A DNAzyme cascade for the amplified detection of Pb2+ ions or l-histidine

Elbaz, Johann; Shlyahovsky, Bella; Willner, Itamar

doi:10.1039/b716774a

Cited by 207 publications

(128 citation statements)

References 15 publications

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“…For several enzymes, the metal-binding affinity and specificity are so high that they were used as components for metal-ion biosensors, such as Pb II sensors. [22][23][24][25][26][27] These successes led us to purposefully employ in vitro selection to obtain metal-specific DNAzymes for metal-sensing applications. For example, we have recently selected an RNA-cleaving DNAzyme that is active in the presence of UO 2 2 + .…”

Section: Introductionmentioning

confidence: 99%

Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

Brown¹,

Liu²,

He³

et al. 2009

ChemBioChem

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Uranyl ion-specific DNAzyme: A DNAzyme (lower strand) cleaves the substrate (upper strand) in the presence of the uranyl ion. The enzyme folds into a bulged three-way-junction structure with catalytically important nucleotides residing in the bulge. A highly conserved GA mismatch is also crucial for the enzyme's activity.The biochemical characterization of a DNAzyme that is highly specific for uranyl (UO(2) (2+)) ions is described. Sequence alignment, enzyme truncation, and mutation studies have resulted in a conserved sequence that folds into a bulged stem-loop structure. Interestingly, a GA pair next to the scissile site is important for the uranyl ion-specific DNAzyme; this is reminiscent of the GT wobble base pair adjacent to the cleavage site that is crucial for the Pb(II)-specific 8-17 DNAzyme activity. Therefore wobble pairs might be important for formation of metal-specific metal-binding sites in DNAzymes. The DNAzyme binds the uranyl ion with a dissociation constant of 469 nM, which is among the strongest metal-binding affinities in nucleic acid enzymes reported to date. This explains why a catalytic beacon fluorescent sensor based on this enzyme has a detection limit (45 pM) that rivals the most-sensitive analytical instrument. It also has over 1 000 000-fold specificity for the uranyl ion over other metal ions. The DNAzyme can carry out multiple turnover reactions that follow the Michaelis-Menten equation, with a k(cat) of 1.46 min(-1) and a K(M) of 463 nM, similar to that of the 8-17 DNAzyme. The pH profile shows a bell-shaped curve that reaches a maximum at pH 5.5, at which the in vitro selection was carried out; this suggests that in vitro selection can be performed to obtain DNAzymes with optimal performance under specific conditions under which practical applications are required. These findings enrich our fundamental understanding of metal-binding sites in nucleic acids and allow the design of sensors with better performance.

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Section: Introductionmentioning

confidence: 99%

Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

Brown¹,

Liu²,

He³

et al. 2009

ChemBioChem

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“…2,2'-Azinobis(3-ethylbenzothiazoline)-6-sulfonate (ABTS 2À ), tris(hydroxymethyl) aminomethane acetate (TRIS), 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid sodium salt (HEPES), MgCl 2 , cytidine 5'-triphosphate (CTP), and adenosine 5'-triphosphate (ATP) were purchased from Sigma-Aldrich. Oligonucleotides 1,2,3,5,6,7,8,9,10,11,12, and 13 were custom-ordered from Sigma Genosys. The chimeric oligonucleotide 4 was custom-ordered from Integrated DNA Technologies.…”

Section: Resultsmentioning

confidence: 99%

“…[11] Recently, a DNAzyme cascade was activated for amplified detection of Pb 2 + ions and l-histidine. [12] The base sequence in nucleic acids allows us to encode structural Abstract: The activation of a DNAzyme cascade by the cooperative selfassembly of multicomponent nucleic acid structures is suggested as a method for the amplified sensing of DNA, or the specific substrates of aptamers. According to one configuration, the DNA analyte 1 is detected by two tailored nucleic acids 2 and 3 that form a multicomponent supramolecular structure with a ribonucleobase-containing quasi-circular DNA 4, but only upon the concomitant hybridization with 1.…”

Section: Introductionmentioning

confidence: 99%

Cooperative Multicomponent Self‐Assembly of Nucleic Acid Structures for the Activation of DNAzyme Cascades: A Paradigm for DNA Sensors and Aptasensors

Elbaz

Moshe

Shlyahovsky

et al. 2009

Chemistry A European J

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149

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The activation of a DNAzyme cascade by the cooperative self-assembly of multicomponent nucleic acid structures is suggested as a method for the amplified sensing of DNA, or the specific substrates of aptamers. According to one configuration, the DNA analyte 1 is detected by two tailored nucleic acids 2 and 3 that form a multicomponent supramolecular structure with a ribonucleobase-containing quasi-circular DNA 4, but only upon the concomitant hybridization with 1. The resulting supramolecular nucleic acid structure includes the Mg(2+)-dependent DNAzyme that cleaves the ribonucleobase site of 4. The cleavage of the quasi-circular DNA 4 results in the fragmentation of the supramolecular structure and the release of two horseradish peroxidase (HRP) mimicking units that were incorporated in the blocked quasi-circular DNA 4. The HRP-mimicking DNAzyme catalyzed the oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS(2-)) by H(2)O(2) to ABTS(*-), and the product provided the colorimetric readout signal for the analyzed DNA. The method enabled the analysis of DNA with a detection limit of 1 x 10(-12) M. Similarly, an analogous DNAzyme cascade was activated by the low-molecular-weight substrates, adenosine triphosphate (ATP) or cocaine. This was induced by the self-assembly of nucleic acids that included fragments of the respective aptamers and the Mg(2+)-dependent DNAzyme. Furthermore, nucleic acids consisting of fragments of the aptamers against ATP or cocaine and fragments of the HRP-mimicking DNAzyme self-assemble, in the presence of the respective substrates, to the active DNAzyme structure that catalyzes the oxidation of ABTS(2-) by H(2)O(2) to form the colored product ABTS(*-). The resulting product provided the readout signal for the recognition events. The cooperative interaction in the formation of the supramolecular nucleic acid assemblies and the activation of the DNAzymes are discussed.

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“…More and more effort has been taken to adjust and design other G-quadruplex DNAs which can bind hemin as catalytic labels for development of colorimetric and chemiluminescence biosensors, i.e., PW17, AGRO100 and TBA. Willner and his co-workers employed PW17-DNAzyme as labels to detect DNA [5,6], Hg 2 + [7], AMP [8] and investigate telomerse activity [9].They also used Pb 2 + and l-histidine-dependent DNAzyme for colorimetric detection of Pb 2 + and l-histidine [10]. Dong and her co-workers expanded ARGO100-DNAzyme to detect K + [11], Hg 2 + [12] and exploited TBA-DNAzyme to thrombin colorimetric detection [13,14].…”

Section: Introductionmentioning

confidence: 95%

G‐Quadruplex‐Based DNAzymes Aptasensor for the Amplified Electrochemical Detection of Thrombin

Shen¹,

Wang²,

Zhu³

et al. 2010

Electroanalysis

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A novel G-quadruplex-based DNAzymes aptasensor for the amplified electrochemical detection of thrombin has been described. The aptasensor utilized a combination of hemin and guanine-rich thrombin-binding aptamer (TBA) to form horseradish peroxidase (HRP)-mimicking DNAzymes with peroxidase catalytic activity. In the presence of thrombin, the enzyme activity could be extensively promoted, thereby providing the amplified electrochemical readout signals for detecting thrombin. This aptasensor exhibited high sensitivity and selectivity for thrombin determination, which enabled the analysis of thrombin with a detection limit of 6 10 -11 M. On the basis of results, this method could have broad applications in the detection of proteins and other biomolecules.

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A DNAzyme cascade for the amplified detection of Pb2+ ions or l-histidine

Abstract: DNAzyme cascades activated by Pb(2+)- or L-histidine-dependent DNAzymes yield the horseradish peroxidase-mimicking catalytic nucleic acids that enable the colorimetric or chemiluminescence detection of Pb(2+) or L-histidine.

Cited by 207 publications

References 15 publications

Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

Cooperative Multicomponent Self‐Assembly of Nucleic Acid Structures for the Activation of DNAzyme Cascades: A Paradigm for DNA Sensors and Aptasensors

G‐Quadruplex‐Based DNAzymes Aptasensor for the Amplified Electrochemical Detection of Thrombin

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