an H-type pseudoknotted preQ1 riboswitch in dependence of Mg(2+) a

224 on NMR structure of the Kluyveromyces lactis pseudoknot, presented here, reveals that it contains a l

225 ound currents arising from transfer from the pseudoknot probe at lower densities.

226 he absence of a target, the structure of the pseudoknot probe minimizes collisions between the redox

227 le cross-links, especially those including a pseudoknot provided the strongest restraint on conformat

228 e existence of H4a, H4b, Psi(3) and a second pseudoknot (Psi(2)) previously identified in a TCV satel

229 nce between the 3' end of the telomerase RNA pseudoknot region and the 5' end of the DNA primer is ap

230 and thermodynamic properties of the TLC1 RNA pseudoknot region, we have examined the structural and t

231 al frameshifting (-1 PRF) stimulated by mRNA pseudoknots regulates gene expression in many viruses, m

232 ding ubiquitous non-canonical base pairs and pseudoknots, remains a challenge.

233 The preformed pseudoknot represents a structure that is close to the l

234 ion of a competing structure that sequesters pseudoknot residues.

235 The structure of the human TER pseudoknot revealed that the loops interact with the ste

236 Non-pseudoknot RNA aptamers exhibited broad-spectrum inhibit

237 l ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core riboso

238 We generalize the BHG framework to include pseudoknotted RNA structures and systematically study th

239 problem in order to compute all possible non-pseudoknotted RNA structures for RNA sequences.

240 aches such as optical tweezers can track the pseudoknot's unfolding intermediate states by pulling th

241 that our work competes favorably with other pseudoknot search methods.

242 It provides a complementary pseudoknot search tool to Infernal.

243 In this work, we design a pseudoknot search tool using multiple simple sub-structu

244 a practical program, called RNATOPS, for RNA pseudoknot search.

245 gle-molecule FRET, we show that the isolated pseudoknot sequence stably folds into a pseudoknot.

246 turbations in the backbone sugar substituted pseudoknots, show a correlation between thermodynamic st

247 3'CITE is composed of three hairpins and two pseudoknots, similar to the TSS 3'CITE of the carmovirus

248 The pseudoknot stabilization by magnesium, in combination wi

249 and minor-groove triplex structures enhances pseudoknot stem stability and torsional resistance, and

250 e 7 base pairs, represents a balance between pseudoknot structural stability and target affinity.

251 These RNAs fold into a double-nested pseudoknot structure and cleave RNA, yielding 2',3'-cycl

252 y interaction, which serves to stabilize the pseudoknot structure and correlates with translational e

253 ernate gene product, is often triggered by a pseudoknot structure in the mRNA in combination with an

254 ormations similar to the bound form, and the pseudoknot structure is only fully formed upon binding t

255 he R2 ribozyme could be folded into a double pseudoknot structure similar to that of the hepatitis de

256 und form of the SAM-II riboswitch is a loose pseudoknot structure that periodically visits conformati

257 nt to the triple helix (within the conserved pseudoknot structure) of Saccharomyces cerevisiae telome

258 Target binding disrupts the pseudoknot structure, liberating a flexible, single-stra

259 analysis to elucidate the folding of an RNA pseudoknot structure.

260 significant fraction of the RNPs to form the pseudoknot structure.

261 eam of the AUGA motif, including a predicted pseudoknot structure.

262 xity, with some proteins recognizing complex pseudoknot structures and others binding to simple RNA h

263 When pseudoknot structures are vital to the functions of the

264 Pseudoknot structures in messenger RNAs stimulate frames

265 rangements between tandem stem-loop and mRNA pseudoknot structures in two of the strains.

266 dicted folding behavior depending on whether pseudoknotted structures are allowed to occur as folding

267 ms, such as I-shaped, Y-shaped, T-shaped, or pseudoknotted structures, or radiate multiple helices fr

268 In contrast, class 1 RNA pseudoknots, such as aptamer T1.1, are specific for RTs

269 Vertebrate TR contains the template/pseudoknot (t/PK) and CR4/5 domains required for telomer

270 The data reveal that folding of the central pseudoknot (T1), the most crucial structural determinant

271 bility of hairpin secondary structures and a pseudoknot tertiary structure are insensitive to the ion

272 ing a more complex structure surrounding the pseudoknot than previously assumed.

273 Q1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribos

274 ighly conserved intronic long-range tertiary pseudoknot that is absolutely required for deamination o

275 The TCV RSE also contains an internal pseudoknot that is not compatible with the phylogenetica

276 e interactions, including stabilization of a pseudoknot that is part of the regulatory switch.

277 These IRESs require an RNA pseudoknot that mimics a codon-anticodon interaction and

278 iyama et al. (2016) prove the existence of a pseudoknot that stabilizes a nuclease-resistant RNA stru

279 ins a structured 3' region with hairpins and pseudoknots that form a complex network of noncanonical

280 us riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory

281 n previous observations of very slow folding pseudoknots that were trapped in misfolded conformations

282 lding occurs by multiple pathways in the hTR pseudoknot, the isolated structural elements of which ha

283 raction has been suggested to substitute for pseudoknots, thought to be missing in tombusvirid RSEs.

284 tions of backbone ribose 2'-OH groups in the pseudoknot to telomerase catalysis were investigated pre

285 hese results indicate that the resistance of pseudoknots to mechanical unfolding is not a primary det

286 The mechanism by which pseudoknots trigger -1 PRF, however, remains controversi

287 h this design, we provided evidence that the pseudoknot unfolding is a two-step, multistate, metal io

288 The pseudoknot unfolding pathway in the nanopore, either fro

289 ions of the 2'-O-methyl and 2'-H substituted pseudoknots, using UV-monitored thermal denaturation, na

290 sh, we find that it forms in the full-length pseudoknot via an unexpected hairpin.

291 strongly stabilizes 5WJ and the helix (H) 18 pseudoknot, which become tightly folded within the first

292 The SRV-1 pseudoknot, which folds in a highly cooperative manner,

293 il the structure and folding of the isolated pseudoknot, which forms a compact structure with major g

294 Pseudoknots, which are common motifs and have been repea

295 core domain that includes the template and a pseudoknot with extended helical subdomains.

296 bound to preQ(1), which is a unique compact pseudoknot with three loops and two stems that encapsula

297 the active structure as being a constrained pseudoknot with unusual connectivity that may juxtapose

298 ying the mechanical properties of a panel of pseudoknots with frameshifting efficiencies ranging from

299 nt flaviviral RNA, which contains interwoven pseudoknots within a compact structure that depends on h

300 switch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characte