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Journal ArticleDOI: 10.1002/CBIC.202000586

Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications.

02 Mar 2021-ChemBioChem (John Wiley & Sons, Ltd)-Vol. 22, Iss: 5, pp 779-789
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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Topics: Deoxyribozyme (57%)
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10 results found


Journal ArticleDOI: 10.1021/ACS.ANALCHEM.1C00140
Shige Xing1, Yao Lin2, Yao Lin1, Liangyuan Cai1  +6 moreInstitutions (3)
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.

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Topics: Blood serum (57%)

2 Citations


Journal ArticleDOI: 10.1016/J.CHEMPR.2021.08.008
14 Oct 2021-Chem
Abstract: Summary The emerging field of DNA nanotechnology harnesses DNA as a stable and generic material to assemble nanostructures with precisely defined sizes and geometries. The past 40 years have witnessed this field’s originating, branching, blossoming, bridging with, and benefiting many different areas. Interestingly, in nearly the same period, DNA has also been discovered to be able to catalyze various chemical reactions. The catalytic DNAs, especially those that can cleave DNA/RNA, are with a destructive property quite opposite to the fundamental concept of DNA nanotechnology. Nevertheless, in the past decade, they have been successfully blended into DNA nanoconstruction and expanded the construction dimension. Here, we present an overview of recent progress in the development of DNA nanotechnology promoted by the DNA/RNA-cleaving DNAs. Meanwhile, we provide an outlook of how the two seemingly distant types of DNA could further collide with and mutually benefit each other, leading to the unprecedented downstream applications in various areas.

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Topics: DNA origami (55%), DNA nanotechnology (55%), DNA walker (54%)

2 Citations


Journal ArticleDOI: 10.1039/D1QI00105A
Hualin Yang1, Hualin Yang2, Hualin Yang3, Yu Zhou1  +1 moreInstitutions (3)
Abstract: Metalloporphyrins play important roles in biology, such as magnesium porphyrin for photosynthesis and iron porphyrin for carrying and transferring oxygen They are also powerful molecules for the development of biosensors, phototherapy, photocatalysis, photodegradation, light harvesting, and water splitting However, the porphyrin metalation reaction is difficult to achieve at room temperature due to a high kinetic barrier Inspired by the pioneering work in catalytic antibodies, ribozymes, DNAzymes and nanozymes have been developed as enzyme mimics to accelerate this reaction This review summarizes the progress in DNAzymes and nanozymes due to their excellent stability and low cost We first introduce the structure and property of common porphyrins and metalloporphyrins DNAzymes for porphyrin metalation are then reviewed, including early work, recent work using Pb2+ as a cofactor, and non-G-quadruplex DNAzymes The catalytic mechanisms of DNAzymes are also discussed, especially the role of metal ions Subsequently, nanozymes for porphyrin metalation based on graphene and a few other nanomaterials are reviewed In this part, the interactions between the nanozymes and porphyrins are elucidated to describe the catalytic effect In addition, beta-cyclodextrin and some surfactants that can form micelles in water were also found to have catalytic activity Finally, we review the applications of porphyrin metalation reactions for the detection of various metal ions, improving photocatalytic activity, and removing heavy metal ions in water

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Topics: Metalation (54%), Porphyrin (52%), Deoxyribozyme (50%)

1 Citations


Open accessJournal ArticleDOI: 10.1093/NAR/GKAB439
Canyu Zhang1, Qingting Li1, Tianbin Xu1, Wei Li1  +2 moreInstitutions (1)
Abstract: DNA-hydrolyzing DNAs represent an attractive type of DNA-processing catalysts distinctive from the protein-based restriction enzymes. The innate DNA property has enabled them to readily join DNA-based manipulations to promote the development of DNA biotechnology. A major in vitro selection strategy to identify these DNA catalysts relies tightly on the isolation of linear DNAs processed from a circular single-stranded (ss) DNA sequence library by self-hydrolysis. Herein, we report that by programming a terminal hybridization stem in the library, other than the previously reported classes (I & II) of deoxyribozymes, two new classes (III & IV) were identified with the old selection strategy to site-specifically hydrolyze DNA in the presence of Zn2+. Their representatives own a catalytic core consisting of ∼20 conserved nucleotides and a half-life of ∼15 min at neutral pH. In a bimolecular construct, class III exhibits unique broad generality on the enzyme strand, which can be potentially harnessed to engineer DNA-responsive DNA hydrolyzers for detection of any target ssDNA sequence. Besides the new findings, this work should also provide an improved approach to select for DNA-hydrolyzing deoxyribozymes that use various molecules and ions as cofactors.

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Topics: Deoxyribozyme (59%), DNA (56%), Restriction enzyme (55%) ... read more

1 Citations


Open accessJournal ArticleDOI: 10.1002/SMLL.202105439
Jabrane Jouha1, Hai Xiong1Institutions (1)
21 Nov 2021-Small
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.

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References
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110 results found


Open accessJournal ArticleDOI: 10.1021/CR030183I
Juewen Liu1, Zehui Cao1, Yi LuInstitutions (1)
20 Mar 2009-Chemical Reviews
Topics: Nucleic acid methods (74%), Nucleic acid (60%)

1,763 Citations


Open accessJournal ArticleDOI: 10.1073/PNAS.94.9.4262
Stephen W. Santoro1, Gerald F. JoyceInstitutions (1)
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.

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Topics: DNA/RNA non-specific endonuclease (61%), Base pair (60%), Polymerase (60%) ... read more

1,317 Citations


Journal ArticleDOI: 10.1126/SCIENCE.1060331
29 Jun 2001-Science
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

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Topics: Zinc (61%), Cation diffusion facilitator (52%)

1,311 Citations


Journal ArticleDOI: 10.1021/ES071445R
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...

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Topics: Nanoparticle (51%), Particle (50%)

1,117 Citations


Journal ArticleDOI: 10.1016/1074-5521(94)90014-0
Ronald R. Breaker1, Gerald F. Joyce1Institutions (1)
Abstract: BACKGROUND: Several types of RNA enzymes (ribozymes) have been identified in biological systems and generated in the laboratory. Considering the variety of known RNA enzymes and the similarity of DNA and RNA, it is reasonable to imagine that DNA might be able to function as an enzyme as well. No such DNA enzyme has been found in nature, however. We set out to identify a metal-dependent DNA enzyme using in vitro selection methodology. RESULTS: Beginning with a population of 10(14) DNAs containing 50 random nucleotides, we carried out five successive rounds of selective amplification, enriching for individuals that best promote the Pb(2+)-dependent cleavage of a target ribonucleoside 3'-O-P bond embedded within an otherwise all-DNA sequence. By the fifth round, the population as a whole carried out this reaction at a rate of 0.2 min-1. Based on the sequence of 20 individuals isolated from this population, we designed a simplified version of the catalytic domain that operates in an intermolecular context with a turnover rate of 1 min-1. This rate is about 10(5)-fold increased compared to the uncatalyzed reaction. CONCLUSIONS: Using in vitro selection techniques, we obtained a DNA enzyme that catalyzes the Pb(2+)-dependent cleavage of an RNA phosphoester in a reaction that proceeds with rapid turnover. The catalytic rate compares favorably to that of known RNA enzymes. We expect that other examples of DNA enzymes will soon be forthcoming.

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Topics: Base pair (63%), Primase (62%), Deoxyribozyme (61%) ... read more

1,086 Citations


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