ライフサイエンスコーパス: RNA folding

1 bel-free single-molecule analysis of DNA and RNA folding.

2 nstead, they are governed by the kinetics of RNA folding.

3 property of transcription that can influence RNA folding.

4 nents: primary ligand binding and subsequent RNA folding.

5 section of the roles of DEAD box proteins in RNA folding.

6 roup I intron, to address basic questions in RNA folding.

7 osome, and an interesting paradigm for large RNA folding.

8 inants in the energetic balance that governs RNA folding.

9 he energetic contribution of these forces in RNA folding.

10 at nature has not completely optimized P4-P6 RNA folding.

11 acromolecules via comparisons of protein and RNA folding.

12 e-resolved infrared spectroscopy in studying RNA folding.

13 rucial to a detailed understanding of global RNA folding.

14 nactive structures that are kinetic traps in RNA folding.

15 ose continued presence is not required after RNA folding.

16 teractions from the intrinsic free energy of RNA folding.

17 ll picture of the energetics of Mg2+-induced RNA folding.

18 al utility of pyrene fluorescence to monitor RNA folding.

19 tly for the rapid collapse observed early in RNA folding.

20 lows us to extract the elusive prefactor for RNA folding.

21 e generalized to understand protein-assisted RNA folding.

22 hat is not anticipated by current models for RNA folding.

23 lar mechanism of transcriptional pausing and RNA folding.

24 volved in catalysis from those important for RNA folding.

25 ly formed prior to the rate-limiting step in RNA folding.

26 o resolve nonnative structures formed during RNA folding.

27 by demonstrating functional reversibility in RNA folding.

28 sms driving these early compaction events in RNA folding.

29 y, as well as allow genome-scale analyses of RNA folding.

30 pecific RNases and thermodynamic modeling of RNA folding.

31 -loop-helix motifs, serves as a paradigm for RNA folding.

32 interactions as essential driving forces for RNA folding.

33 r for the use of human-guided simulations to RNA folding.

34 ze topological constraints as a key force in RNA folding.

35 act order model will not suffice to describe RNA folding.

36 argely ignored the effects of nonequilibrium RNA folding.

37 synergy between ligand- and Mg(2+)-mediated RNA folding.

38 ia a rugged energy landscape, reminiscent of RNA folding.

39 anging from simple ligand binding to complex RNA folding.

40 sition with regulatory factor binding and/or RNA folding, a direct causal link between pausing and ch

41 eral implementations of Nussinov's classical RNA folding algorithm have been proposed.

42 The RNA folding algorithm mfold indicated that the presence

43 n is an original extension of the underlying RNA folding algorithm to account for the likely existenc

44 Based on our experimental results and an RNA folding algorithm, we predict that RepE binding to t

45 ructural elements were utilized in the Mfold RNA-folding algorithm.

46 extensive RNA structure was predicted using RNA folding algorithms and confirmed by selective 2'-hyd

47 oximately 150 nt 3'-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phyl

48 vity data that can be used as constraints in RNA folding algorithms to predict structures on par with

49 singly apparent over the last several years: RNA folding algorithms underlie numerous applications in

50 Here we evaluate 11 different RNA folding algorithms' riboSNitch prediction performanc

51 those predicted by commonly used regulatory RNA-folding algorithms.

52 et out to explore dynamic aspects of twister RNA folding along the cleavage reaction coordinate.

53 In silico RNA folding analysis and translational reporter assays r

54 r results indicate substantial modularity in RNA folding and assembly and suggest that these processe

55 understanding of the roles of metal ions in RNA folding and catalysis and have applications in struc

56 us cofactor for nucleic acids, with roles in RNA folding and catalysis as well as in processing of nu

57 Many studies of RNA folding and catalysis have revealed conformational h

58 To exert control over RNA folding and catalysis, both molecular engineering st

59 Mg(2+) is essential for RNA folding and catalysis.

60 s is important for high-precision studies of RNA folding and catalytic behavior, but photodamage accr

61 f the physical origins of the DeltaC(P)s for RNA folding and consider their impact on biological func

62 eight specific pRNA sites without perturbing RNA folding and dimer formation, and a total of 17 inter

63 To advance our understanding of RNA folding and dynamics it is critical to know the flex

64 Thus, an understanding of RNA folding and function will require deep and incisive

65 play central, currently unexplored, roles in RNA folding and function.

66 a tool for rationally tuning and optimizing RNA folding and function.

67 study conformational changes associated with RNA folding and function.

68 bozyme is a minimalist paradigm for studying RNA folding and function.

69 with magnesium (Mg2+) ions are essential for RNA folding and function.

70 ors, recent advances in our understanding of RNA folding and functions have motivated the use of RNA

71 Our results highlight multiple pathways in RNA folding and illustrate how kinetic competitions betw

72 NA structural motifs play essential roles in RNA folding and interaction with other molecules.

73 hese findings provide a global assessment of RNA folding and its significant regulatory effects in a

74 des may function as molecular timers in many RNA folding and ligand recognition reactions.

75 retical model describing the linkage between RNA folding and magnesium ion binding.

76 ing to an understanding of the principles of RNA folding and of the molecular interactions that under

77 landscape, with sequential and hierarchical RNA folding and protein binding events finally convergin

78 d mutation assay, we show that strengthening RNA folding and reducing R-loop formation by synonymous

79 for quantitative, time-resolved analysis of RNA folding and ribonucleoprotein (RNP) assembly mechani

80 A collapsed states play fundamental roles in RNA folding and ribonucleoprotein assembly processes, th

81 ertiary interactions are critical for proper RNA folding and ribozyme catalysis.

82 st general strategies to enhance fidelity in RNA folding and ribozyme cleavage.

83 re powerful in NMR spectroscopic analysis of RNA folding and RNA ligand interactions.

84 ial 30S ribosomes involves a large number of RNA folding and RNA-protein binding steps.

85 bility, uncover rG4-dependent differences in RNA folding and show evolutionarily conserved enrichment

86 Toward our mechanistic studies of RNA folding and structures with heterogeneous backbones,

87 e native state is not a universal feature of RNA folding and that there is an alternative paradigm in

88 between the early conformational changes in RNA folding and the "burst phase" changes and molten glo

89 abilizing transient RNA conformations, while RNA folding and the early stages of protein binding are

90 of problems including protein-ssNA binding, RNA folding and the polymer nature of NAs.

91 These findings provide a new paradigm for RNA folding and they underscore the diversity of RNA bio

92 alized conformational events contributing to RNA folding and unfolding that could not be observed by

93 s a powerful method to study the kinetics of RNA folding and unfolding transitions.

94 to investigate the biophysical mechanisms of RNA folding and unfolding, its interactions with ligands

95 d connectivity are important determinants of RNA folding, and demonstrates the potential of coarse-gr

96 Counterions are required for RNA folding, and divalent metal ions such as Mg(2+) are

97 red to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent

98 ng been recognized as a key factor governing RNA folding, and is crucial for many diverse functions o

99 ysical processes such as chromosome packing, RNA folding, and molecular recognition.

100 ess: specific binding by a few copies of CP, RNA folding, and then cooperative binding of CP to the "

101 RS3D is widely applicable to a variety of RNA folding architectures currently present in the struc

102 yRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed.

103 Using RNA folding as a test case, we demonstrate that protein-

104 deal system for investigating this aspect of RNA folding as ligand-dependent termination is obligator

105 lead to a superior fluorescence signal upon RNA folding, as demonstrated by equilibrium titrations w

106 lly active RNA structure is still limited by RNA folding, as visualized directly using time-resolved

107 To dissect RNA folding at the molecular level, we performed simulat

108 ghlight the importance of chain stiffness to RNA folding; at 10 mM Mg2 +, a stiff hinge limits the ra

109 tive framework for describing key aspects of RNA folding behavior and also provide the first evidence

110 now begin to build more detailed models for RNA folding behavior.

111 remely stable, likely due to the cooperative RNA folding behavior.

112 Intermediates play important roles in RNA folding but can be difficult to characterize when sh

113 , is not designed for applications involving RNA folding but rather offers a stable RNA structure for

114 tead we propose that higher [Mg(2+)] can aid RNA folding by decreasing the entropic penalty of counte

115 stigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization

116 order from ten different RNAs suggests that RNA folding can be divided into two classes.

117 ctivation of PKR and provide a model for how RNA folding can be related to human disease.

118 strated that the local free-energy minima of RNA folding can be used to detect the positions of the s

119 While the computational analysis of RNA folding can make use of well-established models of t

120 For RNA, folding can only begin after the polyelectrolyte pr

121 perimental results for the thermodynamics of RNA folding cannot be explained by simple pairwise hydro

122 ses, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated

123 m whereby metabolite-dependent alteration of RNA folding controls splicing and alternative 3' end pro

124 oss protein-coding transcripts that indicate RNA folding demarcates regions of protein translation an

125 ructure determines the speed and accuracy of RNA folding, docking of a tetraloop with its receptor in

126 s and was greatly facilitated by a conserved RNA folding domain (1,470 to 1,877 nucleotides upstream)

127 s a communication module to render disparate RNA folding domains interdependent.

128 We explore the temperature dependence of RNA folding due to the ubiquitous GAAA tetraloop-recepto

129 Overall, this study demonstrates that RNA folding during HIV-1 transcription is dynamic and th

130 RNA folding during transcription directs an order of fol

131 RNA folding during transcription resembles folding in a

132 iptional pausing may be a general feature of RNA folding during transcription.

133 We simulated co-transcriptional RNA folding dynamics to identify competing secondary str

134 Existing models have focused on how RNA folding energetics control translation initiation ra

135 extracted from the data correlate well with RNA folding energies obtained from cotranscriptional fol

136 of transcriptome organization in the form of RNA folding energies.

137 active folds occurs unexpectedly high on the RNA folding energy landscape, resulting in partially irr

138 aled two sequential steps of protein-induced RNA folding, establishing a hierarchical RNP assembly me

139 e function of assembly factors and ribosomal RNA folding events are lacking.

140 os or significantly shorter than large scale RNA folding events.

141 resistance that we used with mutagenesis and RNA folding experiments to show that Xrn1-resistant RNAs

142 energetic linkage between Mg(2+) binding and RNA folding for both of these systems without requiring

143 ial release covers parameters for predicting RNA folding free energy and enthalpy changes.

144 melting experiments were also used to obtain RNA-folding free energies.

145 Cation-mediated RNA folding from extended to compact, biologically activ

146 in the eventual quantitative description of RNA folding from its secondary and tertiary structural e

147 are a primeval motif, with pivotal roles in RNA folding, function and evolution.

148 the experimental study of cotranscriptional RNA folding has been limited by the lack of easily appro

149 The influence of DeltaC(P) on RNA folding has been widely overlooked and is poorly und

150 insights into electrostatic contributions to RNA folding; however, it can be challenging to isolate t

151 Finally, our data suggest that RNA folding impact the aggregation behavior of the funct

152 free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a m

153 RNA folding in the cell occurs during transcription.

154 ms, yet the thermodynamic forces which drive RNA folding in vitro may not be sufficient to predict st

155 and II introns are prone to kinetic traps in RNA folding in vivo and that the splicing of both types

156 RNA folding in vivo is significantly influenced by trans

157 e contribution of thermodynamic stability to RNA folding in vivo.

158 The data support a mechanistic model of RNA folding in which the element is comprised of both ca

159 ifs carry out a wide variety of functions in RNA folding, in RNA-RNA and RNA-protein interactions.

160 ulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping b

161 We conclude that RNA folding intermediates adopt extended conformations d

162 he opportunity to determine the structure of RNA folding intermediates and conformational trajectorie

163 to act as an RNA chaperone or by stabilizing RNA folding intermediates.

164 These findings have consequences in RNA folding, intermolecular interaction, and packing, in

165 iological processes, including initiation of RNA folding into complex tertiary shapes, promotion of d

166 ch backbone heterogeneity is compatible with RNA folding into defined three-dimensional structures th

167 s suggest that the protein cofactor-assisted RNA folding involves sequential non-specific and specifi

168 RNA folding is a complicated kinetic process.

169 RNA folding is a remarkably complex problem that involve

170 The process of large RNA folding is believed to proceed from many collapsed s

171 We propose that the major barrier to RNA folding is dominated by entropy changes when counter

172 RNA folding is enabled by interactions between the nucle

173 milarity in tertiary structure suggests that RNA folding is independent of sequence and length.

174 RNA folding is initiated by addition of Mg(2+) or protei

175 NA condensation is well known, their role in RNA folding is less understood.

176 This suggests that RNA folding is non-sequential under a variety of differe

177 crowding environment, the impact of which on RNA folding is poorly understood.

178 We further reveal that RNA folding is significantly anticorrelated with overall

179 Current models assume that RNA folding is strongly hierarchical such that the base-

180 ent of the bI3 RNP are thus not independent: RNA folding is strongly nonhierarchical.

181 A requirement for specific RNA folding is that the free-energy landscape discrimina

182 A fundamental question in RNA folding is the mechanism of thermodynamic stability.

183 A fundamental question in RNA folding is the nature of the rate-limiting step.

184 key issues in the theoretical prediction of RNA folding is the prediction of loop structure from the

185 energy, enthalpy, and entropy landscapes of RNA folding is unknown.

186 counting for this phenomenon of Mg2+-induced RNA folding, it is necessary to independently determine

187 Simulating RNA folding kinetics can provide unique insight into RNA

188 the rugged energy landscapes and multistate RNA folding kinetics even for small RNA systems such as

189 a general computational approach to simulate RNA folding kinetics that can be used to extract populat

190 tions, we propose a new analytical model for RNA folding kinetics.

191 rategies previously used for the analysis of RNA folding kinetics.

192 ically without incurring associated costs in RNA folding kinetics.

193 an unprecedented view of the topology of an RNA folding landscape and the RNA structural features th

194 identify the same biases in a computational RNA-folding landscape as well as regulatory sequence bin

195 oximating the set of local minima in partial RNA folding landscapes associated with a bounded-distanc

196 esults show that RNA chaperones can simplify RNA folding landscapes by weakening intramolecular inter

197 e data demonstrate that severe ruggedness of RNA folding landscapes extends into conformational space

198 RNA folding landscapes have been described alternately a

199 The study of rugged RNA folding landscapes holds the key to answer these que

200 Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA

201 motions have the greater potential to govern RNA folding, ligand recognition, and ribonucleoprotein a

202 quitous nature of misfolded intermediates in RNA folding, little is known about their physical proper

203 oped thermodynamic scanning method predicted RNA folding mapping precisely to regions of SSSV and at

204 he perspective that a generalizable model of RNA folding may be developed from understanding of the f

205 he weak capacity of Tris-borate to stabilize RNA folding may reflect relatively unfavorable interacti

206 d with temperature-dependent single-molecule RNA folding measurements, which identify that crowding e

207 ous thermodynamics-based models of a general RNA folding mechanism, our observations indicate that st

208 on in bacterial cells, putrescine2+, and how RNA folding might be influenced by the three ions in com

209 ly developed "Vfold" model (a coarse-grained RNA folding model) provides an effective method to gener

210 , may ultimately lead to an all-encompassing RNA folding model.

211 To broaden the scope of RNA folding models and to better understand group II int

212 ment and conformational energetics that make RNA folding more complex than protein folding.

213 tion (GAIT)-elements relies on the conserved RNA folding motifs rather than the conserved sequence mo

214 eat interest to understand the repertoire of RNA folding motifs.

215 Expedient RNA folding must avoid the formation of undesirable stru

216 uring the linkage between Mg(2+) binding and RNA folding must be reinterpreted.

217 biophysical factors, such as the kinetics of RNA folding; no current implementation considers both ev

218 er the potential for intramolecular rod-like RNA folding nor the presence of the delta protein confer

219 Globally RNA folding occurs in multiple stages involving chain co

220 RNA folding occurs via a series of transitions between m

221 RNA folding parameters including specific heat, contact

222 These results identify the RNA folding pathway during telomerase biogenesis and def

223 rder of protein binding, suggesting that the RNA folding pathway forms the basis for early steps of r

224 stitute kinetic traps in the CYT-18-assisted RNA-folding pathway.

225 RET methods to address the thermodynamics of RNA folding pathways by probing the intramolecular docki

226 ellular polyamine concentrations could alter RNA folding pathways.

227 determine the relative flux through parallel RNA folding pathways.

228 lysis, m-values (change in DeltaG degrees of RNA folding per molal concentration of osmolyte) have be

229 RNA folding plays an important role in controlling prote

230 econdary structures of the HIV-2 RRE and two RNA folding precursors have been identified using the SH

231 elegant and efficient solution, the inverse RNA folding problem appears to be hard.

232 ates that successful designs for the inverse RNA folding problem does not necessarily have to rely on

233 However, whereas the RNA folding problem from an algorithmic viewpoint has an

234 Decades of study of the RNA folding problem have revealed that diverse and compl

235 raction with a combinatorial approach to the RNA folding problem in order to compute all possible non

236 o-scale designs, the interest in the inverse RNA folding problem is bound to increase.

237 A critical step toward solving the RNA folding problem is the characterization of the assoc

238 At the heart of the RNA folding problem is the number, structures, and relat

239 d RNA-protein interactions are present in an RNA folding problem.

240 troviral therapy and represents a compelling RNA folding problem.

241 ity in folding is an important aspect of the RNA folding problem.

242 , indicating Mg(2+) and Na(+) synergy in the RNA folding process.

243 complex energy landscapes often observed for RNA folding processes and lays the groundwork for a sign

244 activation enthalpies generally observed for RNA folding processes.

245 RNA folding programs applied to the TER sequences show t

246 Sequence alignment software, thermodynamic RNA folding programs, and classical comparative phylogen

247 ion is not predicted by available predictive RNA folding programs, is the major conformer at physiolo

248 ding of the mechanism by which urea enhances RNA folding rates.

249 s to promote only the final few angstroms of RNA folding rather than mediate global conformational re

250 acts may be a general property of elementary RNA folding reactions.

251 ent manner and are important determinants of RNA folding, recognition, and functions.

252 nding the linkage between Mg(2+) binding and RNA folding requires a proper theoretical model describi

253 oteins to DNA and RNA, DNA condensation, and RNA folding, requires an understanding of the ion atmosp

254 An RNA folding/RNA secondary structure prediction algorithm

255 h that used mechanistic modeling and kinetic RNA folding simulations to engineer RNA-regulated geneti

256 eveloped an open software for coarse-grained RNA folding simulations, guided by human intuition.

257 As a result, strengthening RNA folding simultaneously curtails genotypic and phenot

258 Using RNA folding software mfold, we found that the predicted

259 ucleotide as a comprehensive function of the RNA folding state.

260 resis is a powerful approach for visualizing RNA folding states and folding intermediates.

261 -pair resolution while also allowing for the RNA folding statistics of smaller RNA sequences to be co

262 V is involved in a critical Mg(2+)-dependent RNA folding step in group II introns and demonstrate the

263 ndicate that cellular factors delay specific RNA folding steps to ensure the quality of assembly.

264 of ribosomal proteins and numerous ribosomal RNA folding steps.

265 Possible RNA folding structures of presumed antitermination seque

266 RNA and its use merits careful evaluation in RNA folding studies.

267 biophysical effects that are known to affect RNA folding such as chemical nucleotide modifications an

268 es about the cellular environment effects in RNA folding, such as molecular crowding and cotranscript

269 kinetic and thermodynamic profiles for this RNA folding system when stabilized by potassium versus m

270 We describe a protocol developed to study RNA folding that can be readily tailored to particular a

271 s a new and important level of complexity in RNA folding that could be relevant to the biological fun

272 CP-induced folding is distinct from RNA folding that depends on base-pairing to stabilize te

273 opose a new regulatory mechanism mediated by RNA folding that may also explain the dual properties of

274 undational for a predictive understanding of RNA folding that will allow manipulation of RNA folding

275 nce information as well as simple aspects of RNA folding that would be occurring during the RNA/capsi

276 e of their frequent transcription and strong RNA folding, the latter also improves translational fide

277 rary to the expectation that Mg2+ stabilizes RNA folding, the mtRNAMet D-domain structure was unfolde

278 ugh DEAD-box proteins play multiple roles in RNA folding, the physiological function of Mss116p in aI

279 es in the development of a new generation of RNA folding theories and models.

280 hypothesis inspired by this modularity-that RNA folding thermodynamics and kinetics can be quantitat

281 RNA folding that will allow manipulation of RNA folding thermodynamics and kinetics.

282 RNA folding thermodynamics are crucial for structure pre

283 -molecular-weight polyethylene glycol on the RNA folding thermodynamics is dramatic, with up to Delta

284 r atomic resolution accuracy and analysis of RNA folding thermodynamics.

285 teins or other ligands can require extensive RNA folding to create an induced fit.

286 lecular processes, spanning from protein and RNA folding to functional transitions in molecular machi

287 The sensitivity of RNA folding to the combination of Mg2+ and putrescine2+

288 roblems, from fibril structure prediction to RNA folding to the design of new protein interfaces, to

289 radius and temperature on counterion-induced RNA folding transitions.

290 extension (SHAPE)-directed ensemble for the RNA folding under different conditions, and we project t

291 optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated.

292 s permit crowding effects on the kinetics of RNA folding/unfolding to be explored for the first time

293 though we have illustrated the complexity of RNA folding using hTR as a case study, general arguments

294 matic structure probing indicated that local RNA folding was not completely altered.

295 o study the role of sequence and topology in RNA folding, we determined the kinetic folding pathways

296 ne the role of topology and contact order in RNA folding, we screened for circular permutants of the

297 the massively parallel genetic algorithm for RNA folding, we show that the core region of the 3'-untr

298 iversal mechanism for monovalent facilitated RNA folding, whereby an increasing monovalent concentrat

299 turn provides an excellent, simple model for RNA folding, which can be dissected at the atomic level.

300 Synchronization of factor binding and/or RNA folding with the RNA polymerase position is a major