Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications.
TL;DR: The applications of these DNAzymes as biosensors for Zn2+, as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed, with an emphasis on RNA‐/DNA‐cleaving reactions.
Abstract: Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn2+ is a very important one among them. Zn2+ has good biocompatibility and can be used for intracellular applications. Chemically, Zn2+ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn2+ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn2+ a unique cofactor for DNAzyme reactions. This review summarizes Zn2+ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn2+ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn2+ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn2+ , which can facilitate practical applications of Zn2+ -dependent DNAzymes.
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TL;DR: A comprehensive overview of exciting developments in the design of photoresponsive DNA materials is provided, and a range of applications in catalysis, sensing and drug delivery/release are showcased.
Abstract: Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
25 citations
TL;DR: In this paper, the authors report Zn2+ -driven RNA self-assembly forming spherical nanoparticles while retaining the integrity and biological function of RNA, and demonstrate that assembled nanospheres possess a superior RNAloading efficiency, pharmacokinetics, and bioavailability.
Abstract: Metal-coordination-directed biomolecule crosslinking in nature has been used for synthesizing various biopolymers, including DNA, peptides, proteins, and polysaccharides. However, the RNA biopolymer has been avoided so far, as due to the poor stability of the RNA molecules, the formation of a biopolymer may alter the biological function of the molecules. Herein, for the first time, we report Zn2+ -driven RNA self-assembly forming spherical nanoparticles while retaining the integrity and biological function of RNA. Various functional RNAs of different compositions, shapes, and lengths from 20 to nearly 1000 nucleotides were used, highlighting the versatility of this approach. The assembled nanospheres possess a superior RNA-loading efficiency, pharmacokinetics, and bioavailability. In-vitro and in-vivo evaluation demonstrated mRNA delivery for expressing GFP proteins, and microRNA delivery to triple-negative breast cancer. This coordination-directed self-assembly behavior amplifies the horizons of RNA coordination chemistry and the application scope of RNA-based therapeutics.
15 citations
TL;DR: A novel dual-mode nanoprobe, including "turn on" fluorescence and "turn off" SERS, which can be used for sensitive and selective Ca2+ determination and has good versatility in various cell lines, which is helpful to better understand the role of Ca1+ in cellular pathways.
Abstract: As a universal second messenger, Ca2+ plays an important role in many cellular processes. In this work, we have developed a novel dual-mode nanoprobe, including "turn on" fluorescence and "turn off" SERS, which can be used for sensitive and selective Ca2+ determination. The proposed nanoprobe combines gold nanostars (AuNSs) and DNAzyme (recognition element), among which AuNSs are used to quench fluorescence and enhance Raman signals. When the substrate chain modified with Cy5 hybridizes with the enzyme chain on the surface of AuNSs, a Ca2+-specific DNAzyme is formed. At this time, the fluorescence is quenched and the SERS signal is strong. With the help of Ca2+, Cy5-labeled substrate chain is cleaved and released from the surface of AuNSs, which leads to the reduction of the SERS signal and the recovery of fluorescence signal. The proposed strategy is also successfully used to monitor Ca2+ in the process of T-2 toxin-induced apoptosis. This is the first report of the simultaneous fluorescence-SERS imaging technique using DNAzyme to detect Ca2+ in cells. The proposed nanoprobe combines the advantages of SERS and fluorescence and has good versatility in various cell lines, which is helpful to better understand the role of Ca2+ in cellular pathways.
15 citations
TL;DR: In this article, a review of DNAzyme-nanomaterial bioconjugates with metal-organic frameworks (MOFs), gold nanoparticles (AuNPs), graphene oxide (GO), and molybdenum disulfide (MoS2) is presented.
Abstract: DNAzyme-nanomaterial bioconjugates are a popular hybrid and have received major attention for diverse biomedical applications, such as bioimaging, biosensor development, cancer therapy, and drug delivery. Therefore, significant efforts are made to develop different strategies for the preparation of inorganic and organic nanoparticles (NPs) with specific morphologies and properties. DNAzymes functionalized with metal-organic frameworks (MOFs), gold nanoparticles (AuNPs), graphene oxide (GO), and molybdenum disulfide (MoS2 ) are introduced and summarized in detail in this review. Moreover, the focus is on representative examples of applications of DNAzyme-nanomaterials over recent years, especially in bioimaging, biosensing, phototherapy, and stimulation response delivery in living systems, with their several advantages and drawbacks. Finally, the perspective regarding the future directions of research addressing these challenges is also discussed and highlighted.
14 citations
TL;DR: In this paper, a photocaged chelator, XDPAdeCage, was used to extract the Zn2+ from the blood serum and then released the chelated Zn 2+ into a buffer using 365 nm light for quantification by an 8-17 DNAzyme sensor.
Abstract: DNAzymes have emerged as a powerful class of sensors for metal ions due to their high selectivity over a wide range of metal ions, allowing for on-site and real-time detection. Despite much progress made in this area, detecting and quantifying tightly bound metal ions, such as those in the blood serum, remain a challenge because the DNAzyme sensors reported so far can detect only mobile metal ions that are accessible to bind the DNAzymes. To overcome this major limitation, we report the use of a photocaged chelator, XDPAdeCage to extract the Zn2+ from the blood serum and then release the chelated Zn2+ into a buffer using 365 nm light for quantification by an 8-17 DNAzyme sensor. Protocols to chelate, uncage, extract, and detect metal ions in the serum have been developed and optimized. Because DNAzyme sensors for other metal ions have already been reported and more DNAzyme sensors can be obtained using in vitro selection, the method reported in this work will significantly expand the applications of the DNAzyme sensors from sensing metal ions that are not only free but also bound to other biomolecules in biological and environmental samples.
13 citations
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1,915 citations
TL;DR: An in vitro selection procedure was used to develop a DNA enzyme that can be made to cleave almost any targeted RNA substrate under simulated physiological conditions, and its activity is dependent on the presence of Mg2+ ion.
Abstract: An in vitro selection procedure was used to develop a DNA enzyme that can be made to cleave almost any targeted RNA substrate under simulated physiological conditions. The enzyme is comprised of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of seven to eight deoxynucleotides each. The RNA substrate is bound through Watson–Crick base pairing and is cleaved at a particular phosphodiester located between an unpaired purine and a paired pyrimidine residue. Despite its small size, the DNA enzyme has a catalytic efficiency (kcat/Km) of ≈109 M−1⋅min−1 under multiple turnover conditions, exceeding that of any other known nucleic acid enzyme. Its activity is dependent on the presence of Mg2+ ion. By changing the sequence of the substrate-recognition domains, the DNA enzyme can be made to target different RNA substrates. In this study, for example, it was directed to cleave synthetic RNAs corresponding to the start codon region of HIV-1 gag/pol, env, vpr, tat, and nef mRNAs.
1,411 citations
TL;DR: The mechanism of zinc sensors that control metal uptake or export in Escherichia coli are determined and their response against the thermodynamically defined free zinc concentration suggests an extraordinary intracellular zinc-binding capacity.
Abstract: Intracellular zinc is thought to be available in a cytosolic pool of free or loosely bound Zn(II) ions in the micromolar to picomolar range To test this, we determined the mechanism of zinc sensors that control metal uptake or export in Escherichia coli and calibrated their response against the thermodynamically defined free zinc concentration Whereas the cellular zinc quota is millimolar, free Zn(II) concentrations that trigger transcription of zinc uptake or efflux machinery are femtomolar, or six orders of magnitude less than one atom per cell This is not consistent with a cytosolic pool of free Zn(II) and suggests an extraordinary intracellular zinc-binding capacity Thus, cells exert tight control over cytosolic metal concentrations, even for relatively low-toxicity metals such as zinc
1,389 citations
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: Care needs to be taken in toxicity testing in ascribing toxicity to nanoparticles per se when the effects may be related, at least in part, to simple solubility, as this study has shown.
Abstract: Metal oxide nanoparticles are finding increasing application in various commercial products, leading to concerns for their environmental fate and potential toxicity. It is generally assumed that nanoparticles will persist as small particles in aquatic systems and that their bioavailability could be significantly greater than that of larger particles. The current study using nanoparticulate ZnO (ca. 30 nm) has shown that this is not always so. Particle characterization using transmission electron microscopy and dynamic light scattering techniques showed that particle aggregation is significant in a freshwater system, resulting in flocs ranging from several hundred nanometers to several microns. Chemical investigations using equilibrium dialysis demonstrated rapid dissolution of ZnO nanoparticles in a freshwater medium (pH 7.6), with a saturation solubility in the milligram per liter range, similar to that of bulk ZnO. Toxicity experiments using the freshwater alga Pseudokirchneriella subcapitata revealed c...
1,221 citations