ライフサイエンスコーパス: internal loop

1 s simplest UAUU motif was a small asymmetric internal loop.

2 elix, a 12-base terminal loop, and an 8-base internal loop.

3 s form and that sheared GA pairs form in the internal loop.

4 the active conformation of the cleavage site internal loop.

5 AP binding site is in close proximity to the internal loop.

6 a single bond within the 5 nt strand of the internal loop.

7 iously determined structures of the inactive internal loop.

8 tain helical domains separated by a bulge or internal loop.

9 -bulge motif in place of the R1.1 asymmetric internal loop.

10 arget and a large downstream pyrimidine-rich internal loop.

11 ntified two Mg2+ binding sites in the active internal loop.

12 hree-helix junction, and the second being an internal loop.

13 ontains a point mutation within a ubiquitous internal loop.

14 h is mediated by conserved bases in the next internal loop.

15 te consisting of a six-nucleotide asymmetric internal loop.

16 helices that are linked by a highly stacked internal loop.

17 tructure containing a purine-rich asymmetric internal loop.

18 odon, is a large hairpin with two asymmetric internal loops.

19 provide insights into structural features of internal loops.

20 ch; it includes five stems separated by four internal loops.

21 t, functionally important, and highly mobile internal loops.

22 ) base pairs and of various 2 x 2 nucleotide internal loops.

23 ins with aldehyde tags at either terminus or internal loops.

24 imations for stabilities of 3 x 3 and larger internal loops.

25 if is illustrated by its presence in complex internal loops.

26 s are predicted to form hairpinned flaps and internal loops.

27 are purine rich, which is also true of other internal loops.

28 al loops and potential G.U pairs adjacent to internal loops.

29 are classified: 2104 hairpin loops and 3776 internal loops.

30 m loops, seven in hairpin loops and three in internal loops.

31 , and dynamic characteristics of purine rich internal loops.

32 specific nucleotides are also present within internal loops.

33 in two distinct helical domains that include internal loops.

34 oribonucleotides containing small asymmetric internal loops.

35 he free energy increments of 2 x 3 and 1 x 3 internal loops.

36 thin dsRNA containing mismatches, bulges and internal loops.

37 t exists as a free molecule or is flanked by internal loops.

38 in kissing interactions using its apical and internal loops.

39 yn-anti orientations for 1 x 1 nucleotide AA internal loops.

40 with 31 previously studied 2 x 3 nucleotide internal loops.

41 al structural elements including hairpin and internal loops.

42 side preferentially binds different types of internal loops.

43 or predicting stabilities of medium-size RNA internal loops.

44 n 3 x 3 nucleotide and larger size-symmetric internal loops.

45 al, whereas positions 485 and 1119 (putative internal loops 5 and 7) only were accessible after perme

46 The structures of internal loops 5' 1009CUAAG1013 3'/3' 1168GAAGC1164 5' a

47 an unusually stable and relatively abundant internal loop, 5'GGA3'/3'AAG5'.

48 This purine-rich asymmetric internal loop, 5'GGAAG/3'UAGU, is also thermodynamically

49 The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has been studied by N

50 Internal loop A, composed of six purines, forms a flexib

51 ts of a 3-bp lower stem, a 5-by-2 asymmetric internal loop, a 6-bp upper stem, and a hexaloop at the

52 served UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical l

53 e most frequently occurring 1 x 2 nucleotide internal loops, a database of 955 RNA secondary structur

54 surrounded by two symmetric adenine-rich 1-2 internal loops, A-bulges.

55 This analysis revealed a conserved internal loop adjacent to the SAM binding site that sign

56 One site is in the internal loop, adjacent to the scissile bond, while the

57 base-pair closing the terminal loop, or the internal loop affected binding of rpS14 to helix 23.

58 deletion of 11 nt in a 5' asymmetric G-rich internal loop (AGIL) of Bvht (bvht(dAGIL)) dramatically

59 he potential of a bubble column (BCR) and an internal loop airlift (ALR) bioreactors of 2.3 L for the

60 site is composed of a 1 x 1 nucleotide all-U internal loop and a 2 x 1 nucleotide all-A internal loop

61 We show that while Mg2+ binds to the internal loop and arrests these internal motions, it pre

62 in RNA structure include the kinking of the internal loop and distortion of the terminal tetraloop.

63 Point mutations in the predicted U-rich internal loop and in the flanking stems abolish the ENE'

64 ive but not the inactive conformation of the internal loop and is likely important for catalysis.

65 cisplatin treatment has potential to create internal loop and other unusual cross-links in structura

66 e analogues interfere with the folding of an internal loop and the C terminus, which are essential fo

67 e widely occurring motifs in RNA, located in internal loops and associated with many biological funct

68 Our results support a model in which the internal loops and bulges in HDV RNA contribute flexibil

69 e in vitro binding activity of RNAs in which internal loops and bulges were mutated and of synthetica

70 anded helical segments are interspersed with internal loops and bulges.

71 t base-paired segments are interspersed with internal loops and bulges.

72 Since cPot1 can bind internal loops and directly adjacent DNA-binding sites,

73 terminus spaced by single-stranded regions, internal loops and hairpins with embedded GNRA-like moti

74 ng the structure and dynamics of purine-rich internal loops and potential G.U pairs adjacent to inter

75 s mostly base paired but also has asymmetric internal loops and single-base bulges.

76 loop has higher rates of evolution than the internal loops and transmembrane segments, suggesting th

77 ins: P2ab (helices P2a and P2b with a 5/6-nt internal loop) and the minimal pseudoknot (P2b-P3 and as

78 RNAs, including 12 k-turn and 23 non k-turn internal loops, and compare the results to solved struct

79 ngle-stranded regions such as hairpin loops, internal loops, and junctions.

80 indicating that the two helices bounding the internal loop are closer than was previously assumed.

81 they revealed that the terminal loop and an internal loop are larger than originally thought.

82 substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.

83 Thermodynamic data for RNA 1 x 2 nucleotide internal loops are lacking.

84 RNA internal loops are often important sites for folding and

85 RNA hairpin and internal loops are often represented as unstructured on

86 Most natural 3 x 3 internal loops are purine rich, which is also true of ot

87 Most natural internal loops are purine rich.

88 All studied selected internal loops are specific for the aminoglycoside that

89 The 3 x 3 nucleotide internal loops are the smallest size symmetric loops wit

90 derived from bending and torsion measures of internal loops as well as radii of gyration for known RN

91 cal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C.

92 lled conformational switch that opens up the internal loop at higher pH.

93 pairs within the phylogenetically conserved internal loop at the base of D3.

94 The absolutely conserved four-purine internal loop B is instead conformationally and thermody

95 Internal loop base triples are classified in SCOR accord

96 NOEs and nucleotide conformations within the internal loop be made.

97 consensus ACACAGA sequence, which forms the internal loop between helices I and III; (2) the four-wa

98 mine, and 6''-azido-tobramycin, the selected internal loops bind with approximately 10-fold higher af

99 conformational change in U1A-hairpin and U1A-internal loop binding using a hybrid of molecular mechan

100 We now observe formation of the internal loop/bulge (IL/B structure) in the IRE (iron-re

101 op (HL) CAGUGX] with helical distortions: an internal loop/bulge (IL/B) (UGC/C) or C-bulge.

102 Conversion of the internal loop/bulge in the ferritin-IRE to a C-bulge, by

103 ructural elements such as helical junctions, internal loops, bulges and loop-loop interactions.

104 finds possible 3D geometries for hairpin and internal loops by matching loop sequences to motif group

105 Specificity was quantified for 16 selected internal loops by studying their binding to each of the

106 E (chideltaC-L2), E-F (chideltaA-L2), and an internal loop C-D (chideltaH-L2); into the h4 helix (chi

107 Thus, thermodynamically destabilizing internal loops can be preorganized for tertiary interact

108 Residues in internal loops can have pKa values shifted close to neut

109 al elements: a four-way RNA junction and two internal loops carried by adjacent arms of the junction.

110 me is a small catalytic RNA comprised of two internal loops carried on two adjacent arms of a four-wa

111 itiation, multibranch loop initiation, AU/GU internal loop closure and AU/GU helix end parameters wer

112 lations, and theory to study the kinetics of internal loop closure in disordered biopolymers such as

113 show that both these and previously reported internal loop closure kinetics of unfolded proteins are

114 ed 12-mer and 14-mer that form an asymmetric internal loop consisting of G-G and G-A noncanonical bas

115 rminal beta-strand and loop, and an extended internal loop constitute an RNA binding cleft.

116 Many folding motifs are internal loops containing GA base pairs, which are usual

117 es comprising two phylogenetically conserved internal loops create a unique surface for protein recog

118 nal change in three adenosine residues of an internal loop, critical for high-affinity antibiotic bin

119 the internal loop, forming an intramolecular internal loop cross-link in BBD and an analogous intermo

120 Thus, internal loops delineate helix ends for ADAR1.

121 n, we describe the identification of the RNA internal loops derived from a 4096 member 3 x 3 nucleoti

122 et if given a choice of binding all possible internal loops derived from an A-site-like library.

123 The sequence identity of the internal loops differs greatly between the BS15 mRNA and

124 igand interactions for ligands that bind the internal loop displayed in these hairpins.

125 The active internal loop displays different base-pairing interactio

126 molecular architecture comprising two docked internal loop domains folded into a wishbone shape, whos

127 interaction between two independently folded internal loop domains, A and B.

128 The base on residue 27 in an internal loop exists in at least three conformational st

129 ting begins with pre-mRNA cleavage within an internal loop flanked by upstream and downstream duplexe

130 These comprise an internal loop flanked on one side by a 2-bp stem and a h

131 and-binding site is defined by an asymmetric internal loop, flanked by a pair of helices.

132 gy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement

133 program mc-search, we identified the active internal loop fold in other RNA structures.

134 ed of a stem and a stem-loop separated by an internal loop folded into a kinked helix because of the

135 zed the most frequently occurring bulges and internal loops for each RNA class and found that the sma

136 Surprisingly, internal loop forces changed erratically as the amount o

137 at the relationship between the timescale of internal loop formation and the positions of the monomer

138 Three helices emanate from a structured internal loop, forming a Y-shaped structure, where helix

139 -link G nucleobases on opposing sides of the internal loop, forming an intramolecular internal loop c

140 The internal loop forms a different structure in solution an

141 The K ligand binds the 2 x 2 pyrimidine-rich internal loops found in the DM2 RNA with high affinity.

142 The internal loop functions as a discrete structural element

143 including G247, A271, G272, G273) or a 1 x 1 internal loop (G247 x G273) near a two-base bulge (A269-

144 ecause of the cross-strand stacking of three internal loop guanines.

145 These histidine-binding RNAs have a common internal loop-hairpin loop structure, based on a conserv

146 The internal loop has contacts with ribosomal protein L20 an

147 We find that adenines within the internal loop have pK(a) values ranging from 4.8 to 5.8,

148 C or U and R representing A or G) stabilize internal loops having 6-10 nucleotides.

149 Consecutive noncanonical pairs can form in internal loops having at least two nucleotides on each s

150 icted structure of the ENE in which a U-rich internal loop hybridizes with the 3'-polyadenylate (poly

151 n, modification of only Cys-357 in the third internal loop (IL3) led to loss of activity.

152 haracterized internal motions induced by the internal loop in an SL1 monomer that may promote the kis

153 uctural comparisons between variants of this internal loop in crystal structures of the 58-nt domain

154 s own expression by binding to a purine-rich internal loop in its pre-mRNA and mRNA.

155 20% for a 23mer model of a 1 x 3 asymmetric internal loop in SL1.

156 lin binding peptide as an affinity tag in an internal loop in the apical domain of the CCT3 subunit,

157 m this study indicate that a flexible, long, internal loop in the ARID motif is likely to be importan

158 Here, we present evidence that an internal loop in the essential yeast ribosomal protein r

159 to form than expected: the two strands in an internal loop in the folded ssDNA structure prefer to br

160 son-Crick C-A and A-C base pairs comprise an internal loop in the middle of the duplex, which is inco

161 such as the palindromic loop and the G-rich internal loop in the SL1 RNA.

162 h primary and secondary cleavage sites in an internal loop in the stem-loop structure.

163 minimum conformation of 1 x 1 nucleotide AA internal loops in r(CAG) repeats is anti-anti but can ad

164 oned alkyne and azide moieties bind adjacent internal loops in r(CCUG)(exp), the causative agent of m

165 Internal loops in RNA are important for folding and func

166 Internal loops in RNA are important for folding and func

167 Internal loops in RNA are important for folding and func

168 ic stabilities of 2 x 2 nucleotide tandem AG internal loops in RNA range from -1.3 to +3.4 kcal/mol a

169 of two U1A proteins bind specifically to two internal loops in the 3' untranslated region (3' UTR) of

170 o adjacent base pairs flanked by symmetrical internal loops in the 3'-terminal SL were shown to be re

171 stable RNA hairpins with regularly repeating internal loops in the stem and have deleterious effects

172 N-terminal tail with the positively charged internal loops in the transmembrane domain, as this mech

173 Some E. coli RNase III substrates contain an internal loop, in which is located the single scissile p

174 n products rearrange from 5'-flaps to stable internal loops inside the repeat tract.

175 e new statistical potentials for hairpin and internal loops integrated into the new version of RNAfol

176 tly binds the microtubule lattice, while the internal loop interacts with the plus end of microtubule

177 E, a stem-loop structure containing a U-rich internal loop, interacts with a downstream A-rich tract

178 Evidently, molecular recognition of this internal loop involves induced fit binding, which could

179 The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA

180 l comparisons indicated that the purine-rich internal loop is dynamic in the free RNA but becomes ord

181 Its asymmetric internal loop is flanked by C-G base pairs on one side a

182 The sequence of this internal loop is highly conserved in rRNA.

183 In contrast, base 10 in a second internal loop is mostly preorganized in the free RNA, co

184 st that this thermodynamically destabilizing internal loop is partially preorganized for tertiary int

185 between the SL1 stems on either side of the internal loop is probable.

186 found that substrate recognition around the internal loop is sequence-independent and that completel

187 s of 70, 60, 40, 20 and 17 nt show that this internal loop is the simplest sequence that can meet the

188 Evaluating all possible internal loops is one of the key steps in predicting the

189 We propose a new algorithm for evaluating internal loops, its run-time is O(M(*)log(2)L), M < L(2)

190 )), comprising part of the H/ACA domain, the internal loop J7b/8a and the CR7 domain, that was found

191 ere employed to identify the single-stranded internal loop J7b/8a as an important and specific hTR.hT

192 The T7 R1.1 internal loop lacks elements of local tertiary structure

193 probed for binding to a 3 x 3 nucleotide RNA internal loop library (81,920 interactions probed in dup

194 ng a 16384-member bacterial rRNA A-site-like internal loop library using two-dimensional combinatoria

195 irpin promoter, contains a large symmetrical internal loop (LSL) with sequence complementary to 3'-te

196 artial melting of three base-pairs above the internal loop making them key nucleation sites for excha

197 We also found an internal loop motif that can significantly increase the

198 or extending our bulge-directed framework to internal loop motifs and implying a simplified link betw

199 als how conserved nucleotides within the two internal loop motifs establish the architecture of the m

200 In contrast, mCherry fused to an internal loop (MreB-RFP(SW)) does not induce helices.

201 Experiments with model proteins show that internal loops must be surprisingly long to engage the p

202 dominantly (K(D) = 12 microM), a symmetrical internal loop of 3 nt per side.

203 rized the reaction between cisplatin and the internal loop of a 41-nucleotide subdomain derived from

204 n fluorescent protein (CFP) inserted into an internal loop of alphas, localized to the plasma membran

205 Here we show that the conserved internal loop of fission yeast Ndc80 directly binds the

206 rted green fluorescent protein (GFP) into an internal loop of Galpha(q).

207 at initially binds the universally conserved internal loop of newly synthesized RpL4 via its superhel

208 with mutant RRE sequences indicate that the internal loop of RRE is required for specific binding of

209 observable metal ion interactions within the internal loop of the A domain.

210 The large, adenine-rich internal loop of the B domain allows us to determine ade

211 rmation of a triple helix between the U-rich internal loop of the ENE and the 3'-poly(A) tail.

212 ional analysis of the asymmetric [4 nt/5 nt] internal loop of the phage T7 R1.1 substrate reveals tha

213 L30 and its RNA complex showed that both the internal loop of the RNA as well as a region of the prot

214 iary interaction may form between the active internal loop of the substrate and the catalytic domain

215 ontains the conserved AGC triad; and (3) the internal loop of the U6 intra-molecular stem loop (ISL).

216 at PTB RRMs 1 and 2 bind the pyrimidine-rich internal loop of U1 snRNA stem loop 4.

217 f oligoribonucleotides that form purine-rich internal loops of 5-10 nucleotides, including kink-turn

218 Unlike the PAN ENE, the U-rich internal loops of both predicted cellular ENEs are inter

219 d on a 23-member data set of 2 x 3 loops and internal loops of other sizes.

220 Found in internal loops of the 23 S rRNA, as well as in RNase P R

221 of the hairpin ribozyme, embedded within the internal loops of the two domains, must interact with on

222 to short AU sequences (UAAUU) located in two internal loops of the WNV3'(-)SL RNA structure.

223 st, the free energy increments for symmetric internal loops of two noncanonical pairs with GU closing

224 er dataset of 1 x 2 nucleotide loops or from internal loops of various sizes.

225 ng site within the pseudouridylation pocket (internal loop) of the guide RNA.

226 mains (omega = 0.55, P = 1.18 x 10(-12)) and internal loops (omega = 0.51, P = 7.04 x 10(-5)), but no

227 However, SMAD3 binds RNA with large internal loops or bulges with high apparent affinity.

228 ic RNA structural motifs, such as asymmetric internal loops or hairpin loop-stem junctions, by aminog

229 D motifs (such as sarcin-ricin and kink-turn internal loops or T- and GNRA hairpin loops) in any PDB

230 elements are flanked by helix (e.g., bulges, internal loops, or branches).

231 stems and, proximal to them, purine-rich 1-3 internal loops, or G-bulges, are the least stable parts

232 Internal loops play an important role in structure and f

233 RNA internal loop preferences for three aminoglycosides were

234 have explored the structure of two conserved internal loops proximal to the palindromic sequence of S

235 NH2 and COOH termini and the five predicted internal loops, reacted with methanethiosulfonate (MTS)

236 They define a model where the RNA internal loop region "breathes" on a micro- to milliseco

237 the rate of ferritin synthesis, because the internal loop region of the ferritin IRE is distinctive

238 The metal binding internal loop region of the stem contains a partially pr

239 es that blocked oxidation of guanines in the internal loop region were expected to selectively increa

240 For a series of symmetric internal loops related in sequence, larger loops (>/=six

241 preserves and/or activates local mobility at internal loop residues G272 and G273 which are implicate

242 ing these approaches could assignment of the internal loop resonances and identification of the unusu

243 el mobility shifts) to block cleavage of the internal loop RNA site by >50% and seemed to inhibit pro

244 The internal loop, [see text], is about 2 kcal/mol more stab

245 The internal loops selected to bind 5''-azido-neomycin B bin

246 U internal loop and a 2 x 1 nucleotide all-A internal loop separated by a single GC base pair.

247 irpin structures with periodically repeating internal loops separated by two 5'GC/3'CG base pairs.

248 (C vs U) within a six-nucleotide asymmetric internal loop sequence that is the binding site for the

249 leavage reactivity is largely independent of internal loop sequence.

250 in a two-piece construct containing the same internal loop sequence.

251 esidues, to convert an end-to-end loop to an internal loop, sharply decreases the contact rate.

252 rmodynamic and structural insights into such internal loops should improve approximations for their s

253 ch arose by expansion of flexible termini or internal loops, show greater variation in structure and

254 defect in SL1 that can adopt either a 1 x 3 internal loop, SL1i (including G247, A271, G272, G273) o

255 eractions that are expected to stabilize the internal loop structure at low pH.

256 The RNA aptamer internal loop structure has pre-organized features that

257 complex with WRN protein cleaves hairpin and internal loop substrates, we suggest that the GEN activi

258 Increasing the U content of the U-rich internal loop surprisingly decreases stability in vivo b

259 nt of its position; originally, on the first internal loop, SV1 insert or CVLF perform equally well i

260 dies of base and ribose dynamics for the RNA internal loop target of human U1A protein located within

261 The specific features of the internal loop that establish the pattern of single-stran

262 site is comprised of two stems each with an internal loop that forms a series of non-canonical base

263 small nucleolar RNA (snoRNA), with a U-rich internal loop that hybridizes to and protects the PAN RN

264 ontain a highly conserved, basically charged internal loop that interacts with the peptidyl-transfer

265 ee, on sequence of a highly conserved G-rich internal loop that normally limits thermal stability of

266 SL1 contains a highly conserved internal loop that promotes the kissing-duplex transitio

267 Selected internal loops that are unique for each aminoglycoside h

268 This provides consensus RNA internal loops that bind these structures and include: l

269 erein is described the identification of RNA internal loops that bind to derivatives of neomycin B, n

270 These structures include bulges and internal loops that can form tertiary contacts or serve

271 Many internal loops that form tertiary contacts in natural RN

272 identified for both models several isolated internal loops that require further curation.

273 In the [see text] internal loop, the GU pairs form canonical wobble config

274 types of loops, namely, hairpin, bulge, and internal loops, the predicted free energies agree with t

275 age by terbium ion and by the ability of the internal loop to destabilize a small model duplex.

276 as been predicted to use both its apical and internal loops to interact with the X RNA in the 3'-UTR,

277 These internal loop triples contain several examples of a freq

278 ifferent from the values predicted for these internal loops using the predictive models proposed by L

279 cluding base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtain

280 mismatches on the thermodynamic stability of internal loops vary depending on the size and asymmetry

281 ible or mobile N and C termini, and variable internal loops were reduced or eliminated, and ligands s

282 A series of RNA internal loops were studied at different pH by UV absorb

283 goribonucleotides containing different 3 x 3 internal loops were studied by UV melting and imino prot

284 xtended regions, either in the termini or in internal loops, which make extensive contact to the RNA

285 ments is a stem-loop structure containing an internal loop whose sequence is the most highly conserve

286 The RNA structural motif contains a large internal loop with 26 unpaired nucleotides flanked by he

287 The NMR structure reveals an internal loop with no hydrogen bonding between the loop

288 G AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs.

289 revised model for predicting stabilities of internal loops with 6-10 nucleotides is derived by multi

290 pairing and free energy of 2 x 2 nucleotide internal loops with a purine-purine mismatch next to a p

291 Thus, thermodynamic parameters of internal loops with GU closing pairs can contribute to t

292 The thermodynamic stabilities of asymmetric internal loops with GU closing pairs relative to those o

293 ligoribonucleotide duplexes containing small internal loops with GU closing pairs were studied by opt

294 An understanding of internal loops with propensities to form a particular st

295 In internal loops with three or more nucleotides on each si

296 lso thermodynamically more stable than other internal loops with two GU closing pairs and three nucle

297 -loop structure emanating from a purine-rich internal loop, with both sequence and structure playing

298 The decoding site, a small internal loop within the 16S rRNA, is the molecular targ

299 l predicts free energies of 2 x 3 nucleotide internal loops within 0.4 kcal/mol, on average, of the e

300 ote selectivity, we investigated the role of internal loops within ADAR substrates.