A Highly Selective DNAzyme Sensor for Mercuric Ions

Hollenstein, Marcel; Hipolito, Christopher J.; Lam, Curtis H.; Dietrich, David; Perrin, David M.

doi:10.1002/ange.200800960

Cited by 78 publications

(50 citation statements)

References 94 publications

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“…[24] Many divalent metals have been detected by DNAzymes,s uch as Pb 2 + , [25] Zn 2 + , [26] Cu 2 + , [27,28] UO 2 2 + , [29] Cd 2 + , [30] and Hg 2 + . [31] Recently, progressw as also made for monovalentN a + [32,33] and Ag + , [34] and trivalent lanthanide ions. [35][36][37][38] The interaction between chromiuma nd DNA was studied mainly in biological systems.…”

Section: Introductionmentioning

confidence: 99%

In Vitro Selection of Chromium‐Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI)

Zhou

Vazin

et al. 2016

Chemistry A European J

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Chromium is a very important analyte for environmental monitoring, and developing biosensors for chromium is a long-standing analytical challenge. In this work, in vitro selection of RNAcleaving DNAzymes was carried out in the presence of Cr 3+ . The most active DNAzyme turned out to be the previously reported lanthanide-dependent Ce13d DNAzyme. While the Ce13d activity was ~150-fold lower with Cr 3+ compared to that with lanthanides, the activity of lanthanides and other competing metals was masked by using a phosphate buffer, leaving Cr 3+ the only metal that can activate Ce13d. With 100 µM Cr 3+ , the cleavage rate is 1.6 h -1 at pH 6.Using a molecular beacon design, Cr 3+ was measured with a detection limit of 70 nM, significantly lower than the U.S. Environmental Protection Agency (EPA) limit (11 μM). Cr(VI) was measured after its reduction by NaBH4 to Cr 3+ , and it can be sensed with a similar detection limit of 140 nM Cr(VI), lower than the EPA limit of 300 nM. This sensor was tested for chromium speciation analysis in a real sample, supporting its application for environmental monitoring. At the same time, it has enhanced our understanding on the interaction between chromium and DNA.3

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Section: Introductionmentioning

confidence: 99%

In Vitro Selection of Chromium‐Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI)

Zhou

Vazin

et al. 2016

Chemistry A European J

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“…[12] DNAzymesa re DNA-based catalysts isolated from in vitro selection. By using specific metal ions during selection, many DNAzymes have been obtained with high specificityf or Na + , [13,14] Pb 2 + , [15,16] Zn 2 + , [17] Cu 2 + , [18,19] UO 2 2 + , [20] Cd 2 + , [21] Hg 2 + , [22] and trivalentl anthanides. [23][24][25][26][27] In principle, the metal specificity is associated with am etal-binding site, however it is quite challenging to extract aptamer motifs from DNAzymes.…”

Section: Introductionmentioning

confidence: 99%

A Selective Na⁺ Aptamer Dissected by Sensitized Tb³⁺ Luminescence

2016

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A previous comparative study between two RNA-cleaving DNAzymes named NaA43 and Ce13d revealed the possibility of a common Na + aptamer in these two DNAzymes. Since Na + binding by DNA is a very fundamental biochemical problem, herein the interaction between Ce13d and Na + is studied in detail using sensitized Tb 3+ luminescence spectroscopy. Na + displaces Tb 3+ from the DNAzyme, and thus quenches the emission from Tb 3+ . The overall requirement for Na + binding includes the hairpin and the highly conserved 16-nucleotide loop in the enzyme strand along with a few unpaired nucleotides in the substrate. Mutations studies indicate a good correlation between Na + binding and the DNAzyme cleavage activity, suggesting the critical role of Na + binding for the enzyme activity. Ce13d displays a Kd of ~20 mM Na + , while other monovalent cations are in the ~40-60 mM range. The measured Kd for other metal ions are mainly due to non-specific competition. With a single nucleotide mutation, the specific Na + binding is lost, while another mutant improved the Kd to 8 mM Na + . This study has demonstrated a Na + aptamer with important biological implications and analytical applications. It has also defined the structural requirements for Na + binding and produced an improved mutant.

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“…[4][5][6][7] Although most early studies on these enzymes employed Mg II as the metal cofactor, many research groups, including ours, also pursued the possibility of using transitionmetal ions, and many transition-metal-specific nucleic acid enzymes have been obtained, thanks mainly to the development of a combinatorial method called in vitro selection. [4,[8][9][10][11][12] For example, in vitro selection has resulted in DNAzymes that are specific for Pb II , [3,13,14] Co II , [15] Mn II , [16] Zn II , [17] Hg II , [18] and Cu II . [19][20][21] These experiments firmly established that nucleic acid enzymes can bind metal ions specifically, just like metalloprotein enzymes.…”

Section: Introductionmentioning

confidence: 99%

“…[18,19,45] In one case, the inhibitory effect at high metal concentrations was attributed to the disruption of DNA base-pairing interactions by nonspecific metal/DNA interactions. [45] To understand the mechanism of inhibition in the current uranium DNAzyme, we tested the activity of the Pb II -specific DNAzyme (Figure 1 C) in the presence of 100 mm uranium, and similar inhibition effects were also observed (data not shown).…”

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confidence: 95%

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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A Highly Selective DNAzyme Sensor for Mercuric Ions

Cited by 78 publications

References 94 publications

In Vitro Selection of Chromium‐Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI)

In Vitro Selection of Chromium‐Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI)

A Selective Na⁺ Aptamer Dissected by Sensitized Tb³⁺ Luminescence

Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

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A Highly Selective DNAzyme Sensor for Mercuric Ions

Cited by 78 publications

References 94 publications

In Vitro Selection of Chromium‐Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI)

In Vitro Selection of Chromium‐Dependent DNAzymes for Sensing Chromium(III) and Chromium(VI)

A Selective Na+ Aptamer Dissected by Sensitized Tb3+ Luminescence

Biochemical Characterization of a Uranyl Ion‐Specific DNAzyme

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A Selective Na⁺ Aptamer Dissected by Sensitized Tb³⁺ Luminescence