ライフサイエンスコーパス: ribozyme

1 vidual RNA molecule with catalytic activity (ribozyme).

2 nition (e.g., aptamers) and catalysis (e.g., ribozymes).

3 ype networks of two catalytic RNA molecules (ribozymes).

4 n on the folding and function of the hairpin ribozyme.

5 ate, docked into the catalytic domain of the ribozyme.

6 3' end produced by self-cleavage of a delta ribozyme.

7 the poor turnover efficiency of the twister ribozyme.

8 re-catalytic structure of the twister-sister ribozyme.

9 ound previously also for the related twister ribozyme.

10 ays soft, non-specific interactions with the ribozyme.

11 inase ribozyme, making this a first-in-class ribozyme.

12 -way junctional twister-sister self-cleaving ribozyme.

13 actorial origins of catalysis by the twister ribozyme.

14 ubdomain of the 'Tetrahymena' group I intron ribozyme.

15 rtiary free-energy landscape of the Azoarcus ribozyme.

16 es that were replicated by an RNA polymerase ribozyme.

17 e the structure and catalytic mechanism of a ribozyme.

18 structure of a 2'-OCH3 -U5 modified twister ribozyme.

19 for destabilizing mutations in the Azoarcus ribozyme.

20 ectivity prevent the complete folding of the ribozyme.

21 ind RNA-puzzle challenge, the lariat-capping ribozyme.

22 wo-fragment form of the ancestral polymerase ribozyme.

23 ditions amenable to catalysis by the hairpin ribozyme.

24 zyme assembly strongly inhibit the resulting ribozyme.

25 ur along an unfolding pathway of the Twister ribozyme.

26 ce of interactions specific to the misfolded ribozyme.

27 rising conclusion that B2 is a self-cleaving ribozyme.

28 e closely similar to those in the hammerhead ribozyme.

29 ically and with the same mechanism as the WT ribozyme.

30 ontain an RNA of interest flanked by Twister ribozymes.

31 operated before the emergence of polymerase ribozymes.

32 ularly of long, structured sequences such as ribozymes.

33 NA molecules including rRNA, tRNA, snRNA and ribozymes.

34 ustain a genome long enough to encode active ribozymes.

35 tic strategies employed by small nucleolytic ribozymes.

36 of the 5'-exon) catalyzed by group II intron ribozymes.

37 serving as unfolded templates and effective ribozymes.

38 ort ribozymes from libraries containing many ribozymes.

39 used to both analyze and engineer allosteric ribozymes.

40 examine several cases of highly promiscuous ribozymes.

41 d DeltaVs comparable to those of the hairpin ribozymes.

42 athways to self-replication and, eventually, ribozymes.

43 or naturally occurring hammerhead and pistol ribozymes.

44 al structures available for all of the known ribozymes, a major challenge involves relating functiona

45 l possible single and double mutants of this ribozyme across a series of ligand concentrations, deter

46 th, the resulting internal dilution produced ribozyme activation.

47 A model of the ribozyme active site is proposed that accommodates these

48 teraction, is sufficient for stabilizing the ribozyme active site, including alignment of the attacki

49 pproach are carried out to control localized ribozyme activities and to label RNAs with dual-color fl

50 stabilized to Mg(2+), which is required for ribozyme activity and RNA synthesis.

51 Ribozyme activity depends on Mg(+2) and monovalent catio

52 rs, B2 and ALU may represent the predominant ribozyme activity in mammalian cells.

53 this network of tertiary interactions reduce ribozyme activity in physiological Mg(2+) concentrations

54 tatic behaviour: the maintenance of constant ribozyme activity per unit volume during protocell volum

55 onucleotides within fatty acid vesicles, and ribozyme activity was inhibited.

56 h specific and random sequence, can modulate ribozyme activity.

57 Real-time observation of single ribozymes after photo-deprotection showed that the precl

58 iFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a

59 ) to a CRISPR RNA (crRNA) array flanked with ribozymes, along with a DRT flanked with either ribozyme

60 f matR expression via synthetically designed ribozymes altered the processing of various introns, inc

61 gs from genetic screens of three proteins, a ribozyme and a protein interaction reveal 3D contacts wi

62 integrate RNA-RNA interaction with available ribozyme and aptamer elements, providing new ways to eng

63 rmined a new crystal structure of the pistol ribozyme and have shown that G40 acts as general base in

64 s, we co-encapsulated high concentrations of ribozyme and oligonucleotides within fatty acid vesicles

65 tion is required for complete folding of the ribozyme and stabilization of the active site.

66 des resulting from the 3' end created by the ribozyme and the 5' end created from an endolytic cleava

67 lations to investigate the mechanism of this ribozyme and to elucidate the roles of the catalytic met

68 folding of certain genetic variants of this ribozyme and use in vitro selection followed by deep seq

69 multiple nucleic acid enzymes including two ribozymes and a deoxyribozyme, underscoring the generali

70 assembly of several altered hammerhead (HH) ribozymes and a singly modified HH substrate.

71 two constructs, an exact monomer flanked by ribozymes and a trihelix-forming RNA with requisite 5' a

72 es, which enables better characterization of ribozymes and aptamers.

73 ng membraneless compartments that accumulate ribozymes and enhance catalysis, and offering a mechanis

74 nalysis efficiently identified highly active ribozymes and estimated catalytic activity with good acc

75 Group II introns are self-splicing ribozymes and mobile genetic elements.

76 roup II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily

77 doknot, which plays a key role in folding of ribozymes and riboswitches, is not addressed in most alg

78 In this review, the chemistry of ribozymes and the influence of pressure is described.

79 been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been ex

80 nucleic acid (SNA) architecture to stabilize ribozymes and transfect them into live cells is reported

81 the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute es

82 nally, the gRNAs linked by the self-cleaving ribozymes and tRNA could be expressed from RNA polymeras

83 ension products long enough to encode active ribozymes and/or aptamers inside model protocells sugges

84 hat multiple gRNAs linked with self-cleaving ribozymes and/or tRNA could be simultaneously expressed

85 stabilization of the transition state by the ribozyme, and functional group substitution at G33 indic

86 t the accessible conformational space of the ribozyme, and that these so-called topological constrain

87 react just 50- to 80-fold slower than the WT ribozyme, and this rate can be improved to near WT by mo

88 , followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic

89 h functional nucleic acids like aptamers and ribozymes, and in some cases key cosolutes localize with

90 complex structured RNAs, including aptamers, ribozymes, and, in low yield, even tRNA.

91 We suggest that while de novo ribozymes appear to be promiscuous in general, they are

92 that large hepatitis delta virus (HDV)-like ribozymes are activated by peripheral domains that bring

93 Self-cleaving ribozymes are found in all domains of life and are belie

94 Ribozymes are highly structured RNA sequences that can b

95 The resulting ribozymes are readily designed for specific target sites

96 The two ribozymes are related but mechanistically distinct.

97 Such new ribozymes are used as biochemical tools, or to address q

98 intron recognition duplex of a self-splicing ribozyme as a model system to study the influence of Mg(

99 tertiary structure formation of the hairpin ribozyme as a model to probe the effects of polyethylene

100 matic nonmonotonic shape fluctuations in the ribozyme as it folds with increasing Mg(2+) or Ca(2+) co

101 design of fast-cleaving engineered synthetic ribozymes as RNA nucleolytic reagents and as subjects fo

102 se the splint oligonucleotides used to drive ribozyme assembly strongly inhibit the resulting ribozym

103 and free energy calculations of the twister ribozyme at different stages along the reaction path to

104 ng and helix assembly of a bacterial group I ribozyme at different temperatures and in different MgCl

105 Here, we show using simulations of Azoarcus ribozyme, based on an accurate coarse-grained three-site

106 We identify new ribozyme-based RNA devices that respond to theophylline,

107 RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have disti

108 tive refolding of a misfolded group I intron ribozyme by CYT-19, a Neurospora crassa DEAD-box protein

109 activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize funct

110 n be circumvented by assembling a functional ribozyme by the templated ligation of short oligonucleot

111 The evolved ribozyme can assemble long RNAs from a mixture of trinuc

112 a three-way junction variant of the hairpin ribozyme can be stabilized by specific insertion of a sh

113 The reverse transcriptase ribozyme can incorporate all four dNTPs and can generate

114 Here we show that RNA polymerase ribozymes can assemble from simple catalytic networks of

115 Ribozymes can catalyze phosphoryl or nucleotidyl transfe

116 The Varkud satellite ribozyme catalyses site-specific RNA cleavage and ligati

117 ivating RNA substrates are incompatible with ribozyme catalysis, it remains unclear how prebiotic sys

118 Nucleolytic ribozymes catalyze site-specific cleavage of their phosp

119 he canonical RNA world in which RNA enzymes (ribozymes) catalyze replication of the RNA genomes of pr

120 ics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying.

121 tudy delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage.

122 the origin of life prior to the evolution of ribozyme-catalyzed RNA replication.

123 of higher-energy substrates required to fuel ribozyme-catalyzed RNA synthesis in the absence of a hig

124 The glmS ribozyme catalyzes a self-cleavage reaction at the phosp

125 econd thiophosphorylation, implying that the ribozyme catalyzes both phosphoryl and nucleotidyl trans

126 The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligati

127 the Varkud satellite, hairpin and hammerhead ribozyme classes.

128 ments is found to result in the emergence of ribozyme cleavage function, thus establishing a connecti

129 Similarities to the hairpin ribozyme cleavage loop activation suggest general strate

130 egies to enhance fidelity in RNA folding and ribozyme cleavage.

131 o a library containing hundreds of different ribozyme clusters that catalyze the triphosphorylation o

132 osome and the RNA subunit of RNase P are the ribozyme components required for catalysis.

133 Endonucleolytic ribozymes constitute a class of non-coding RNAs that cat

134 Pistol ribozymes constitute a new class of small self-cleaving

135 obtained in the case of small self-cleaving ribozymes containing adenine bulges are consistent with

136 viously thought; the catalytic repertoire of ribozymes continues to expand, approaching the goal of s

137 ides are brought into close proximity at the ribozyme core through long-range interactions mediated b

138 n a linked transition and assembles with the ribozyme core via three tertiary contacts: a kissing loo

139 talysis of bond scission in these hammerhead ribozymes could be restored by putative t2M/t4M refoldin

140 unctional switches in a family of hammerhead ribozymes deactivated by stem or loop replacement with a

141 However, the two ribozymes differ in the nature of the general acid.

142 For ribozymes, divalent cations are known to be more efficie

143 t are applied by aptamers, riboswitches, and ribozymes/DNAzymes.

144 n at very low Mg(2+) concentrations when the ribozyme does not form tertiary interactions.

145 helices in diverse structured RNAs including ribozyme domains, riboswitch aptamers, and viral RNA dom

146 ionally insulated from each other by placing ribozymes downstream of terminators to block nuclear exp

147 ve-site Mg(2+) cation to N7 of G33 makes the ribozyme drastically slower.

148 showed that Mg(2+) and Mn(2+) ions increase ribozyme efficiency by making transitions to the high en

149 the P4-P6 domain of the Tetrahymena group I ribozyme embedded in Xenopus egg extract demonstrate the

150 However, how such replicase ribozymes emerged from the pools of short RNA oligomers

151 Our variant ribozymes enabled in vivo regulation of adeno-associated

152 anges are required in the minimal hammerhead ribozyme enzyme strand sequence (providing that the natu

153 Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg(2+) concentrations, and are

154 hows that the landscape contains three major ribozyme families (landscape peaks).

155 Most ribozyme families have distinct catalytic cores stabiliz

156 imates of catalytic activity for hundreds of ribozyme families.

157 hows that, while local optimization within a ribozyme family would be possible, optimization of activ

158 The most efficient new ribozyme (FH14) shows excellent specificity toward its t

159 essful proof-of-principle use of multiplexed ribozyme flanked gRNAs to induce mutations in vivo in Dr

160 Self-cleaving ribozymes fold into intricate structures, which orient a

161 ingle-molecule fluorescence detection of the ribozyme folding pathway.

162 anonical RNA-binding proteins that stabilize ribozyme folding; the apparent chaperoning activity of t

163 spontaneously cleave their own RNA when the ribozyme folds into its active conformation.

164 When Mg(2+) is replaced by Ca(2+) the ribozyme folds, but the active site remains unstable.

165 the conserved evolutionary mechanism used by ribozymes for catalysis.

166 tile trans-acting 2'-5' adenylyl transferase ribozymes for covalent and site-specific RNA labeling.

167 e a significant part of an active hammerhead ribozyme, forging a link between nonenzymatic polymeriza

168 ndividual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously

169 ibe a combinatorial method to identify short ribozymes from libraries containing many ribozymes.

170 of the large sequence space relevant to the ribozyme function.

171 o transcribed tRNA, which are purified after ribozyme-fusion transcription by automated size exclusio

172 ut high in promiscuity, and that these early ribozymes gave rise to specialized descendants with high

173 By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotid

174 diting system for Plasmodium that utilizes a ribozyme-guide-ribozyme (RGR) single guide RNA (sgRNA) e

175 issing loop junction of the Varkud Satellite ribozyme has been experimentally characterized, the dyna

176 Neither in splicing nor for self-cleaving ribozymes has the role of the two Mg(2+) ions been estab

177 For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that ut

178 Small self-cleaving ribozymes have been discovered in all evolutionary domai

179 Additionally, self-cleaving ribozymes have been the subject of extensive engineering

180 ons, as the hammerhead, hairpin, and twister ribozymes have guanines at a similar position as G40.

181 free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-l

182 ndicate that secondary structure assists the ribozyme in navigating the otherwise rugged tertiary fol

183 al model for the active state of the twister ribozyme in solution that is consistent with these and o

184 The ribosome has been described as a ribozyme in which ribosomal RNA is responsible for pepti

185 ife, we evolved populations of self-cleaving ribozymes in an anoxic atmosphere with varying pH in the

186 he docked, catalytically active state of the ribozyme, in part through excluded volume effects; unexp

187 f functional molecules, such as aptamers and ribozymes, in the starting sequence pools.

188 n other ribozymes such as the hairpin and VS ribozymes, in the twister ribozyme there may be a twist.

189 ation and reveals the importance of avoiding ribozyme inhibition by complementary oligonucleotides.

190 e is the O2' of G8, while that of the pistol ribozyme is a hydrated metal ion.

191 The improved polymerase ribozyme is able to synthesize a variety of complex stru

192 The self-cleaving activity of the hammerhead ribozyme is also slowed down by pressure on the basis of

193 A minimal version of the twister ribozyme is reported that lacks the phylogenetically con

194 The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of t

195 cate that the general acid of the hammerhead ribozyme is the O2' of G8, while that of the pistol ribo

196 s of ribose hydroxyls to catalysis by kinase ribozyme K28.

197 From this selected ribozyme library, the shortest ribozyme that was previou

198 owed for the efficient assembly of an active ribozyme ligase.

199 er has previously been reported for a kinase ribozyme, making this a first-in-class ribozyme.

200 re, we explore the idea that these two large ribozymes may have begun their evolutionary odyssey as a

201 Base-modifying ribozymes may have played important roles in early RNA w

202 embranes and encapsulated catalysts, such as ribozymes, may have acted in conjunction with each other

203 ey positions, a mechanistic insight into the ribozyme-mediated cleavage is gained.

204 ules are hydrolyzed during refolding of each ribozyme molecule.

205 network suggests that chance emergence of a ribozyme motif would be more important than optimization

206 Structured RNAs such as ribozymes must fold into specific 3D structures to carry

207 This compensation helps explains why ribozyme mutations are often less deleterious in the cel

208 covery of a new class of small self-cleaving ribozymes named Pistol.

209 otif represents a new class of self-cleaving ribozymes of yet unknown biological function.

210 RNA precursors, monomers, active ribozymes, oligonucleotides and lipids are shown to (1)

211 ozymes, along with a DRT flanked with either ribozymes or crRNA targets, produces primary transcripts

212 tatively more promiscuous than later evolved ribozymes or protein enzymes.

213 nditional mutations that alter the wild-type ribozyme phenotype under a stressful environmental condi

214 obtained a complete activity profile of the ribozyme pool which was used to both analyze and enginee

215 More than 90% of the positively designed ribozymes possess self-cleaving activity, whereas more t

216 In the case of the hairpin ribozyme, pressure slowed down the self-cleavage reactio

217 by some endoribonucleases and self-cleaving ribozymes produces RNA fragments with 5'-hydroxyl (5'-OH

218 ficult to study, however, because the active ribozyme rapidly converts to product.

219 The ribozymes rapidly undergo autocatalytic cleavage, leavin

220 profiling, all 54 genetic parts (promoters, ribozymes, RBSs, terminators) are parameterized and used

221 Most ribozymes react just 50- to 80-fold slower than the WT r

222 cleophile for the required inline hammerhead ribozyme reaction mechanism.

223 ATP hydrolysis that occurs in the absence of ribozyme refolding, we find that approximately 100 ATPs

224 By comparing the rates of ATP hydrolysis and ribozyme refolding, we find that several hundred ATP mol

225 he substrate and the catalytic domain of the ribozyme, resulting in a rearrangement of the substrate

226 tro for the ability to synthesize functional ribozymes, resulting in the markedly improved ability to

227 onal structures of the hammerhead and pistol ribozymes reveals many close similarities, so in this wo

228 or Plasmodium that utilizes a ribozyme-guide-ribozyme (RGR) single guide RNA (sgRNA) expression strat

229 ts application to a model RNA: the core glmS ribozyme riboswitch, which performs a ligand-dependent s

230 hese structures are functionally relevant in ribozymes, riboswitches, rRNA, and during replication.

231 cies, which undergo 5'-end maturation by the ribozyme RNase P.

232 th ribosomal subunits enhance RNA polymerase ribozyme (RPR) function, as do derived homopolymeric pep

233 The protocol is analogous to (deoxy)ribozyme selections, but it enables the development of f

234 Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine b

235 hat attempt to predict pseudoknot-containing ribozymes, self-cleavage activity has not been tested.

236 transition of a newly synthesized hammerhead ribozyme sequence from its inactive, duplex state to its

237 tuating environmental conditions can allow a ribozyme sequence to alternate between acting as a templ

238 s a structural and functional mapping of the ribozyme sequence, revealing the catalytic consequences

239 is helpful to identify the shortest possible ribozymes since they are easier to deploy as a tool, and

240 The properties of this novel ribozyme-SNA are characterized in the context of the tar

241 es such as PEG stabilize a bacterial group I ribozyme so that the RNA folds in low Mg(2+) concentrati

242 dissociation, thus maintaining near-constant ribozyme specific activity throughout protocell growth.

243 in previously observed variations in hairpin ribozyme stability.

244 concentration and decreases with decreasing ribozyme stability.

245 Our findings expand the repertoire of ribozyme structures and highlight the conserved evolutio

246 Small ribozymes such as Oryza sativa twister spontaneously cle

247 acid acting through the N1 position in other ribozymes such as the hairpin and VS ribozymes, in the t

248 nd phosphate mutations in the twister-sister ribozyme, suggest contributions to the cleavage chemistr

249 y expanding our toolset of highly functional ribozyme switches.

250 ings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and ha

251 ting aptamers that exhibit ligand-responsive ribozyme tertiary interactions.

252 The correct folding of the active site and ribozyme tertiary structure is also regulated by metal i

253 including a previously described polymerase ribozyme that catalyzes the template-directed synthesis

254 ter RNA is a recently discovered nucleolytic ribozyme that is present in both bacteria and eukarya.

255 We report a single ribozyme that performs both reactions, with a nucleobase

256 rt a 3.3 A crystal structure of the complete ribozyme that reveals the active, shifted conformation o

257 this selected ribozyme library, the shortest ribozyme that was previously identified had a length of

258 Group II introns are Mg(2+)-dependent ribozymes that are considered to be the evolutionary anc

259 Group II introns are large, autocatalytic ribozymes that catalyze RNA splicing and retrotransposit

260 d RNA pool allowed for in vitro evolution of ribozymes that modify a predetermined nucleotide in cis

261 xizymes (transfer RNA (tRNA) synthetase-like ribozymes that recognize synthetic leaving groups) have

262 2/ALU SINEs may be classified as "epigenetic ribozymes" that function as transcriptional switches dur

263 ly known methods to generate catalytic RNAs (ribozymes) that do not exist in nature.

264 been reported of a new catalytic RNA, the TS ribozyme, that has been identified through comparative g

265 two-piece version of the Tetrahymena group I ribozyme, the separated P5abc subdomain folds to local n

266 the hairpin and VS ribozymes, in the twister ribozyme there may be a twist.

267 the case of the hepatitis delta virus (HDV) ribozyme, there are three high-resolution crystal struct

268 linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we

269 ded would have depended on an RNA polymerase ribozyme to copy functional RNA molecules, including cop

270 The unexpected ability of an RNA polymerase ribozyme to copy RNA into DNA has ramifications for unde

271 cient ligation but which allow the assembled ribozyme to remain active.

272 we engineered a class of type III hammerhead ribozymes to develop RNA switches that are highly effici

273 r molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg(2+) concentrations

274 The ability of enzymes, including ribozymes, to catalyze side reactions is believed to be

275 airing interaction in the minimal hammerhead ribozyme transforms an RNA sequence possessing typically

276 first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with fu

277 red from structure, and suggest that the HDV ribozyme transition state resembles the cleavage product

278 tabilized the active structure of the mutant ribozymes under physiological conditions.

279 ause of earlier findings that ~90% of global ribozyme unfolding cycles lead back to the kinetically p

280 appears that the solution of the hammerhead ribozyme used in this study contains two populations of

281 Herein, we design double-pseudoknot HDV ribozymes using an inverse RNA folding algorithm and tes

282 Our results suggest that group I ribozymes utilize the same interactions with specific me

283 tative characterization of greater than 1000 ribozyme variants in a single experiment.

284 We generated a library of predefined ribozyme variants that were converted to DNA and analyze

285 h concentrations, and dilution activates the ribozyme via inhibitor dissociation, thus maintaining ne

286 f P4-P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance ene

287 Here the class I RNA polymerase ribozyme was evolved in vitro for the ability to synthes

288 A highly evolved RNA polymerase ribozyme was found to also be capable of functioning as

289 rotocol on the library of triphosphorylation ribozymes, we identified a 17-nucleotide sequence motif

290 rinting polymers, peptide nucleic acids, and ribozymes were encompassed as "products" of biomimetic c

291 nsional structure is essential, including as ribozymes where they catalyze chemical reactions.

292 eled adenine at this position in the twister ribozyme, which is significantly shifted compared to the

293 y, whereas more than 70% of negative control ribozymes, which are predicted to fold to the necessary

294 Ribozymes, which carry out phosphoryl-transfer reactions

295 It has been speculated that the earliest ribozymes, whose emergence marked the origin of life, we

296 to the genetic code would be the reaction of ribozymes with activated amino acids, such as 5(4 H)-oxa

297 Thus, fast-cleaving functional ribozymes with multiple pseudoknots can be designed comp

298 Kinetic analysis of ribozymes with systematically altered length and stabili

299 rresponds to an inability to restructure the ribozyme without losing activity.

300 e bearing on the question of whether de novo ribozymes would be quantitatively more promiscuous than