ライフサイエンスコーパス: deoxyribozyme

1 tion step involving the 3'-5'-selective 8-17 deoxyribozyme.

2 ded onto the catalytic core of a ribozyme or deoxyribozyme.

3 says based on the ribonuclease activity of a deoxyribozyme.

4 by RCA, codes for a fluorescence generating deoxyribozyme.

5 that flank the 40-nt catalytic region of the deoxyribozyme.

6 faster than our previously identified 15HA9 deoxyribozyme.

7 han our previously reported Mg(2+)-dependent deoxyribozymes.

8 f the well-known 10-23 and 8-17 RNA-cleaving deoxyribozymes.

9 cular beacon stem-loops with hammerhead-type deoxyribozymes.

10 interest for the in vitro selection of novel deoxyribozymes.

11 interest for the in vitro selection of novel deoxyribozymes.

12 and localizes cleavage sites of thousands of deoxyribozymes.

13 enables identification of amide-hydrolyzing deoxyribozymes.

14 pSer lyase deoxyribozymes, named Dha-forming deoxyribozymes 1 and 2 (DhaDz1 and DhaDz2), each functio

15 Furthermore, we demonstrate that deoxyribozyme 10-12opt can be utilized to cleave certain

16 The best new deoxyribozyme, 15MZ36, catalyzes covalent Tyr modificati

17 cleavage activity of the histidine-dependent deoxyribozyme 3 (HD3).

18 tion was previously used to identify a small deoxyribozyme, 7Q10, that ligates RNA with formation of

19 Among these, deoxyribozyme 8-17 is the most common small DNA motif ca

20 For synthesis of branched DNA, the best new deoxyribozyme, 8LV13, has k(obs) on the order of 0.1 min

21 For synthesis of branched RNA, two new deoxyribozymes, 8LX1 and 8LX6, were identified with broa

22 antisense oligodeoxynucleotides and a 10-23 deoxyribozyme active against the positive-strand 3'-X re

23 ate reaction vessels wherein the products of deoxyribozyme adenylation are purified before their use

24 gether our data showed that treatment with a deoxyribozyme against XT-1 mRNA decreased the amount of

25 The deoxyribozymes all function by forming a three-helix-jun

26 that allow differential pairing between the deoxyribozyme and each substrate.

27 re the cleavage status and sequences of both deoxyribozyme and RNA substrate.

28 tensive Watson-Crick complementarity between deoxyribozyme and substrate, the parent 10MD5 is inheren

29 ors are designed using modified RNA-cleaving deoxyribozymes and detect analytes that act as allosteri

30 feasibility of mid-down approaches based on deoxyribozymes and underscored their potential in the an

31 2)(+) as used by our previous branch-forming deoxyribozymes, and each has an initially random region

32 cleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin

33 ytic DNAs, an ATP-dependent self-adenylating deoxyribozyme (AppDNA) and a self-ligating deoxyribozyme

34 The deoxyribozyme approach may become a contributing factor

35 The pH profile and reaction products of this deoxyribozyme are similar to those reported for hammerhe

36 Some of the new deoxyribozymes are general with regard to the amino acid

37 , although these particular Zn(2+)-dependent deoxyribozymes are likely not useful for this practical

38 broadly sequence-tolerant and site-specific deoxyribozymes are readily identified for hydrolysis of

39 These RNA ligase deoxyribozymes are the first that create native 3'-5' RN

40 le logic gates and one constitutively active deoxyribozyme arrayed in nine wells (3x3) corresponding

41 also suggest the longer-term feasibility of deoxyribozymes as artificial proteases.

42 avidin molecule as an inert 'body' and three deoxyribozymes as catalytic 'legs'-show elementary robot

43 cessing, for example as shown by the classic deoxyribozyme-based automaton that plays tic-tac-toe(42)

44 We designed a deoxyribozyme-based DNA machine that can i) recognize th

45 We developed deoxyribozyme-based graphics processing units able to mo

46 required the design of a generic three-input deoxyribozyme-based logic gate that can use any three-wa

47 port that molecular computation performed by deoxyribozyme-based logic gates can be used to control t

48 We report herein a set of deoxyribozyme-based logic gates capable of generating an

49 constructed a solution-phase array of three deoxyribozyme-based logic gates that behaves as a half-a

50 cular scale events that can be achieved with deoxyribozyme-based logic gates.

51 The sum output consisted of four new deoxyribozyme-based logic gates: an ANDAND gate and thre

52 A deoxyribozyme-based molecular automaton.

53 We have developed an array of seven deoxyribozyme-based molecular logic gates that behaves a

54 ched RNA are extremely limited in scope, the deoxyribozyme-based route using 7S11 will enable many ex

55 The vast majority of deoxyribozyme-based sensors are designed using modified

56 Here we report a novel RNA-cleaving deoxyribozyme called 10-12opt that functions with an equ

57 e able to show that small molecule modifying deoxyribozymes can be converted to analyte sensors by co

58 The newly identified deoxyribozymes can function with multiple turnover using

59 In addition, the binary deoxyribozymes can read non-natural nucleotides and writ

60 This "deoxyribozyme" can self-cleave or can operate as a bimol

61 We recently reported that a DNA catalyst (deoxyribozyme) can site-specifically hydrolyze DNA on th

62 We previously reported that DNA catalysts (deoxyribozymes) can hydrolyze DNA phosphodiester linkage

63 We show that DNA enzymes (deoxyribozymes) can introduce azide functional groups at

64 leic acid elements (aptamers, ribozymes, and deoxyribozymes) can serve as inputs and outputs to the e

65 Deoxyribozymes capable of catalyzing sequence-specific R

66 Members of class I deoxyribozymes carry a catalytic core composed of only 1

67 DNA strands hybridize to 16S rRNA to form 32 deoxyribozyme catalytic cores that produce a fluorescent

68 by using the analyte as the substrate for a deoxyribozyme catalyzed self-phosphorylation reaction.

69 The final ligation step of the deoxyribozyme-catalyzed sequence of reactions mimics the

70 Each deoxyribozyme catalyzes the transfer of the AMP moiety o

71 mental insights into the interplay among key deoxyribozyme characteristics of tolerance and selectivi

72 This deoxyribozyme contains a 14-nucleotide catalytic core th

73 ed the selection strategy to demand that the deoxyribozymes create linear 3'-5' linkages by introduci

74 Some of the Zn(2+)-dependent deoxyribozymes create native 3'-5' RNA linkages (with k(

75 The best deoxyribozyme decreases the half-life for phosphoserine

76 that makes use of in vitro transcription and deoxyribozyme digestion of the transcripts to produce th

77 his system, we used the self-phosphorylating deoxyribozyme Dk2 to detect as little as 25 nM GTP even

78 Most deoxyribozymes (DNA catalysts) require metal ions as cof

79 We recently reported deoxyribozymes (DNA enzymes) that synthesize 2',5'-branc

80 in vitro selection of several Mg2+-dependent deoxyribozymes (DNA enzymes) that synthesize a 2'-5' RNA

81 Two new deoxyribozymes (DNA enzymes) were identified by in vitro

82 We show that DNA catalysts (deoxyribozymes, DNA enzymes) can phosphorylate tyrosine

83 Catalytic DNA sequences (deoxyribozymes, DNA enzymes, or DNAzymes) have been iden

84 de, many catalytically active DNA molecules (deoxyribozymes; DNA enzymes) have been identified by in

85 , we knocked down XT-1 mRNA using a tailored deoxyribozyme (DNAXTas) and hypothesized that this would

86 sed for the in vitro selection of a modified deoxyribozyme (DNAzyme) capable of the sequence-specific

87 our knowledge) Na(+)-specific, RNA-cleaving deoxyribozyme (DNAzyme) with a fast catalytic rate [obse

88 Deoxyribozymes (DNAzymes) and aptamers are of interest t

89 Deoxyribozymes (DNAzymes) are single-stranded DNA that c

90 RNA-cleaving deoxyribozymes (DNAzymes) are synthetic single-stranded

91 tides, small interfering RNA, ribozymes, and Deoxyribozymes (DNAzymes) have been used to tackle neuro

92 Although deoxyribozymes (DNAzymes) have been widely used as biose

93 ctures consisting of temporarily inactivated deoxyribozymes (DNAzymes).

94 The deoxyribozymes do not require redox-active metal ions an

95 ntrol which of the two strands bind with the deoxyribozyme during the branch-forming reaction.

96 ith different components of a multicomponent deoxyribozyme (DZ) sensor.

97 eriments have identified numerous RNA ligase deoxyribozymes, each of which can synthesize either 2',5

98 Surprisingly, the new deoxyribozymes evolved from 8-17 create only 2'-5' linka

99 roducing protein-like functional groups into deoxyribozymes for identifying new catalytic function.

100 nstrated substantially broader generality of deoxyribozymes for site-specific DNA hydrolysis.

101 o selection experiments to identify improved deoxyribozymes for synthesis of branched DNA and RNA.

102 Several new deoxyribozymes for Tyr modification (and several for Ser

103 DNA catalysts (deoxyribozymes) for a variety of reactions have been ide

104 tail that is complementary to a G-quadruplex deoxyribozyme-forming sequence.

105 results suggest that this novel RNA-cleaving deoxyribozyme forms a distinct catalytic structure than

106 An optimized deoxyribozyme from this selection requires L-histidine o

107 Each deoxyribozyme generates both superoxide (O2(-*) or HOO(*

108 The self-ligating deoxyribozyme has also been reconfigured to generate a t

109 The compact 7Q10 deoxyribozyme has both practical utility and the potenti

110 This deoxyribozyme has higher activity in the presence of tra

111 ghly efficient Zn(II)-dependent RNA-cleaving deoxyribozymes has been obtained through in vitro select

112 Alternatively, numerous deoxyribozymes have been identified for catalysis of RNA

113 Since that time, many other RNA-cleaving deoxyribozymes have been identified.

114 RNA-cleaving deoxyribozymes have found broad application as useful to

115 The deoxyribozymes have little or no selectivity for the ami

116 ssays show that some of the newly identified deoxyribozymes have promise for ligating RNA in a sequen

117 On this basis, Zn(2+)-dependent deoxyribozymes have promise for synthesis of native 3'-5

118 The current deoxyribozymes have some RNA substrate sequence requirem

119 of RNA ligation products by Zn(2+)-dependent deoxyribozymes highlights the versatility of transition

120 These data support the utility of deoxyribozymes in creating synthetic 2',5'-branched RNAs

121 All of the new deoxyribozymes indeed create only linear 3'-5' RNA, conf

122 nsional architecture such that the resulting deoxyribozymes inherently cannot function with free pept

123 Some of the new Zn(2+)-dependent deoxyribozymes instead create non-native 2'-5' linkages,

124 ved upon evolution of the 10-23 RNA-cleaving deoxyribozyme into an RNA ligase.

125 nd involvement of superoxide and H2O2 by the deoxyribozymes is not yet defined.

126 pproach to obtain 3'-5'-selective RNA ligase deoxyribozymes is particularly important for ongoing sel

127 They share a common motif with the '8-17' deoxyribozyme isolated under different conditions, inclu

128 found that reselection of a DNA-hydrolyzing deoxyribozyme leads either to transesterification or hyd

129 he AppDNA and that of the 3' terminus of the deoxyribozyme ligase limit the range of sequences that c

130 tial rate constant (k(obs)) of the optimized deoxyribozyme ligase was found to be 1 x 10(-)(4) min(-)

131 The binary deoxyribozyme ligases could potentially be used in a var

132 Selected deoxyribozyme ligases could use all five substrates, alb

133 We have engineered binary deoxyribozyme ligases whose two components are brought t

134 The new deoxyribozymes ligate RNA with k(obs) values up to 0.5 h

135 The 7Q10 deoxyribozyme ligates any RNA substrates that form the s

136 purified before their use as substrates for deoxyribozyme ligation.

137 ategy termed magnetic field-activated binary deoxyribozyme (MaBiDZ) sensor that enables both efficien

138 Each self-phosphorylating deoxyribozyme makes use of one or more of the eight stan

139 entification of numerous new DNA-hydrolyzing deoxyribozymes, many of which require merely two particu

140 some substrates, nearly half of the selected deoxyribozymes mediate a ligation reaction involving the

141 The in vitro-selected 9F7 and 9F21 deoxyribozymes mediate reaction of a branch-site adenosi

142 Therefore, deoxyribozyme-mediated formation of a non-native 2'-5' p

143 Bimolecular deoxyribozyme-mediated strand scission proceeds with a k

144 Each new Zn(2+)-dependent deoxyribozyme mediates the reaction of a specific nucleo

145 Two deoxyribozymes mimic i(1)ANDNOTi(2) and i(2)ANDNOTi(1) g

146 The third deoxyribozyme mimics an i(1)ANDi(2) gate and cleaves the

147 Two new pSer lyase deoxyribozymes, named Dha-forming deoxyribozymes 1 and 2

148 Here we have found that deoxyribozymes newly selected to use uridine as the bran

149 b(3+) was confirmed for related RNA-ligating deoxyribozymes, pointing toward favorable activation of

150 Although most prototypic deoxyribozymes poorly differentiate between the ribose a

151 This reaction creates a modified deoxyribozyme product that can be circularized and subje

152 Under these conditions, the ligase deoxyribozyme promotes DNA ligation at least 10(5)-fold

153 The new Mg(2+)-dependent deoxyribozymes provide 50-60% yield of ligated RNA in ov

154 that cleave the RNA substrate, mimicking the deoxyribozyme reaction.

155 Most but not all of these deoxyribozymes require a divalent metal ion cofactor suc

156 A 41-nucleotide class 1 deoxyribozyme requires Cu(2+) as a cofactor and adopts a

157 Each deoxyribozyme requires Zn(2+), and most additionally req

158 Each of the new deoxyribozymes requires Mn(2)(+) as a cofactor, rather t

159 utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors.

160 Here, we describe the compact 6CE8 deoxyribozyme (selected using a 20 nt random region) tha

161 via this approach shows that the outcome of deoxyribozyme selection experiments can be dramatically

162 ation of drug resistant mutants using binary deoxyribozyme sensors (BiDz).

163 In one case, the same deoxyribozyme sequence without the modifications still r

164 The practical impact of RNA-cleaving deoxyribozymes should continue to increase as additional

165 The binary deoxyribozymes show great specificity, can discriminate

166 nteresting structure near this region of the deoxyribozyme-substrate complex.

167 Unexpectedly, other Zn(2+)-dependent deoxyribozymes synthesize one of three unnatural linkage

168 The 7S11 deoxyribozyme synthesizes 2',5'-branched RNA by mediatin

169 This two-deoxyribozyme system was able to report the presence of

170 tro evolution was used to transform the 8-17 deoxyribozyme that cleaves RNA into a family of DNA enzy

171 d on the highly efficient 10-23 RNA-cleaving deoxyribozyme that is capable of exponential amplificati

172 ic core of 7Q10, a previously reported small deoxyribozyme that is unrelated in sequence to 9A2.

173 tification by in vitro selection of 10MD5, a deoxyribozyme that requires both Mn2+ and Zn2+ to hydrol

174 used in vitro selection to identify 7S11, a deoxyribozyme that synthesizes 2',5'-branched RNA.

175 We recently described 7S11, a deoxyribozyme that was identified by in vitro selection

176 monstrated its utility by discovery of novel deoxyribozymes that allow for cleaving challenging RNA t

177 tly used in vitro selection to identify many deoxyribozymes that catalyze DNA phosphodiester bond hyd

178 Here we describe in vitro selection of deoxyribozymes that catalyze Tyr side chain modification

179 Several deoxyribozymes that cleave RNA have utility for in vitro

180 This article focuses on deoxyribozymes that cleave RNA substrates.

181 Deoxyribozymes that could catalyze the formation of an i

182 In all cases, we again find deoxyribozymes that create only 2'-5' linkages.

183 7.5, versus pH 9.0 for many of our previous deoxyribozymes that form branched RNA.

184 The automaton is a Boolean network of deoxyribozymes that incorporates 23 molecular-scale logi

185 To obtain deoxyribozymes that instead create linear 3'-5'-linked (

186 Previously, deoxyribozymes that join a 5'-hydroxyl and a 2',3'-cycli

187 Deoxyribozymes that ligate RNA expand the scope of nucle

188 Deoxyribozymes that ligate RNA should be particularly us

189 We report Zn(2+)-dependent deoxyribozymes that ligate RNA.

190 In vitro selection was used to identify deoxyribozymes that ligate two RNA substrates.

191 tro selection to identify several classes of deoxyribozymes that mediate RNA ligation by attack of a

192 vitro selection to identify Mg(2+)-dependent deoxyribozymes that mediate the ligation reaction of an

193 We recently described several deoxyribozymes that modify tyrosine (Tyr) or serine (Ser

194 Twelve classes of deoxyribozymes that promote an ATP-dependent "self-cappi

195 on and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DN

196 at the 3'-5' selection pressure was applied, deoxyribozymes that specifically create 3'-5' linkages q

197 Using in vitro selection, we identified deoxyribozymes that transfer the 2'-azido-2'-deoxyadenos

198 Using in vitro selection, we identified deoxyribozymes that transfer the gamma-phosphoryl group

199 whereas all of our previous Mg(2+)-dependent deoxyribozymes that use a 2',3'-cyclic phosphate create

200 Tyrosine kinase deoxyribozymes that use pppRNA were identified from each

201 focuses on the development of DNA catalysts (deoxyribozymes) that modify side chains of peptide subst

202 Additionally, compared to control deoxyribozyme, the DNAXTas treatment resulted in a 9-fol

203 Here we subjected the 9A2 deoxyribozyme to re-selection for improved ligation rate

204 ted the possible application of RNA-cleaving deoxyribozymes to control the number and size of cleavag

205 We use one of the new deoxyribozymes to modify free peptide substrates by atta

206 We have previously used deoxyribozymes to synthesize several types of branched n

207 g deoxyribozyme (AppDNA) and a self-ligating deoxyribozyme, to create a ligation system that covalent

208 c acid enzymes including two ribozymes and a deoxyribozyme, underscoring the generality of this appro

209 An optimized ATP-dependent deoxyribozyme uses ATP >40,000-fold more efficiently tha

210 Using Tb(3+) as accelerating cofactor for deoxyribozymes, various labeled guanosines were site-spe

211 n, we present a facile method implementing a deoxyribozyme, VMC10, which preferentially cleaves the u

212 The previously reported deoxyribozyme was covalently modified with biotin and us

213 A bimolecular version of the ATP-dependent deoxyribozyme was further engineered to phosphorylate sp

214 One of the new deoxyribozymes was used to prepare by ligation the Tetra

215 The aromatic amide-hydrolyzing deoxyribozymes were examined using linear free energy re

216 In these efforts, all of the deoxyribozymes were identified via a common in vitro sel

217 used in vitro selection to identify the 7S11 deoxyribozyme, which catalyzes formation of 2',5'-branch

218 st that with further development, pSer lyase deoxyribozymes will have broad practical utility for sit

219 This includes deoxyribozymes with an arrangement that favors 3'-5' lin

220 Deoxyribozymes with fluorescence-based reporting have th

221 two to six attached nucleic acid catalysts (deoxyribozymes), with phosphodiesterase activity.