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1 ive riboswitch (P(tac)-riboswitch and P(BAD)-riboswitch).
2 lorimetry, explaining the specificity of the riboswitch.
3 ry site (IRES) and the flavin-mononucleotide riboswitch.
4 ine riboswitch and as the second for the ZMP riboswitch.
5 d metabolite-bound closed state of the SAM-I riboswitch.
6 e folding free energy landscape of the SAM-I riboswitch.
7 folding free energy landscape of the SAM-II riboswitch.
8 s strong co-transcriptional effects for this riboswitch.
9 and the P3 helix is a bottleneck in the apo riboswitch.
10 7-aminomethyl-7-deazaguanine (preQ1)-sensing riboswitch.
11 is distinctly different from that in the apo riboswitch.
12 evealed new tertiary interactions in the TPP riboswitch.
13 n-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch.
14 positive bacteria are regulated by the T box riboswitch.
15 edge, of translational regulation in a T box riboswitch.
16 P(tac) > P(BAD) > P(BAD)-riboswitch > P(tac)-riboswitch.
17 orce spectroscopy trajectory for multi-state riboswitch.
18 ding landscape that controls the fate of the riboswitch.
19 le RNA and the Bacillus cereus crcB fluoride riboswitch.
20 omeostasis is controlled by yybP-ykoY family riboswitches.
21 Gram-positive bacteria is monitored by T-box riboswitches.
22 egion (UTR) derives from bacterial and other riboswitches.
23 regulation implemented by a wide variety of riboswitches.
24 t in Archaea is controlled by FMN-responsive riboswitches.
25 development of efficient cis-acting aptazyme riboswitches.
26 ersity of naturally occurring ligand-binding riboswitches.
27 t the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 angstrom and 4.1 a
28 strand-specific RNA sequencing to identify 4 riboswitches, 13 trans-acting (intergenic), and 22 cis-a
29 standard inducible promoters and orthogonal riboswitches, a multi-layered modular genetic control ci
30 ap, we prepared 15 mutants of the preQ(1)-II riboswitch-a structurally and biochemically well-charact
32 cted toward the identification of artificial riboswitch activators by establishing high-throughput sc
37 ong evidence that translationally regulating riboswitches also regulate mRNA levels through an indire
40 he aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, incl
41 first of all submissions for the L-glutamine riboswitch and as the second for the ZMP riboswitch.
42 structure upstream of the characterized HIV riboswitch and demonstrates the basal translation rate o
43 s ON-OFF transition of the full length SAM-I riboswitch and its magnesium concentration dependence.
45 ession platform of the P3 helix in the bound riboswitch and the P3 helix is a bottleneck in the apo r
47 ional interactions-e.g., at switch points in riboswitches and at a complex nucleation site in HIV.
48 ensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA inte
49 ross species, which correspond to many known riboswitches and further suggest novel putative regulato
50 ecent studies have identified new classes of riboswitches and have revealed new insights into the mol
51 ods that have been developed to engineer new riboswitches and highlight applications of natural and s
56 n streamlines design of synthetic allosteric riboswitches and small molecule-nucleic acid complexes.
57 ural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch re
59 B. subtilis at a global level by binding to riboswitches and to different classes of transport prote
60 from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation
61 long-lost ligand sensed by the ykkC class of riboswitches, and identified that members of its regulon
66 ions were used to target the guanine-sensing riboswitch aptamer domain (GSR(apt)) of the xpt-pbuX ope
68 y determining four structures of the adenine riboswitch aptamer domain during the course of a reactio
69 ring ligand recognition of the preQ1 class-I riboswitch aptamer from Thermoanaerobacter tengcongensis
70 stal structure of the ligand-bound yybP-ykoY riboswitch aptamer from Xanthomonas oryzae at 2.96 angst
73 cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacter
74 yclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose st
75 structured RNAs including ribozyme domains, riboswitch aptamers, and viral RNA domains with a single
83 However, a significant proportion of glycine riboswitches are comprised of single aptamers (singleton
85 irillum indicum The regulatory mechanisms of riboswitches are influenced by the kinetics of ligand in
100 rRNA, and the aptamer domain of the adenine riboswitch) are in excellent agreement with experiments
101 pseudoknot of a class-I translational preQ1 riboswitch as a highly structured RNA model whose confor
102 rize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON ribosw
104 ussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus
105 ach for the design of synthetic theophylline riboswitches based on secondary structure prediction.
108 ssment of the translational potential of FMN riboswitch binders against wild-type Gram-negative bacte
110 determined crystal structures of the SAM/SAH riboswitch bound to SAH, SAM and other variant ligands a
111 SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unkno
112 ve analyzed the ligand-binding properties of riboswitches, but this work has outpaced our understandi
114 transcriptional RNA, the translational metI riboswitch can make multiple reversible regulatory decis
115 at the two alternate secondary structures of riboswitches can be accurately predicted once the 'switc
116 ption of essential genes controlled by T-box riboswitches can be directly modulated by commonly used
117 f the ykkC motif RNA, the longest unresolved riboswitch candidate, naturally sense and respond to gua
118 s pipeline that can uncover novel, but rare, riboswitch candidates as well as other noncoding RNA str
119 ure and mutagenesis analyses revealed a VB12-riboswitch, cbiMCbl (140 bp), within the 5' UTR that con
121 NA-mediated regulators (e.g., thermosensors, riboswitches, cis- and trans-encoded RNAs) used for adap
122 scoveries are unique variants of the guanine riboswitch class that most tightly bind the nucleoside 2
123 ition, we identified variants of the glycine riboswitch class that no longer recognize this amino aci
124 roups of protein enzymes and receptors, some riboswitch classes have evolved to change their ligand s
125 a procedure to systematically analyze known riboswitch classes to find additional variants that have
127 ls in Gram--negative bacteria, translational riboswitches--commonly embedded in messenger RNAs (mRNAs
130 the utility of the tightly inducible P(BAD)-riboswitch construct using the dynamic activity of type
132 uggesting that the majority of known E. coli riboswitches control transcription termination by using
135 functional analysis in live bacteria using a riboswitch-controlled GFPuv-reporter assay revealed that
136 The widespread Mn(2+)-sensing yybP-ykoY riboswitch controls the expression of bacterial Mn(2+) h
138 same RNA structural transitions related to a riboswitch decision-making process that we previously id
139 er, our findings suggest that tandem glycine riboswitches degrade into functional singletons, with th
141 olving mechanisms such as dynamic folding of riboswitches during translation initiation or the synthe
142 f the phylogenetically widespread classes of riboswitches, each specific to a particular metabolite o
148 ngle-molecule FRET analysis reveals that the riboswitch exists in two distinct conformations, and tha
149 has been very successful in identifying new riboswitch families and defining their distributions, sm
150 cture similar to other members of the purine riboswitch family, but contains key differences within t
153 n plastids, but the application of synthetic riboswitches for the regulation of nuclear-encoded genes
154 t broadly distributed and numerous bacterial riboswitches for which the cognate ligand was unknown.
156 iron responsive elements (29 nt), a fluoride riboswitch from Bacillus anthracis(48 nt), and a frame-s
157 d approach was used to re-engineer the PreQ1 riboswitch from Bacillus subtilis into an orthogonal OFF
158 e show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of t
159 sed readouts of 15 mutants of the preQ(1)-II riboswitch from Lactobacillus rhamnosus demonstrates tha
160 ion by the aptamer domain of a guanidine III riboswitch from Legionella pneumophila has a different e
161 ide resolution for the I-A type 2'dG-sensing riboswitch from Mesoplasma florum by NMR spectroscopy.
162 case of the thiamine 5'-pyrophosphate (TPP) riboswitch from the Escherichia coli thiM gene encoding
163 hich targets the flavin mononucleotide (FMN) riboswitch, from a compound lacking whole-cell activity
164 pling of synthesis and folding essential for riboswitch function, revealing the importance of metasta
167 xhibit Mn2+ sensitivity, revealing that this riboswitch functions as a failsafe 'on' signal to preven
168 lts suggest that the S. pneumoniae yybP-ykoY riboswitch functions to regulate Ca2+ efflux under these
170 and show that leakiness for P(tac) > P(tac)-riboswitch > P(BAD); while the newly developed P(BAD)-ri
174 epresentative members of the SAM-I family of riboswitches has been extensively analyzed using approac
175 genic approach to demonstrate that cobalamin riboswitches have a broad spectrum of preference for the
179 alian gene expression with ligand-responsive riboswitches have been hindered by lack of a general met
180 ntal importance in bacteria gene regulation, riboswitches have been proposed as antibacterial drug ta
182 inomethyl-7-deazaguanine, preQ(1)) bacterial riboswitches have been studied, but the functional conse
183 Mg2+ ions suggests that some single-aptamer riboswitches have exploited the coupling of cellular lev
185 uggests the need for alternative methods for riboswitch identification, possibly based on features in
187 e determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 ang
189 ure of the eukaryotic thiamine pyrophosphate riboswitch in the context of a hexanucleotide loop seque
190 fied and characterized a translational S-box riboswitch in the metI gene from Desulfurispirillum indi
191 MN-induced "turn-off" activities of both FMN riboswitches in Bacillus subtilis, allowing rib gene exp
192 hlight applications of natural and synthetic riboswitches in enzyme and strain engineering, in contro
193 single-molecule monitoring captures folding riboswitches in multiple states, including an intermedia
194 amin riboswitch and a model for the complete riboswitch, including its expression platform domain.
196 Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA syn
200 st that the correlation network in the bound riboswitch is distinctly different from that in the apo
202 esented whereby in the absence of ligand the riboswitch is largely unfolded, lacking the PK helix so
208 determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallogr
209 ene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of m
211 nosine, suggesting that a subset of 2'-dG-II riboswitches may bind either molecule to regulate gene e
214 control by the cyclic AMP receptor protein, riboswitch-mediated transcription attenuation in respons
215 h previously and newly discovered classes of riboswitches might reveal subgroups of RNAs that respond
217 tructured, cis-encoded RNA elements known as riboswitches modify gene expression upon binding a wide
218 many of these changes are not present in TPP riboswitch mutant plants, demonstrating their lack of me
219 described Arabidopsis (Arabidopsis thaliana) riboswitch mutant plants, which accumulate thiamin vitam
220 n photorespiration and the TCA cycle, as TPP riboswitch mutants accumulate less photorespiratory inte
224 The discovery, design and reengineering of riboswitches offer an alternative means by which to cont
228 vailable to support tasks like the design of riboswitches; our analysis of RS3 suggests strong co-tra
229 t have an additional theophylline-responsive riboswitch (P(tac)-riboswitch and P(BAD)-riboswitch).
230 show that one aptamer of the tandem glycine riboswitch pair is typically much more highly conserved,
231 S-box (SAM-I) riboswitches, including the riboswitch present in the Bacillus subtilis metI gene, w
233 eling at three independent positions on each riboswitch, PRRSM accurately classified all apo and liga
234 Our model-based approach for engineering riboswitches quantitatively confirms several physical me
235 i-AMP molecules are bound to the protein and riboswitch receptors and what kinds of interactions acco
237 y, it is less clear how the unbound, sensing riboswitch refolds into the ligand binding-induced outpu
244 ions of these riboswitches with theophylline riboswitches represent logic gates responding to two dif
246 iscriminate between SAM and SAH, the SAM/SAH riboswitch responds to both ligands with similar apparen
247 n riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promisc
248 bolite, a Mg(2+) (0-0.5 mm)-bound apo SAM-II riboswitch RNA exists in a minor ( approximately 10 %) p
249 sequentially releases fluorescently labeled riboswitch RNA from a heteroduplex in a 5'-to-3' directi
250 sing of changes in the environment by use of riboswitches (RNAs that change shape in response to envi
255 itching sequence inside a putative, complete riboswitch sequence, on the basis of pairing behaviors,
257 range tertiary interactions stabilize global riboswitch structure and confer increased ligand specifi
259 curately classified all apo and ligand-bound riboswitch structures, including changes in the size of
261 t there is a great diversity of undiscovered riboswitches, suggests the need for alternative methods
262 r how their sequence controls the physics of riboswitch switching and activation, particularly when c
263 in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits transla
265 nal map of the Vibrio vulnificus add adenine riboswitch that reveals five classes of structures.
266 e used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a
267 tion relationship for translation-regulating riboswitches that activate gene expression, characterize
268 ass, and also variants of c-di-GMP-I and -II riboswitches that might recognize different bacterial si
270 s the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP
271 tomated computational design of 62 synthetic riboswitches that used six different RNA aptamers to sen
275 different combinations of TALE proteins and riboswitches, to rapidly and reproducibly control the ex
276 n, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expressio
277 ic analysis of well-characterized classes of riboswitches uncovered subgroups unable to bind to the r
279 Here, we characterize a yybP-ykoY family riboswitch upstream of the mgtA gene encoding a PII-type
281 eraction found in the tetrahydrofolate (THF) riboswitch using rationally designed self-assembling tec
282 ch by analyzing the fluorescence response of riboswitch variants, each with a single, strategically p
283 te stress-sensing Fusobacterium ulcerans ZTP riboswitch, we apply a single-molecule vectorial folding
284 of the thiamin pyrophosphate-dependent thiM riboswitch, we find that Rho-dependent transcription ter
285 To overcome the associated difficulties with riboswitches, we have designed and introduced a novel ge
286 dentified class of 2'-deoxyguanosine binding riboswitches, we have solved the crystal structure of a
289 ation to a model RNA: the core glmS ribozyme riboswitch, which performs a ligand-dependent self-cleav
290 he Bacillus subtilis adenine-responsive pbuE riboswitch, which regulates gene expression at the trans
291 -AMP binds to a large number of proteins and riboswitches, which are often involved in potassium and
292 tory mechanisms employed by Escherichia coli riboswitches, which are predicted to regulate mostly at
294 t is able to model the switching behavior of riboswitches whose generated ensemble covers both altern
296 th and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and th
298 itable targets for construction of synthetic riboswitches with design approaches based on equilibrium
300 witch as a Mn(2+)-dependent transcription-ON riboswitch, with a approximately 30-40 muM affinity for
301 hetic ligands and drugs that bind tightly to riboswitches without eliciting a biological response.