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 enables identification of amide-hydrolyzing deoxyribozymes.

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

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

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

11 interest for the in vitro selection of novel deoxyribozymes.

12 interest for the in vitro selection of novel deoxyribozymes.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

27 The deoxyribozyme approach may become a contributing factor

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

47 The newly identified deoxyribozymes can function with multiple turnover using

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

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

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

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

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

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

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

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

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

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

58 Each deoxyribozyme catalyzes the transfer of the AMP moiety o

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

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

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

62 The best deoxyribozyme decreases the half-life for phosphoserine

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

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

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

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

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

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

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

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

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

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

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

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

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

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

77 ctures consisting of temporarily inactivated deoxyribozymes (DNAzymes).

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

93 This deoxyribozyme has higher activity in the presence of tra

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

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

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

97 The deoxyribozymes have little or no selectivity for the ami

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

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

100 The current deoxyribozymes have some RNA substrate sequence requirem

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

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

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

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

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

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

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

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

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

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

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

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

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

114 Selected deoxyribozyme ligases could use all five substrates, alb

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

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

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

118 purified before their use as substrates for deoxyribozyme ligation.

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

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

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

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

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

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

125 Bimolecular deoxyribozyme-mediated strand scission proceeds with a k

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

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

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

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

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

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

132 Although most prototypic deoxyribozymes poorly differentiate between the ribose a

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

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

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

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

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

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

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

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

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

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

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

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

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

146 The binary deoxyribozymes show great specificity, can discriminate

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

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

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

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

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

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

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

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

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

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

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

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

159 Several deoxyribozymes that cleave RNA have utility for in vitro

160 This article focuses on deoxyribozymes that cleave RNA substrates.

161 Deoxyribozymes that could catalyze the formation of an i

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

163 7.5, versus pH 9.0 for many of our previous deoxyribozymes that form branched RNA.

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

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

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

167 Deoxyribozymes that ligate RNA expand the scope of nucle

168 Deoxyribozymes that ligate RNA should be particularly us

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

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

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

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

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

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

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

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

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

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

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

180 Tyrosine kinase deoxyribozymes that use pppRNA were identified from each

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

197 Deoxyribozymes with fluorescence-based reporting have th

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