ライフサイエンスコーパス: RNA folding

1 amic RNA folding processes and principles of RNA folding.

2 anging from simple ligand binding to complex RNA folding.

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

4 property of transcription that can influence RNA folding.

5 nents: primary ligand binding and subsequent RNA folding.

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

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

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

9 inants in the energetic balance that governs RNA folding.

10 flaviviruses with a thermodynamic model for RNA folding.

11 he energetic contribution of these forces in RNA folding.

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

13 acromolecules via comparisons of protein and RNA folding.

14 e-resolved infrared spectroscopy in studying RNA folding.

15 rucial to a detailed understanding of global RNA folding.

16 nactive structures that are kinetic traps in RNA folding.

17 ose continued presence is not required after RNA folding.

18 teractions from the intrinsic free energy of RNA folding.

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

20 al utility of pyrene fluorescence to monitor RNA folding.

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

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

23 e generalized to understand protein-assisted RNA folding.

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

25 lar mechanism of transcriptional pausing and RNA folding.

26 volved in catalysis from those important for RNA folding.

27 teract with RNA is relevant in understanding RNA folding.

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

29 o resolve nonnative structures formed during RNA folding.

30 nsight into nucleotide positions critical to RNA folding.

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

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

33 interactions as essential driving forces for RNA folding.

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

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

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

37 argely ignored the effects of nonequilibrium RNA folding.

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

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

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

41 le-pseudoknot HDV ribozymes using an inverse RNA folding algorithm and test their kinetic mechanisms

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

43 The RNA folding algorithm mfold indicated that the presence

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

45 Our work, though inexact, is the first RNA folding algorithm to achieve linear runtime (and lin

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

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

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

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

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

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

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

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

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

55 In silico RNA folding analysis and translational reporter assays r

56 t functional folds establishes principles of RNA folding and applications in biotechnology.

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

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

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

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

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

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

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

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

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

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

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

68 study conformational changes associated with RNA folding and function.

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

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

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

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

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

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

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

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

77 ifications might affect the kinetic rates of RNA folding and other conformational transitions that ar

78 erstanding how the interplay between nascent RNA folding and protein binding determines the fate of t

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

98 in the context of transcription elongation, RNA folding, and ligand binding.

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

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

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

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

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

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

105 We examined RNA folding at both the secondary and tertiary structura

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

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

108 y affecting splicing of nascent transcripts, RNA folding, base modification, transport, localization,

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 Therefore, understanding RNA folding conformations, in particular, RNA secondary

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

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

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

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

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 provide a general mechanism to shape nascent RNA folding during RNP assembly.

131 RNA folding during transcription directs an order of fol

132 RNA folding during transcription resembles folding in a

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

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

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

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

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

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

139 elop an algorithm that we name 'detection of RNA folding ensembles using expectation-maximization' (D

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

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

142 systematic approach to automatically detect RNA folding events from these datasets to reduce human b

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

144 ong-range tertiary interaction guides native RNA folding for both secondary and tertiary structure.

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

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

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

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

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

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

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

152 on containing a mixture of both ion types on RNA folding has remained a challenging problem for decad

153 Although many algorithms for inverse RNA folding have been developed, the pseudoknot, which p

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

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

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

157 Small molecule ligands can thus promote RNA folding in cells, and thus allow single mRNA imaging

158 RNA folding in the cell occurs during transcription.

159 ongation confirmed the importance of nascent RNA folding in transcription.

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

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

162 RNA folding in vivo is significantly influenced by trans

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

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

165 We conclude that RNA folding intermediates adopt extended conformations d

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

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

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

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

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

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

172 RNA folding is a complicated kinetic process.

173 RNA folding is a remarkably complex problem that involve

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

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

176 RNA folding is enabled by interactions between the nucle

177 the SARS-CoV-2 genomic propensity for stable RNA folding is exceptional among RNA viruses, supersedin

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

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

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

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

182 RNA folding is often studied by renaturing full-length R

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

184 Surprisingly, SRP RNA folding is robust to transcription rate changes and

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

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

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

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

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

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

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

192 Simulating RNA folding kinetics can provide unique insight into RNA

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

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

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

196 ically without incurring associated costs in RNA folding kinetics.

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

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

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

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

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

202 RNA folding landscapes have been described alternately a

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

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

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

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

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

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

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

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

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

212 exible application to study broad classes of RNA folding mechanisms.

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

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

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

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

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

218 Expedient RNA folding must avoid the formation of undesirable stru

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

220 Globally RNA folding occurs in multiple stages involving chain co

221 RNA folding occurs via a series of transitions between m

222 RNA folding parameters including specific heat, contact

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

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

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

226 determine the relative flux through parallel RNA folding pathways.

227 ellular polyamine concentrations could alter 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 by multiple proteins overcomes heterogeneous RNA folding, preventing assembly bottlenecks and initiat

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

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

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

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

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

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

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

239 troviral therapy and represents a compelling RNA folding problem.

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

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

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

243 is poised to reveal a wide range of dynamic RNA folding processes and principles of RNA folding.

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

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

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

252 An RNA folding/RNA secondary structure prediction algorithm

253 This tool for light-controlled single RNA folding should offer precise and rapid control of ot

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

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

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

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

258 Here we show that RNA folding stability of SARS-CoV-2 genome is exceptiona

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 O(n3)-time dynamic programming algorithm for RNA folding that is amenable to heuristics that make it

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 te is crucial for an accurate calculation of RNA folding thermodynamics.

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

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

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

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

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

290 vent discovery and generate hypotheses about RNA folding trajectories for further analysis and experi

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

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

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

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

295 d, single-molecule, through-space probing of RNA folding using the RING-MaP correlated chemical probi

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

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

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

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

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