In vitro selection and application of lanthanide-dependent DNAzymes.
TL;DR: In this article, a few such DNAzymes are introduced and methods for in vitro selection of lanthanide-dependent RNA-cleaving DNAZymes are described in detail, including the selection protocols, the DNA sequences used, the characterization of selected DNAz enzymes and their conversion into biosensors.
Abstract: Highly sensitive and selective detection of lanthanide ions is a major analytical challenge. In recent years, the use of DNA for this purpose has been pursued. For such highly charged cations, it is difficult to select their aptamers due to strong nonspecific binding. On the other hand, the use of catalytic DNA or DNAzymes has an advantage to overcome this problem, especially DNAzymes with RNA-cleaving activity. In this chapter, a few such DNAzymes are introduced and methods for in vitro selection of lanthanide-dependent RNA-cleaving DNAzymes are described in detail, including the selection protocols, the DNA sequences used, the characterization of selected DNAzymes and their conversion into biosensors. All of the experiments use only fluorophore-labeled DNA, and radioisotope labeling is completely avoided. The resulting DNAzymes can distinguish lanthanides from non-lanthanide metals, tell the difference between light and heavy lanthanides, and can be used together to discriminate individual lanthanides.
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TL;DR: For example, DNAzymeBuilder as discussed by the authors enables fast and automatic assembly of DNAzymes for the first time by relying on an internal database with information on RNA and DNA cleaving enzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNA enzymes.
Abstract: Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.
3 citations
TL;DR: Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize, and DNAzymeBuilder enables fast and automatic assembly of DNAZymes for the first time.
Abstract: Abstract Nucleic acid cleaving DNAzymes are versatile and robust catalysts that outcompete ribozymes and protein enzymes in terms of chemical stability, affordability and ease to synthesize. In spite of their attractiveness, the choice of which DNAzyme should be used to cleave a given substrate is far from obvious, and requires expert knowledge as well as in-depth literature scrutiny. DNAzymeBuilder enables fast and automatic assembly of DNAzymes for the first time, superseding the manual design of DNAzymes. DNAzymeBuilder relies on an internal database with information on RNA and DNA cleaving DNAzymes, including the reaction conditions under which they best operate, their kinetic parameters, the type of cleavage reaction that is catalyzed, the specific sequence that is recognized by the DNAzyme, the cleavage site within this sequence, and special design features that might be necessary for optimal activity of the DNAzyme. Based on this information and the input sequence provided by the user, DNAzymeBuilder provides a list of DNAzymes to carry out the cleavage reaction and detailed information for each of them, including the expected yield, reaction products and optimal reaction conditions. DNAzymeBuilder is a resource to help researchers introduce DNAzymes in their day-to-day research, and is publicly available at https://iimcb.genesilico.pl/DNAzymeBuilder.
3 citations
01 Jan 2022
TL;DR: This chapter describes the methods of HPLC-based separation followed by ligation to generate a long and fluorescently modified DNAzyme substrate and the use of the modified substrate for activity assay to understand metal binding and for metal ion detection.
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TL;DR: Using in vitro selection techniques, a DNA enzyme is obtained that catalyzes the Pb(2+)-dependent cleavage of an RNA phosphoester in a reaction that proceeds with rapid turnover, and compares favorably to that of known RNA enzymes.
1,225 citations
TL;DR: In this article, the chemistry of different solvent extractants and typical configurations for rare earth separations are reviewed. But the choice of extractants is influenced by both cost considerations and requirements of technical performance.
947 citations
TL;DR: In this article, the authors summarized the occurrence of rare earth elements in the Earth's crust, their mineralogy, different types of deposits both on land and oceans from the standpoint of the new data with more examples from the Indian subcontinent.
Abstract: Rare earth elements (REE) include the lanthanide series elements (La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) plus Sc and Y. Currently these metals have become very critical to several modern technologies ranging from cell phones and televisions to LED light bulbs and wind turbines. This article summarizes the occurrence of these metals in the Earth's crust, their mineralogy, different types of deposits both on land and oceans from the standpoint of the new data with more examples from the Indian subcontinent. In addition to their utility to understand the formation of the major Earth reservoirs, multi-faceted updates on the applications of REE in agriculture and medicine including new emerging ones are presented. Environmental hazards including human health issues due to REE mining and large-scale dumping of e-waste containing significant concentrations of REE are summarized. New strategies for the future supply of REE including recent developments in the extraction of REE from coal fired ash and recycling from e-waste are presented. Recent developments in individual REE separation technologies in both metallurgical and recycling operations have been highlighted. An outline of the analytical methods for their precise and accurate determinations required in all these studies, such as, X-ray fluorescence spectrometry (XRF), laser induced breakdown spectroscopy (LIBS), instrumental neutron activation analysis (INAA), inductively coupled plasma optical emission spectrometry (ICP-OES), glow discharge mass spectrometry (GD-MS), inductively coupled plasma mass spectrometry (including ICP-MS, ICP-TOF-MS, HR-ICP-MS with laser ablation as well as solution nebulization) and other instrumental techniques, in different types of materials are presented.
709 citations
644 citations
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TL;DR: Each metal ion and the known DNA sequences for its sensing are reviewed and the fundamental aspect of metal binding is emphasized, emphasizing the distinct chemical property of each metal.
Abstract: Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers. On the other hand, DNAzymes are powerful tools for metal sensing since they are selected based on catalytic activity, thus bypassing the need for metal immobilization. In the last five years, a new surge of development has been made on isolating new metal-sensing DNA sequences. To date, many important metals can be selectively detected by DNA often down to the low parts-per-billion level. Herein, each me...
618 citations