ライフサイエンスコーパス: hairpin ribozyme

1 ecular bases of these unique features of the hairpin ribozyme.

2 the catalytically essential B domain of the hairpin ribozyme.

3 ls that have been proposed for loop B of the hairpin ribozyme.

4 ty and orientation of the two domains of the hairpin ribozyme.

5 behavior and kinetic folding pathway of the hairpin ribozyme.

6 alysis of four structural derivatives of the hairpin ribozyme.

7 and G36 in the catalytic conformation of the hairpin ribozyme.

8 econdary structure of internal loop B of the hairpin ribozyme.

9 on design on the folding and function of the hairpin ribozyme.

10 ) four-way helical junction derived from the hairpin ribozyme.

11 sly folding molecules, as exemplified by the hairpin ribozyme.

12 ormational states of a model RNA enzyme, the hairpin ribozyme.

13 ing and catalysis of a model RNA enzyme, the hairpin ribozyme.

14 ween structural dynamics and function of the hairpin ribozyme.

15 cellular TF mRNA with the use of a tetraloop hairpin ribozyme.

16 ssential step in the reaction pathway of the hairpin ribozyme.

17 nknown target RNAs recognized and cleaved by hairpin ribozymes.

18 ne base requirements in loops 2 and 4 of the hairpin ribozyme, a comprehensive mutational analysis of

19 The hairpin ribozyme, a small catalytic RNA consisting of tw

20 The hairpin ribozyme accelerates a phosphoryl transfer react

21 The catalytic mechanism by which the hairpin ribozyme accelerates cleavage or ligation of the

22 The hairpin ribozyme accelerates the rate of phosphodiester

23 The hairpin ribozyme achieves catalytic cleavage through int

24 entify two adenines which may participate in hairpin ribozyme active site chemistry.

25 ures that contribute to catalysis within the hairpin ribozyme active site, structures for five base v

26 onsists of a fixed sequence derived from the hairpin ribozyme and an antisense segment whose size and

27 The complex between the hairpin ribozyme and its substrate consists of two domai

28 The complex formed by the hairpin ribozyme and its substrate consists of two indep

29 veral nucleotides in two catalytic RNAs, the hairpin ribozyme and the hepatitis delta virus ribozyme,

30 stablished consensus selection rules for the hairpin ribozyme and were not predicted by examining the

31 sis of purine nucleotide conservation in the hairpin ribozyme, and provides a basis for the design an

32 ely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for t

33 The hairpin ribozyme appears to take up at least one tri- or

34 avage and ligation reactions mediated by the hairpin ribozyme are integral to the polyribonucleotide

35 stallographic and mechanistic studies of the hairpin ribozyme are reported.

36 It is shown that the linear monomeric hairpin ribozymes are active in cleaving RNA targets in

37 monitor tertiary structure formation of the hairpin ribozyme as a model to probe the effects of poly

38 We used two-, three-, and four-way junction hairpin ribozymes as model systems to investigate the th

39 ding kinetics of the natural 4WJ form of the hairpin ribozyme, as well as a minimal construct consist

40 mus of molecular dynamics simulations of the hairpin ribozyme at different stages along the catalytic

41 The hairpin ribozyme belongs to the family of small catalyti

42 All three minimal hairpin ribozymes bound Co(NH(3))(6)(3+) at G21/A40, the

43 Metal ions facilitate the folding of the hairpin ribozyme but do not participate directly in cata

44 lts were used to improve the activity of the hairpin ribozyme by designing new interfaces between the

45 ate that a three-way junction variant of the hairpin ribozyme can be stabilized by specific insertion

46 truncated and fragmented derivatives of the hairpin ribozyme can catalyze ligation of a wide variety

47 ement of this ribozyme and indicate that the hairpin ribozyme can now be engineered to cleave a wider

48 ative amounts; and (iii) that self-processed hairpin ribozymes can be catalytically active in trans d

49 ecent results indicating that hammerhead and hairpin ribozymes can cleave RNA following cellular lysi

50 t that metal ions play a passive role in the hairpin ribozyme catalysed reaction and are probably req

51 The hairpin ribozyme catalyses sequence-specific cleavage of

52 The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dyn

53 U41, U42 and C25) plays an important role in hairpin ribozyme catalysis.

54 se results are consistent with models of the hairpin ribozyme catalytic mechanism in which interactio

55 The hairpin ribozyme catalyzes a reversible RNA cleavage rea

56 The hairpin ribozyme catalyzes reversible phosphodiester bon

57 The hairpin ribozyme catalyzes sequence-specific cleavage of

58 Our model system, the two-way junction hairpin ribozyme, catalyzes a multistep reversible RNA c

59 We developed a quantitative assay of hairpin ribozyme cleavage activity in yeast to learn how

60 ce both in understanding the role of ions in hairpin ribozyme cleavage and in potential therapeutic a

61 Similarities to the hairpin ribozyme cleavage loop activation suggest genera

62 tional rearrangement as an important step in hairpin ribozyme cleavage.

63 The hairpin ribozyme cleaves a phosphodiester bond within a

64 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor an

65 The natural form of the hairpin ribozyme comprises two major structural elements

66 s C, suggesting Mg2+ stabilizes a low-energy hairpin ribozyme conformation.

67 The natural form of the hairpin ribozyme consists of a four-way RNA junction of

68 The tobacco ringspot virus hairpin ribozyme consists of two helix-loop-helix elemen

69 A minimal hairpin ribozyme consists of two helix-loop-helix segmen

70 structure and dynamics of four-way junction hairpin ribozyme constructs.

71 orientations, we have chemically synthesized hairpin ribozymes containing 2'-2' disulphide linkages o

72 ynthesized a series of individually modified hairpin ribozymes containing 2'-analogues of nucleosides

73 (a) of the N1-imino moiety in the context of hairpin ribozyme crystals representative of a "precataly

74 ve complex, the essential nucleotides of the hairpin ribozyme, embedded within the internal loops of

75 ducts with much higher affinity than minimal hairpin ribozymes, evidence that tertiary interactions w

76 functional studies revealed that the minimal hairpin ribozyme exhibited "gain-of-function" cleavage p

77 ned within vesicles, the natural form of the hairpin ribozyme exhibited 50-fold variation in both fol

78 Therefore, the hairpin ribozyme exploits the dynamics of the junction t

79 tent with the role of divalent metal ions in hairpin ribozyme folding, we observed more interdomain c

80 The hairpin ribozyme folds in solution and catalyzes self-cl

81 The solution structure of loop A from the hairpin ribozyme found in the minus strand of tobacco ri

82 ped a selection system based on a randomized hairpin ribozyme gene library to identify cellular facto

83 As a tool for functional genomics, a hairpin ribozyme gene library with randomized target rec

84 We have developed a library of hairpin ribozyme genes that can be delivered and express

85 cal groups required to achieve a functioning hairpin ribozyme have been determined by nucleotide anal

86 Recent mechanistic studies on the hairpin ribozyme have led to models in which protonation

87 Crystallographic studies of hairpin ribozymes have provided high resolution views of

88 recent examples are discussed, including the hairpin ribozyme, Holliday junction, G-quadruplex, Rep h

89 l evidence for the catalytic activity of the hairpin ribozyme in a cellular environment, and indicate

90 This places the hairpin ribozyme in a different mechanistic class to oth

91 (a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states.

92 The hairpin ribozyme in its natural context consists of two

93 nt of the macroscopic pH-rate profile of the hairpin ribozyme in solution and strongly supports A38 a

94 lycoside antibiotics inhibit cleavage of the hairpin ribozyme in the presence of metal ions with the

95 The hairpin ribozyme in the satellite RNA of Tobacco Ringspo

96 in vivo expression of either a hammerhead or hairpin ribozyme in this rat model considerably slows th

97 al synthesis of RNA to create mutants of the hairpin ribozyme in which a nucleoside analogue replaces

98 The hairpin ribozyme, in common with all other small ribozym

99 An initial structural model of the docked hairpin ribozyme included a proposal for a ribose zipper

100 spection of recent crystal structures of the hairpin ribozyme, including a complex with a vanadate tr

101 del is consistent with the literature on the hairpin ribozyme, including pH-rate profiles of wild-typ

102 The proposed three-dimensional model of the hairpin ribozyme incorporates three different crystallog

103 The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribo

104 influence of temperature, ions and pH on the hairpin ribozyme internal equilibrium.

105 These results show that a hairpin ribozyme introduced into CD34+ hematopoietic pro

106 The hairpin ribozyme is a better ligase than it is a nucleas

107 The hairpin ribozyme is a minimalist paradigm for studying R

108 The hairpin ribozyme is a small catalytic motif found in pla

109 The hairpin ribozyme is a small catalytic RNA composed of tw

110 The hairpin ribozyme is a small catalytic RNA comprised of t

111 The hairpin ribozyme is a small catalytic RNA consisting of

112 The hairpin ribozyme is a small catalytic RNA that accelerat

113 The hairpin ribozyme is a small catalytic RNA that achieves

114 The hairpin ribozyme is a small catalytic RNA with reversibl

115 The hairpin ribozyme is a small endonucleolytic RNA motif wi

116 The hairpin ribozyme is a small self-cleaving RNA that can b

117 The hairpin ribozyme is a small, naturally occurring RNA cap

118 The hairpin ribozyme is a small, noncoding RNA (ncRNA) that

119 Hence, the hairpin ribozyme is a unique model to study the role of

120 We find that the junction-based form of the hairpin ribozyme is active in magnesium, calcium, or str

121 ge rates (0.2 min-1), demonstrating that the hairpin ribozyme is an efficient RNA ligase.

122 The hairpin ribozyme is an example of a small catalytic RNA

123 The hairpin ribozyme is an example of a small catalytic RNA

124 The hairpin ribozyme is an RNA enzyme that performs site-spe

125 ese results, a two-dimensional model for the hairpin ribozyme is presented.

126 Catalysis by the hairpin ribozyme is stimulated by a wide range of both s

127 the in vitro synthesis of circular RNAs and hairpin ribozymes is described.

128 periments in which the catalytic activity of hairpin ribozymes is monitored following expression in m

129 ant] ratio = 5 x 10(7) M/min), then the P23H hairpin ribozyme (kcat:K(m) ratio = 9 x 10(5) M/min) and

130 cal junction has revealed two changes in the hairpin ribozyme kinetic mechanism.

131 overy where the intracellular application of hairpin ribozyme libraries was used to identify a novel

132 A hairpin ribozyme library (5 x 10(5) variants) containing

133 se 2'-OH and purine functional groups to the hairpin ribozyme ligation reaction.

134 The hammerhead and hairpin ribozymes may share similarities in the organiza

135 ructural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other funct

136 tobacco ringspot virus satellite RNA, where hairpin ribozyme-mediated self-cleavage and ligation rea

137 evidence has suggested that base A38 of the hairpin ribozyme plays an important role in phosphoryl t

138 The hairpin ribozyme presents an excellent case study for su

139 ture stability is a major determinant of the hairpin ribozyme proficiency as a ligase and illustrates

140 III) complexes are capable of supporting the hairpin ribozyme reaction, with a similar efficiency to

141 Mechanistic studies of hairpin ribozyme reactions provided early evidence that,

142 native explanations for the pH dependence of hairpin ribozyme reactivity are discussed, from which we

143 Combinatorial libraries of hairpin ribozymes representing all possible cleavage spe

144 The hairpin ribozyme requires functional group contributions

145 te-specific RNA cleavage and ligation by the hairpin ribozyme requires the formation of a tertiary in

146 The hairpin ribozyme reversibly cleaves phosphodiesters of R

147 We have designed a hairpin ribozyme (Rz3'X) targeting the HCV minus-strand

148 A hairpin ribozyme, RzCR2A, directed against position 323

149 of an elementary folding reaction where the hairpin ribozyme's two helical domains dock to make seve

150 ng transcription in vitro and in yeast using hairpin ribozyme self-cleavage to assess partitioning be

151 nt in length are constructed to encode both hairpin ribozyme sequences and ribozyme-cleavable sequen

152 The crystal structure of the docked hairpin ribozyme shows an intricate network of hydrogen

153 The RNA cleavage reaction catalyzed by the hairpin ribozyme shows biphasic kinetics, and chase expe

154 ure technique, we evaluated the ability of a hairpin ribozyme specific for simian immunodeficiency vi

155 ly explain previously observed variations in hairpin ribozyme stability.

156 es an important basis for further studies of hairpin ribozyme structure and function.

157 For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolut

158 The relationship between hairpin ribozyme structure, and cleavage and ligation ki

159 e not observed in previous four-way-junction hairpin ribozyme structures due to crystal contacts with

160 Recent physical characterization of hairpin ribozyme structures using fluorescence resonance

161 located within all the required loops of the hairpin ribozyme-substrate complex and allowed for the d

162 The hairpin ribozyme-substrate complex contains two independ

163 es for all positions in loops 1 and 5 of the hairpin ribozyme-substrate complex was carried out using

164 The two domains of the hairpin ribozyme-substrate complex, usually depicted as

165 identified the catalytic core of the active hairpin ribozyme-substrate complex.

166 A hairpin ribozyme targeting G575 of the Sindbis virus gen

167 We have previously shown that hairpin ribozymes targeting the human immunodeficiency v

168 e detection of cellular target molecules for hairpin ribozymes, termed C-SPACE (cleavage-specific amp

169 cal junction determines the stability of the hairpin ribozyme tertiary structure and thus its catalyt

170 The enhanced ligation activity of hairpin ribozymes that contain a four-way helical juncti

171 Hairpin ribozymes that incorporate the natural four-way

172 l screening method has been used to identify hairpin ribozymes that inhibit hepatitis B virus (HBV) r

173 Here we report the selection of hairpin ribozymes that inhibit human immunodeficiency vi

174 Besides its presence in the hairpin ribozyme, the loop E motif is also apparent in h

175 In the active form of the hairpin ribozyme, the loops are in proximity.

176 ociated cations contributes significantly to hairpin ribozyme thermodynamics.

177 In a few cases, including loop B of the hairpin ribozyme, this unusual arrangement gives rise to

178 We engineered a variant of the hairpin ribozyme to catalyze addition of all four N>p's

179 Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphoryla

180 have carried out molecular modelling of the hairpin ribozyme to learn how the two domains (A and B)

181 g transcripts containing active and inactive hairpin ribozymes together with cleavable and non-cleava

182 mistic folding/unfolding simulations for the hairpin ribozyme using a Monte Carlo algorithm.

183 structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissil

184 d pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substit

185 our-way helical junction compared to minimal hairpin ribozyme variants.

186 ants for tertiary structure stability in the hairpin ribozyme, we evaluated the energetic contributio

187 Hairpin ribozymes were engineered to cleave a specific s

188 oter expression constructs for corresponding hairpin ribozymes were generated and cotransfected into

189 crystal structures of minimal, junctionless hairpin ribozymes were solved in native (U39), and mutan

190 One of the most striking examples is the hairpin ribozyme, which was shown to exhibit two to thre

191 self-cleavage reaction in a fully functional hairpin ribozyme with a unique 8azaA at position 38.

192 ddress this discrepancy, we investigated the hairpin ribozyme with an expanded set of pK(a) perturbed

193 ngement rationalizes the observed ability of hairpin ribozymes with a circularized substrate-binding