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1 tion conditions amenable to catalysis by the hairpin ribozyme.
2 ing and catalysis of a model RNA enzyme, the hairpin ribozyme.
3 ecular bases of these unique features of the hairpin ribozyme.
4  the catalytically essential B domain of the hairpin ribozyme.
5 ls that have been proposed for loop B of the hairpin ribozyme.
6 ty and orientation of the two domains of the hairpin ribozyme.
7  behavior and kinetic folding pathway of the hairpin ribozyme.
8 alysis of four structural derivatives of the hairpin ribozyme.
9 and G36 in the catalytic conformation of the hairpin ribozyme.
10 econdary structure of internal loop B of the hairpin ribozyme.
11 activity of folding-deficient mutants of the hairpin ribozyme.
12 on design on the folding and function of the hairpin ribozyme.
13 ) four-way helical junction derived from the hairpin ribozyme.
14 sly folding molecules, as exemplified by the hairpin ribozyme.
15 ormational states of a model RNA enzyme, the hairpin ribozyme.
16 ween structural dynamics and function of the hairpin ribozyme.
17 cellular TF mRNA with the use of a tetraloop hairpin ribozyme.
18 ssential step in the reaction pathway of the hairpin ribozyme.
19 eters and DeltaVs comparable to those of the hairpin ribozymes.
20 nknown target RNAs recognized and cleaved by hairpin ribozymes.
21 ne base requirements in loops 2 and 4 of the hairpin ribozyme, a comprehensive mutational analysis of
22                                          The hairpin ribozyme, a small catalytic RNA consisting of tw
23                                          The hairpin ribozyme accelerates a phosphoryl transfer react
24         The catalytic mechanism by which the hairpin ribozyme accelerates cleavage or ligation of the
25                                          The hairpin ribozyme accelerates the rate of phosphodiester
26                                          The hairpin ribozyme achieves catalytic cleavage through int
27 entify two adenines which may participate in hairpin ribozyme active site chemistry.
28 ures that contribute to catalysis within the hairpin ribozyme active site, structures for five base v
29 onsists of a fixed sequence derived from the hairpin ribozyme and an antisense segment whose size and
30                      The complex between the hairpin ribozyme and its substrate consists of two domai
31                    The complex formed by the hairpin ribozyme and its substrate consists of two indep
32 veral nucleotides in two catalytic RNAs, the hairpin ribozyme and the hepatitis delta virus ribozyme,
33 ed conformation characteristic of the active hairpin ribozyme and the triplex structure.
34 stablished consensus selection rules for the hairpin ribozyme and were not predicted by examining the
35 sis of purine nucleotide conservation in the hairpin ribozyme, and provides a basis for the design an
36 ely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for t
37                                          The hairpin ribozyme appears to take up at least one tri- or
38 avage and ligation reactions mediated by the hairpin ribozyme are integral to the polyribonucleotide
39 stallographic and mechanistic studies of the hairpin ribozyme are reported.
40        It is shown that the linear monomeric hairpin ribozymes are active in cleaving RNA targets in
41  monitor tertiary structure formation of the hairpin ribozyme as a model to probe the effects of poly
42  We used two-, three-, and four-way junction hairpin ribozymes as model systems to investigate the th
43 ding kinetics of the natural 4WJ form of the hairpin ribozyme, as well as a minimal construct consist
44 mus of molecular dynamics simulations of the hairpin ribozyme at different stages along the catalytic
45                                          The hairpin ribozyme belongs to the family of small catalyti
46                            All three minimal hairpin ribozymes bound Co(NH(3))(6)(3+) at G21/A40, the
47     Metal ions facilitate the folding of the hairpin ribozyme but do not participate directly in cata
48 lts were used to improve the activity of the hairpin ribozyme by designing new interfaces between the
49 ate that a three-way junction variant of the hairpin ribozyme can be stabilized by specific insertion
50  truncated and fragmented derivatives of the hairpin ribozyme can catalyze ligation of a wide variety
51 ement of this ribozyme and indicate that the hairpin ribozyme can now be engineered to cleave a wider
52 ative amounts; and (iii) that self-processed hairpin ribozymes can be catalytically active in trans d
53 ecent results indicating that hammerhead and hairpin ribozymes can cleave RNA following cellular lysi
54 t that metal ions play a passive role in the hairpin ribozyme catalysed reaction and are probably req
55                                          The hairpin ribozyme catalyses sequence-specific cleavage of
56                   The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dyn
57 U41, U42 and C25) plays an important role in hairpin ribozyme catalysis.
58 se results are consistent with models of the hairpin ribozyme catalytic mechanism in which interactio
59                                          The hairpin ribozyme catalyzes a reversible RNA cleavage rea
60                                          The hairpin ribozyme catalyzes reversible phosphodiester bon
61                                          The hairpin ribozyme catalyzes sequence-specific cleavage of
62       Our model system, the two-way junction hairpin ribozyme, catalyzes a multistep reversible RNA c
63         We developed a quantitative assay of hairpin ribozyme cleavage activity in yeast to learn how
64 ce both in understanding the role of ions in hairpin ribozyme cleavage and in potential therapeutic a
65                          Similarities to the hairpin ribozyme cleavage loop activation suggest genera
66 tional rearrangement as an important step in hairpin ribozyme cleavage.
67                                          The hairpin ribozyme cleaves a phosphodiester bond within a
68  angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor an
69                      The natural form of the hairpin ribozyme comprises two major structural elements
70 s C, suggesting Mg2+ stabilizes a low-energy hairpin ribozyme conformation.
71                      The natural form of the hairpin ribozyme consists of a four-way RNA junction of
72                   The tobacco ringspot virus hairpin ribozyme consists of two helix-loop-helix elemen
73                                    A minimal hairpin ribozyme consists of two helix-loop-helix segmen
74  structure and dynamics of four-way junction hairpin ribozyme constructs.
75 orientations, we have chemically synthesized hairpin ribozymes containing 2'-2' disulphide linkages o
76 ynthesized a series of individually modified hairpin ribozymes containing 2'-analogues of nucleosides
77 (a) of the N1-imino moiety in the context of hairpin ribozyme crystals representative of a "precataly
78 ve complex, the essential nucleotides of the hairpin ribozyme, embedded within the internal loops of
79 ducts with much higher affinity than minimal hairpin ribozymes, evidence that tertiary interactions w
80 functional studies revealed that the minimal hairpin ribozyme exhibited "gain-of-function" cleavage p
81 ned within vesicles, the natural form of the hairpin ribozyme exhibited 50-fold variation in both fol
82                               Therefore, the hairpin ribozyme exploits the dynamics of the junction t
83 tent with the role of divalent metal ions in hairpin ribozyme folding, we observed more interdomain c
84                                          The hairpin ribozyme folds in solution and catalyzes self-cl
85    The solution structure of loop A from the hairpin ribozyme found in the minus strand of tobacco ri
86 ped a selection system based on a randomized hairpin ribozyme gene library to identify cellular facto
87         As a tool for functional genomics, a hairpin ribozyme gene library with randomized target rec
88               We have developed a library of hairpin ribozyme genes that can be delivered and express
89 cal groups required to achieve a functioning hairpin ribozyme have been determined by nucleotide anal
90            Recent mechanistic studies on the hairpin ribozyme have led to models in which protonation
91                  Crystallographic studies of hairpin ribozymes have provided high resolution views of
92 recent examples are discussed, including the hairpin ribozyme, Holliday junction, G-quadruplex, Rep h
93 l evidence for the catalytic activity of the hairpin ribozyme in a cellular environment, and indicate
94                              This places the hairpin ribozyme in a different mechanistic class to oth
95 (a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states.
96                                          The hairpin ribozyme in its natural context consists of two
97 nt of the macroscopic pH-rate profile of the hairpin ribozyme in solution and strongly supports A38 a
98 lycoside antibiotics inhibit cleavage of the hairpin ribozyme in the presence of metal ions with the
99                                          The hairpin ribozyme in the satellite RNA of Tobacco Ringspo
100 in vivo expression of either a hammerhead or hairpin ribozyme in this rat model considerably slows th
101 al synthesis of RNA to create mutants of the hairpin ribozyme in which a nucleoside analogue replaces
102                                          The hairpin ribozyme, in common with all other small ribozym
103    An initial structural model of the docked hairpin ribozyme included a proposal for a ribose zipper
104 spection of recent crystal structures of the hairpin ribozyme, including a complex with a vanadate tr
105 del is consistent with the literature on the hairpin ribozyme, including pH-rate profiles of wild-typ
106  The proposed three-dimensional model of the hairpin ribozyme incorporates three different crystallog
107          The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribo
108    Here, we studied how encapsulation of the hairpin ribozyme inside model protocells affects ribozym
109 influence of temperature, ions and pH on the hairpin ribozyme internal equilibrium.
110                    These results show that a hairpin ribozyme introduced into CD34+ hematopoietic pro
111                                          The hairpin ribozyme is a better ligase than it is a nucleas
112                                          The hairpin ribozyme is a minimalist paradigm for studying R
113                                          The hairpin ribozyme is a small catalytic motif found in pla
114                                          The hairpin ribozyme is a small catalytic RNA composed of tw
115                                          The hairpin ribozyme is a small catalytic RNA comprised of t
116                                          The hairpin ribozyme is a small catalytic RNA consisting of
117                                          The hairpin ribozyme is a small catalytic RNA that accelerat
118                                          The hairpin ribozyme is a small catalytic RNA that achieves
119                                          The hairpin ribozyme is a small catalytic RNA with reversibl
120                                          The hairpin ribozyme is a small endonucleolytic RNA motif wi
121                                          The hairpin ribozyme is a small self-cleaving RNA that can b
122                                          The hairpin ribozyme is a small, naturally occurring RNA cap
123                                          The hairpin ribozyme is a small, noncoding RNA (ncRNA) that
124                                   Hence, the hairpin ribozyme is a unique model to study the role of
125  We find that the junction-based form of the hairpin ribozyme is active in magnesium, calcium, or str
126 ge rates (0.2 min-1), demonstrating that the hairpin ribozyme is an efficient RNA ligase.
127                                          The hairpin ribozyme is an example of a small catalytic RNA
128                                          The hairpin ribozyme is an example of a small catalytic RNA
129                                          The hairpin ribozyme is an RNA enzyme that performs site-spe
130 ese results, a two-dimensional model for the hairpin ribozyme is presented.
131                             Catalysis by the hairpin ribozyme is stimulated by a wide range of both s
132  the in vitro synthesis of circular RNAs and hairpin ribozymes is described.
133 periments in which the catalytic activity of hairpin ribozymes is monitored following expression in m
134 ant] ratio = 5 x 10(7) M/min), then the P23H hairpin ribozyme (kcat:K(m) ratio = 9 x 10(5) M/min) and
135 cal junction has revealed two changes in the hairpin ribozyme kinetic mechanism.
136 overy where the intracellular application of hairpin ribozyme libraries was used to identify a novel
137                                            A hairpin ribozyme library (5 x 10(5) variants) containing
138 se 2'-OH and purine functional groups to the hairpin ribozyme ligation reaction.
139                           The hammerhead and hairpin ribozymes may share similarities in the organiza
140 ructural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other funct
141  tobacco ringspot virus satellite RNA, where hairpin ribozyme-mediated self-cleavage and ligation rea
142  evidence has suggested that base A38 of the hairpin ribozyme plays an important role in phosphoryl t
143                                          The hairpin ribozyme presents an excellent case study for su
144                           In the case of the hairpin ribozyme, pressure slowed down the self-cleavage
145 ture stability is a major determinant of the hairpin ribozyme proficiency as a ligase and illustrates
146 III) complexes are capable of supporting the hairpin ribozyme reaction, with a similar efficiency to
147                       Mechanistic studies of hairpin ribozyme reactions provided early evidence that,
148 native explanations for the pH dependence of hairpin ribozyme reactivity are discussed, from which we
149                   Combinatorial libraries of hairpin ribozymes representing all possible cleavage spe
150                                          The hairpin ribozyme requires functional group contributions
151 te-specific RNA cleavage and ligation by the hairpin ribozyme requires the formation of a tertiary in
152                                          The hairpin ribozyme reversibly cleaves phosphodiesters of R
153                           We have designed a hairpin ribozyme (Rz3'X) targeting the HCV minus-strand
154                                            A hairpin ribozyme, RzCR2A, directed against position 323
155  of an elementary folding reaction where the hairpin ribozyme's two helical domains dock to make seve
156 ng transcription in vitro and in yeast using hairpin ribozyme self-cleavage to assess partitioning be
157  nt in length are constructed to encode both hairpin ribozyme sequences and ribozyme-cleavable sequen
158          The crystal structure of the docked hairpin ribozyme shows an intricate network of hydrogen
159   The RNA cleavage reaction catalyzed by the hairpin ribozyme shows biphasic kinetics, and chase expe
160 ure technique, we evaluated the ability of a hairpin ribozyme specific for simian immunodeficiency vi
161 ly explain previously observed variations in hairpin ribozyme stability.
162 es an important basis for further studies of hairpin ribozyme structure and function.
163        For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolut
164                     The relationship between hairpin ribozyme structure, and cleavage and ligation ki
165 e not observed in previous four-way-junction hairpin ribozyme structures due to crystal contacts with
166          Recent physical characterization of hairpin ribozyme structures using fluorescence resonance
167 located within all the required loops of the hairpin ribozyme-substrate complex and allowed for the d
168                                          The hairpin ribozyme-substrate complex contains two independ
169 es for all positions in loops 1 and 5 of the hairpin ribozyme-substrate complex was carried out using
170                       The two domains of the hairpin ribozyme-substrate complex, usually depicted as
171  identified the catalytic core of the active hairpin ribozyme-substrate complex.
172                                            A hairpin ribozyme targeting G575 of the Sindbis virus gen
173                We have previously shown that hairpin ribozymes targeting the human immunodeficiency v
174 e detection of cellular target molecules for hairpin ribozymes, termed C-SPACE (cleavage-specific amp
175 cal junction determines the stability of the hairpin ribozyme tertiary structure and thus its catalyt
176            The enhanced ligation activity of hairpin ribozymes that contain a four-way helical juncti
177                                              Hairpin ribozymes that incorporate the natural four-way
178 l screening method has been used to identify hairpin ribozymes that inhibit hepatitis B virus (HBV) r
179              Here we report the selection of hairpin ribozymes that inhibit human immunodeficiency vi
180                  Besides its presence in the hairpin ribozyme, the loop E motif is also apparent in h
181                    In the active form of the hairpin ribozyme, the loops are in proximity.
182 ociated cations contributes significantly to hairpin ribozyme thermodynamics.
183      In a few cases, including loop B of the hairpin ribozyme, this unusual arrangement gives rise to
184               We engineered a variant of the hairpin ribozyme to catalyze addition of all four N>p's
185                  Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphoryla
186  have carried out molecular modelling of the hairpin ribozyme to learn how the two domains (A and B)
187 g transcripts containing active and inactive hairpin ribozymes together with cleavable and non-cleava
188 mistic folding/unfolding simulations for the hairpin ribozyme using a Monte Carlo algorithm.
189 structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissil
190 d pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substit
191 our-way helical junction compared to minimal hairpin ribozyme variants.
192 ants for tertiary structure stability in the hairpin ribozyme, we evaluated the energetic contributio
193                                              Hairpin ribozymes were engineered to cleave a specific s
194 oter expression constructs for corresponding hairpin ribozymes were generated and cotransfected into
195  crystal structures of minimal, junctionless hairpin ribozymes were solved in native (U39), and mutan
196     One of the most striking examples is the hairpin ribozyme, which was shown to exhibit two to thre
197 self-cleavage reaction in a fully functional hairpin ribozyme with a unique 8azaA at position 38.
198 ddress this discrepancy, we investigated the hairpin ribozyme with an expanded set of pK(a) perturbed
199 ngement rationalizes the observed ability of hairpin ribozymes with a circularized substrate-binding

 
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