Ultrasensitive DNAzyme Beacon for Lanthanides and Metal Speciation

Huang, Po‐Jung Jimmy; Lin, Jenny; Vazin, Mahsa; Liu, Juewen

doi:10.1021/ac403762s

Cited by 138 publications

(251 citation statements)

References 50 publications

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“…We also converted Dy35 into a trans-cleaving form and it is also active (the last lane in Figure 1D). Since Dy10a appears to be different from all the previously reported Ln 3+ -dependent DNAzymes, [28][29][30] we characterized it in detail. With only two active sequences, the information from the DNA library is limited, only supporting the overall secondary structure and two mutable nucleotides.…”

Section: Resultsmentioning

confidence: 97%

“…Y 3+ has a size similar to Ho 3+ and it can activate the previously reported DNAzymes. [28][29][30] Interestingly, 5 µM Pb 2+ did not show any cleavage. Based on previous studies, Pb 2+ is active with many DNAzymes.…”

Section: Dy10a Is Highly Specific For Lnmentioning

confidence: 85%

“…This trend is different from any known DNAzyme. We already reported four other lanthanide-specific DNAzymes, [28][29][30][31] and this is the fifth one. By accumulating sufficient number of such DNAzymes, we may be able to distinct each lanthanide by designing a sensor array, mimicking the human tongue.…”

mentioning

confidence: 85%

“…For comparison, Ce13d works optimally with 10 µM Ln 3+ . 28 We used 10 to 50 At higher metal concentrations, the rate drops due to DNAzyme inhibition by Sm 3+ .…”

Section: Dy10a Is Highly Specific For Lnmentioning

confidence: 99%

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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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Section: Resultsmentioning

confidence: 97%

Section: Dy10a Is Highly Specific For Lnmentioning

confidence: 85%

mentioning

confidence: 85%

“…For comparison, Ce13d works optimally with 10 µM Ln 3+ . 28 We used 10 to 50 At higher metal concentrations, the rate drops due to DNAzyme inhibition by Sm 3+ .…”

Section: Dy10a Is Highly Specific For Lnmentioning

confidence: 99%

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

2016

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“…For example, RNA-cleaving DNAzymes specific for Na + , 23,24 Pb 2+ , 25,26 Zn 2+ , 27 UO2 2+ , 28 and lanthanide ions [29][30][31] were reported. These DNAzymes are fast, highly selective, and versatile in biosensor design.…”

Section: Introductionmentioning

confidence: 99%

An Ultrasensitive Light-up Cu²⁺ Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate

2016

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Cu 2+ is a very important metal ion in biology, environmental science, and industry. Developing biosensors for Cu 2+ is a key topic in analytical chemistry. DNAzyme-based sensors are highly attractive for their excellent sensitivity, stability, and programmability. In the past decade, a few Cu 2+ biosensors were reported using DNAzymes with DNA cleavage or DNA ligation activity.However, they require unstable ascorbate or imidazole activation. So far, no RNA-cleaving DNAzymes specific for Cu 2+ are known. In this work, a phosphorothioate (PS) RNA containing library was used for in vitro selection, and a few new Cu 2+ -specific RNA-cleaving DNAzymes were isolated. Among them, a DNAzyme named PSCu10 was studied further. It has only eight nucleotides in the enzyme loop with a cleavage rate of 0.1 min -1 in the presence of 1 µM Cu 2+ at pH 6.0 (its optimal pH). Between the two diastereomers of the PS RNA chiral center, the Rp isomer is 37 times more active than the Sp one. Among the other divalent metal ions, only Hg 2+ can cleave the substrate due to its extremely high thiophilicity. A catalytic beacon sensor was designed with a detection limit of 1.6 nM Cu 2+ and extremely high selectivity. PSCu10 is specific for Cu 2+ and it has no cleavage in the presence of ascorbate, which reduces Cu 2+ to Cu + .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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Ultrasensitive DNAzyme Beacon for Lanthanides and Metal Speciation

Cited by 138 publications

References 50 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

An Ultrasensitive Light-up Cu²⁺ Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate

DNA ‐Enabled Heavy Metal Detection in Water

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Ultrasensitive DNAzyme Beacon for Lanthanides and Metal Speciation

Cited by 138 publications

References 50 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

An Ultrasensitive Light-up Cu2+ Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate

DNA ‐Enabled Heavy Metal Detection in Water

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An Ultrasensitive Light-up Cu²⁺ Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate