DNA as Sensors and Imaging Agents for Metal Ions

Xiang, Yu; Lu, Yi

doi:10.1021/ic4019103

Cited by 142 publications

(106 citation statements)

References 351 publications

(814 reference statements)

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“…DNA is very useful and versatile platform for biosensor development [17][18][19][20][21][22]. DNA is attractive for their programmability, easy to modify, and amenable to in vitro selection.…”

Section: Introductionmentioning

confidence: 99%

Adsorption of Selenite and Selenate by Metal Oxides Studied with Fluorescent DNA Probes for Analytical Application

Liu

2017

J. Anal. Test.

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Selenium is a required micronutrient at low concentrations, while it becomes toxic at high concentrations. Inorganic selenium exists mainly as SeO 3 2-(selenite or Se(IV)) and SeO 4 2-(selenate or Se(VI)). Currently, few biosensors can effectively measure these selenium species in water. In this work, we study the adsorption of selenite/ selenate by various metal oxide nanoparticles including CeO 2 , CoO, Cr 2 O 3 , Fe 2 O 3 , Fe 3 O 4 , In 2 O 3 , Mn 2 O 3 , NiO, TiO 2 , and ZnO. Fluorescently-labeled DNA molecules are used as probes and first adsorbed on these oxides, resulting in quenched fluorescence. Upon addition of selenite, the DNA probes are displaced from the surface with fluorescence recovered for six out of the ten oxides, while the response to selenate was much lower in all the cases. The signaling is optimal below 400 mM NaCl at near neutral pH when Fe 3 O 4 nanoparticles were used. Quantitative studies were performed on three oxides with detection limits for selenite being 0.3 lM (CeO 2 ), 2.0 lM (Fe 3 O 4 ), and 3.0 lM (Fe 2 O 3 ), respectively. The system, however, is also responsive to a few other anions such as phosphate and arsenate. Therefore, it can be used as a method for analyzing selenium species when the system is known to be free of such competing anions. This study represents the first effort of designing selenite sensors using DNA as probes, and it may stimulate related work for this important analyte.

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Section: Introductionmentioning

confidence: 99%

Adsorption of Selenite and Selenate by Metal Oxides Studied with Fluorescent DNA Probes for Analytical Application

Liu

2017

J. Anal. Test.

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“…Since then, many DNAzymes have been isolated via this selection process. Among them, RNA-cleaving DNAzymes are of particular interest for metal ion sensing, due to their fast reaction rate and because the cleavage, which is catalyzed by a metal ion cofactor, can easily be converted into a detectable signal (36)(37)(38). Unlike the rational design of either small-molecule or genetically encoded protein sensors, DNAzymes with desired sensitivity and specificity for a metal ion of interest can be selected from a large Significance Monovalent ions, such as Na + , play important roles in biology, yet few sensors that image intracellular Na + have been reported.…”

mentioning

confidence: 99%

In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing

Torabi¹,

Wu²,

McGhee³

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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316

286

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Over the past two decades, enormous progress has been made in designing fluorescent sensors or probes for divalent metal ions. In contrast, the development of fluorescent sensors for monovalent metal ions, such as sodium (Na + ), has remained underdeveloped, even though Na + is one the most abundant metal ions in biological systems and plays a critical role in many biological processes. Here, we report the in vitro selection of the first (to our knowledge) Na + -specific, RNA-cleaving deoxyribozyme (DNAzyme) with a fast catalytic rate [observed rate constant (k obs ) ∼0.1 min −1 ], and the transformation of this DNAzyme into a fluorescent sensor for Na + by labeling the enzyme strand with a quencher at the 3′ end, and the DNA substrate strand with a fluorophore and a quencher at the 5′ and 3′ ends, respectively. The presence of Na + catalyzed cleavage of the substrate strand at an internal ribonucleotide adenosine (rA) site, resulting in release of the fluorophore from its quenchers and thus a significant increase in fluorescence signal. The sensor displays a remarkable selectivity (>10,000-fold) for Na + over competing metal ions and has a detection limit of 135 μM (3.1 ppm). Furthermore, we demonstrate that this DNAzyme-based sensor can readily enter cells with the aid of α-helical cationic polypeptides. Finally, by protecting the cleavage site of the Na + -specific DNAzyme with a photolabile o-nitrobenzyl group, we achieved controlled activation of the sensor after DNAzyme delivery into cells. Together, these results demonstrate that such a DNAzyme-based sensor provides a promising platform for detection and quantification of Na + in living cells.M etal ions play crucial roles in a variety of biochemical processes. As a result, the concentrations of cellular metal ions have to be highly regulated in different parts of cells, as both deficiency and surplus of metal ions can disrupt normal functions (1-4). To better understand the functions of metal ions in biology, it is important to detect metal ions selectively in living cells; such an endeavor will not only result in better understanding of cellular processes but also novel ways to reprogram these processes to achieve novel functions for biotechnological applications.Among the metal ions in cells, sodium (Na + ) serves particularly important functions, as changes in its concentrations influence the cellular processes of numerous living organisms and cells (5-8), such as epithelial and other excitable cells (9). As one of the most abundant metal ions in intracellular fluid (10), Na + affects cellular processes by triggering the activation of many signal transduction pathways, as well as influencing the actions of hormones (11). Therefore, it is important to carefully monitor the concentrations of Na + in cells. Toward this goal, instrumental analyses by atomic absorption spectroscopy (12), Xray fluorescence microscopy (13), and 23 Na NMR (14) have been used to detect the concentration of intracellular Na + . However, it is difficult to use these methods to o...

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“…Significant progress has been made in developing sensors and imaging agents for the detection of metal ions, mostly based on organic molecules, peptides, proteins, or cells [39][40][41][42][43][44][45]. Prof. Yi Li has given a significant insight to the role of DNA as sensors and imaging agents for metal Ions [46], the structure of these systems is illustrated and described in Figure 3. DNA does not appear to be a good candidate for sensing metal ions with high selectivity because the negatively charged phosphodiester backbones of DNA are known to be capable of binding cationic metal ions with poor selectivity for any particular metal ion.…”

Section: Dna As Sensors and Imaging Agents For Metal Ionsmentioning

confidence: 99%

Biomolecules and Pure Carbon Aggregates: An Application Towards “Green Electronics”

Srivastava¹

2018

Green Electronics

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Abstract"Green electronics" is a novel scientific term which aims to identify the compounds of natural origin (economically safe and biodegradable) and establish economically efficient route for production of synthetic materials. The purpose of green electronics is to create path for the production of human and environmental friendly electronics and the integration of electronics with living tissue in particular. These researches may help to fulfill not only the organic electronics to deliver low cost energy efficient materials and devices, but also achieve unimaginable functionalities for electronics. In this chapter we have considered the molecular electronic devices biomolecules: deoxyribonucleic acid (DNA) and pure carbon aggregates: (carbon nanotubes (CNTs)/graphene), their properties and applications.

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DNA as Sensors and Imaging Agents for Metal Ions

Cited by 142 publications

References 351 publications

Adsorption of Selenite and Selenate by Metal Oxides Studied with Fluorescent DNA Probes for Analytical Application

Adsorption of Selenite and Selenate by Metal Oxides Studied with Fluorescent DNA Probes for Analytical Application

In vitro selection of a sodium-specific DNAzyme and its application in intracellular sensing

Biomolecules and Pure Carbon Aggregates: An Application Towards “Green Electronics”

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