A Highly Sensitive and Selective Catalytic DNA Biosensor for Lead Ions

Li, Jing; Lu, Yi

doi:10.1021/ja0021316

Cited by 682 publications

(612 citation statements)

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“…The 17E DNAzyme is the most active with low concentration of Pb 2+ and Zn 2+ can also assist cleavage ( Figure 2C). 23 …”

Section: Ps-modified Enzymesmentioning

confidence: 99%

“…[12][13][14][15][16] Owing to their high catalytic efficiency and versatility in sensor design, RNA-cleaving DNAzymes have emerged as a unique metal sensing platform. 14,[17][18][19][20][21] Since DNAzymes require metal cofactors, by using specific metals during selection, RNA-cleaving DNAzymes selective for Mg 2+ , 13 Pb 2+ , 22,23 UO2 2+24 and lanthanides 25 have been reported. These metals are hard or borderline Lewis acids.…”

Section: Introductionmentioning

confidence: 99%

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Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes

2014

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Cadmium, mercury and lead are collectively banned by many countries and regions in electronic devices due to their extremely high toxicity. To date, no sensing method can detect them as a group and also individually with sufficient sensitivity and selectivity. An RNA-cleaving DNAzyme (Ce13d) was recently reported to be active with trivalent lanthanides, which are hard Lewis acids. In this work, phosphorothioate (PS) modifications were systematically made on Ce13d. A single PS at the substrate cleavage site shifts the activity from being dependent on lanthanide to soft thiophilic metals.By incorporating the PS modification to a few other DNAzymes, a sensor array was prepared to detect each metal. Individual sensors have excellent sensitivity (limit of detection = 4.8 nM Cd 2+ , 2.0 nM Hg 2+ , and 0.1 nM Pb 2+ ). This study provides a new route to obtain metal-specific DNAzymes by atomic replacement and also offers important mechanistic insights into metal binding and DNAzyme catalysis.3

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“…The 17E DNAzyme is the most active with low concentration of Pb 2+ and Zn 2+ can also assist cleavage ( Figure 2C). 23 …”

Section: Ps-modified Enzymesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes

2014

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“…19 At the same time, it is also studied as a model DNAzyme due to its recurrence in many different in vitro selections and high catalytic efficiency. [20][21][22][23][24][25] Examples of using the 8-17 DNAzyme for gene silencing are also known.…”

mentioning

confidence: 99%

“…For example, when an rAC junction was used, barely any cleavage was observed even with 500 mM Mg 2+ ( Figure S1, ESI). Therefore, it is also true for the [10][11][12][13][14][15][16][17][18][19][20][21][22][23] DNAzyme that its cleavage activity for every junction is not the same.…”

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confidence: 99%

Tandem DNAzymes for mRNA cleavage: Choice of enzyme, metal ions and the antisense effect

Wang

Saran

Liu

2015

Bioorganic & Medicinal Chemistry Letters

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“…Metal ions are a natural choice and indeed most nucleic acid enzymes require metal ions for function under physiological conditions and therefore, are metalloenzymes. Even though DNAzymes constitute the newest metalloenzyme family, they have already been used in a number of applications such as therapeutic agents 8 , biosensors [9][10][11][12] , and nanomaterials assembly 13 , often because DNAzymes are more stable against hydrolysis and more cost-effective to produce than proteins or ribozymes. A primary example is the 8-17 DNAzyme which cleaves a DNA substrate containing one RNA base at the cleavage site (Fig.…”

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confidence: 99%

Dissecting metal ion–dependent folding and catalysis of a single DNAzyme

et al. 2007

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Protein metalloenzymes use various modes for functions where metal-dependent global conformational change is required in some cases, but not in others. In contrast, most ribozymes appear to require a global folding that almost always precedes enzyme reactions. Herein we studied metal-dependent folding and cleavage activity of the 8-17 DNAzyme using single molecule fluorescence resonance energy transfer (FRET). Addition of Zn 2+ and Mg 2+ resulted in a folding step followed by cleavage reaction, suggesting that the DNAzyme may require metaldependent global folding for activation. In the presence of Pb 2+ , however, cleavage reaction occurred without a precedent folding step, suggesting that the DNAzyme may be prearranged to accept Pb 2+ for the activity. This feature may contribute to the remarkably fast Pb 2+ -dependent reaction of the DNAzyme. These results suggest that DNAzymes can use all modes of activation that metalloproteins use.Metal ion-dependent folding can play a critical role in metalloenzyme function. Understanding the relationship between folding and reaction is important in obtaining deeper insight into the enzyme mechanism. For protein metalloenzymes, an active-site metal-dependent global folding precedes enzymatic reaction in some cases while such a folding is not required in others 1 . These different modes of activation may fulfill different functions. For example, a reaction preceded by a folding step may be responsible for an allosteric effect in many enzyme functions, or such a folding step may contribute to the overall reaction. Competing Financial Interests StatementThe authors declare there are no competing financial interests. HHS Public Access Author Manuscript Author ManuscriptAuthor Manuscript Author ManuscriptIn the early 1980s, RNA molecules that can catalyze enzymatic reactions were discovered and named ribozymes 2,3 . This discovery was then followed by demonstrations in the 1990s that DNA can also act as enzymes, termed deoxyribozymes or DNAzymes 4-7 . With only four nucleotides as building blocks versus twenty in proteins, nucleic acid enzymes may need to recruit cofactors to perform some functions. Metal ions are a natural choice and indeed most nucleic acid enzymes require metal ions for function under physiological conditions and therefore, are metalloenzymes. Even though DNAzymes constitute the newest metalloenzyme family, they have already been used in a number of applications such as therapeutic agents 8 , biosensors [9][10][11][12] , and nanomaterials assembly 13 , often because DNAzymes are more stable against hydrolysis and more cost-effective to produce than proteins or ribozymes. A primary example is the 8-17 DNAzyme which cleaves a DNA substrate containing one RNA base at the cleavage site (Fig. 1a) Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript DNAzyme constructsThe original 8-17 DNAzyme was labeled with a fluorophore (Alexa fluoro 488) and two quenchers (Dabcyl) for bulk cleavage activity assays (Fig. 1a). To carry out the smFRET...

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A Highly Sensitive and Selective Catalytic DNA Biosensor for Lead Ions

Cited by 682 publications

References 34 publications

Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes

Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes

Tandem DNAzymes for mRNA cleavage: Choice of enzyme, metal ions and the antisense effect

Dissecting metal ion–dependent folding and catalysis of a single DNAzyme

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A Highly Sensitive and Selective Catalytic DNA Biosensor for Lead Ions

Cited by 682 publications

References 34 publications

Sensing Parts-per-Trillion Cd2+, Hg2+, and Pb2+ Collectively and Individually Using Phosphorothioate DNAzymes

Sensing Parts-per-Trillion Cd2+, Hg2+, and Pb2+ Collectively and Individually Using Phosphorothioate DNAzymes

Tandem DNAzymes for mRNA cleavage: Choice of enzyme, metal ions and the antisense effect

Dissecting metal ion–dependent folding and catalysis of a single DNAzyme

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Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes

Sensing Parts-per-Trillion Cd²⁺, Hg²⁺, and Pb²⁺ Collectively and Individually Using Phosphorothioate DNAzymes