Highly Selective Oligonucleotide‐Based Sensor for Mercury(<scp>II</scp>) in Aqueous Solutions

Ono, Akira; Togashi, Humika

doi:10.1002/anie.200454172

Cited by 1,132 publications

(628 citation statements)

References 48 publications

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“…For example, the enzyme strand contains quite a few thymines, which may form base pairs mediated by Hg 2+ . 54 Similar artifacts were observed also for an Ag + -specific DNAzyme. 20 Overall, this sensor has excellent specificity consistent with the gel-based assays.…”

supporting

confidence: 65%

In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage

2016

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Trivalent lanthanide ions (Ln3+) were recently employed to select RNA-cleaving DNAzymes, and three new DNAzymes have been reported so far. In this work, dysprosium (Dy3+) was used with a library containing 50 random nucleotides. After six rounds of in vitro selection, a new DNAzyme named Dy10a was obtained and characterized. Dy10a has a bulged hairpin structure cleaving a RNA/DNA chimeric substrate. Dy10a is highly active in the presence of the five Ln3+ ions in the middle of the lanthanide series (Sm3+, Eu3+, Gd3+, Tb3+, and Dy3+), while its activity descends on the two sides. The cleavage rate reaches 0.6 min–1 at pH 6 with just 200 nM Sm3+, which is the fastest among all known Ln3+-dependent enzymes. Dy10a binds two Ln3+ ions cooperatively. When a phosphorothioate (PS) modification is introduced at the cleavage junction, the activity decreases by >2500-fold for both the R p and S p diastereomers, and thiophilic Cd2+ cannot rescue the activity. The pH–rate profile has a slope of 0.37 between pH 4.2 and 5.2, and the slope was even lower at higher pH. On the basis of these data, a model of metal binding is proposed. Finally, a catalytic beacon sensor that can detect Ho3+ down to 1.7 nM is constructed.

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confidence: 65%

In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage

2016

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“…[5] The adaptive binding property has been used to design fluorescence resonance energy transfer (FRET)-based sensors with end-labeled fluorophores since FRET is known to be sensitive to such distance changes. Many molecules include adenosine/ATP, [6] cocaine, [7] arginiamide, [8] K I , [9][10][11][12] Mg II /Ca II , [13] Ag I , [14] Hg II , [15,16] thrombin, [17] and (platelet-derived growth factor) PDGF [18,19] have been detected using this method. One particularly interesting example is the Hg II binding DNA shown in Figure 1A.…”

Section: Introductionmentioning

confidence: 99%

“…Addition of Hg II folds the DNA into a hairpin. [15,20] can fold both through non-specific metal induced condensation and Hg II induced hairpin formation. F and T denote FAM (donor) and TAMRA (acceptor), respectively.…”

Section: Introductionmentioning

confidence: 99%

“…[25,26] To manage the mercury contamination problem, many sensors have been developed. [27] In particular, a large number of fluorescent, [15,[28][29][30] colorimetric, [31,32] and electrochemical sensors [33,34] have been designed based on the Hg II -thymine binding. In the original paper by Ono et al, [15] the DNA shown in Figure 1A was labeled with a 6-carboxyfluorescein (FAM) and a dark quencher (4-(4-dimethylaminophenyl) diazenylbenzoic acid, Dabcyl), respectively on the two ends.…”

Section: Introductionmentioning

confidence: 99%

“…First, it is possible to carry out ratiometric detection. Compared to the previous "light-off" design, [15] ratiometric detection allows better reproducibility and higher sensitivity. Second, FRET allows us to quantitatively study DNA folding.…”

Section: Introductionmentioning

confidence: 99%

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Metal‐Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications

Kiy

Jacobi

Liu

2011

Chemistry A European J

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Abstract.Metal induced nucleic acid folding has been extensively studied with ribozymes, DNAzymes, tRNA and riboswitches. These RNA/DNA molecules usually have a high content of double-stranded regions to support a rigid scaffold. On the other hand, such rigid structural features are not available for many in vitro selected or rationally designed DNA aptamers; they adopt flexible random coil structures in the absence of target molecules. Upon target binding, these aptamers adaptively fold into a compact structure with a reduced end-to-end distance, making fluorescence resonance energy transfer (FRET) a popular signaling mechanism. However, non-specific folding induced by mono-or divalent metal ions can also reduce the end-to-end distance and thus lead to false positive results. In this study we used a FRET pair labeled Hg II binding DNA and monitored metal induced folding in the presence of various cations. While non-specific electrostatically mediated folding can be very significant, at each tested salt condition, Hg II induced folding was still observed with a similar sensitivity. We also studied the biophysical meaning of the acceptor/donor fluorescence ratio that allowed us to explain the experimental observations. Potential solutions for this ionic strength problem have been discussed. For example, probes designed to signaling the formation of double-stranded DNA showed a lower dependency on ionic strength.3

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DNA ‐Enabled Heavy Metal Detection in Water

Moon

Huang

Liu

2020

Encyclopedia of Analytical Chemistry

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Detection of heavy metal contamination in the environment is an on‐going analytical challenge. In effort of developing portable biosensors, deoxyribonucleic acid (DNA)‐based designs have gained much attention for their high affinity and specificity to metals, stability, cost‐efficiency, ease of modification, and batch‐to‐batch reproducibility. Specific sequences of DNA aptamers and DNAzymes provide grounds for rational designs of fluorescent, colorimetric, and electrochemical detection methods. Aptamers exert only a binding function, while DNAzymes can use heavy metals to catalyze specific chemical and biological transformations. This article starts with a brief introduction of heavy metals and their interactions with DNA. Then DNA aptamers and DNAzymes are respectively reviewed from their in vitro selection, representative DNA sequences, and design of biosensors. For signal transduction, various fluorescent, colorimetric, and electrochemical examples are described. Finally, future perspectives are discussed.

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Highly Selective Oligonucleotide‐Based Sensor for Mercury(II) in Aqueous Solutions

Cited by 1,132 publications

References 48 publications

In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage

In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage

Metal‐Induced Specific and Nonspecific Oligonucleotide Folding Studied by FRET and Related Biophysical and Bioanalytical Implications

DNA ‐Enabled Heavy Metal Detection in Water

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