DNA Catalysis: The Chemical Repertoire of DNAzymes

Hollenstein, Marcel

doi:10.3390/molecules201119730

Cited by 138 publications

(108 citation statements)

References 220 publications

(311 reference statements)

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“…Since that time, many labs have collectively reported hundreds and perhaps thousands of individual deoxyribozyme sequences, encompassing a broad and growing scope of catalytic activity. Several pertinent reviews have addressed the field of deoxyribozymes [16–23], including both general overviews and the relationship of DNA catalysis to other applications of DNA. This review describes the advantages of DNA as a catalyst and highlights recent advances in the scope, applications, and structural investigation of deoxyribozymes.…”

Section: Nucleic Acids As Catalystsmentioning

confidence: 99%

Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes

Silverman

2016

Trends in Biochemical Sciences

310

215

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The discovery of natural RNA enzymes (ribozymes) prompted the pursuit of artificial DNA enzymes (deoxyribozymes) by in vitro selection methods. A key motivation is the conceptual and practical advantages of DNA relative to proteins and RNA. Early studies focused on RNA-cleaving deoxyribozymes, and more recent experiments have expanded the breadth of catalytic DNA to many other reactions. Including modified nucleotides has the potential to widen the scope of DNA enzymes even further. Practical applications of deoxyribozymes include their use as sensors for metal ions and small molecules. Structural studies of deoxyribozymes are just beginning; mechanistic experiments will surely follow. From the first report 21 years ago, the field of deoxyribozymes has promise for both fundamental and applied advances in chemistry, biology, and other disciplines.

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Section: Nucleic Acids As Catalystsmentioning

confidence: 99%

Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes

Silverman

2016

Trends in Biochemical Sciences

310

215

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“…Indeed there have been also reported examples where those ssDNA behave as holoenzymes and require from cofactors to perform its activity. [48][49][50][51] Since their discovery, DNAzymes have been widely exploited in medicine, biology and material sciences because of their advantages over conventional enzymes; which are principally a higher thermal stability and simpler preparation. Unlike enzymes, responsible for a huge number of processes, known processes catalysed by DNAzymes are limited, although efficiently catalysed.…”

Section: Double Stranded Gates Based On Dnazymesmentioning

confidence: 99%

“…The second requirement, which seemed unbridgeable, has been elegantly solved by the use of DNAzymes with nuclease activity. Those strands, able to cleave certain sequences, are then the perfect candidates for the development of triggered in which the gating double strand is released 51 (Figure 4). 55 More recently, the same research group demonstrated the potency of this strategy by reporting an evolved version of this methodology in which the cation-dependent release system is also sensitive to pH.…”

Section: Double Stranded Gates Based On Dnazymesmentioning

confidence: 99%

Recent applications of the combination of mesoporous silica nanoparticles with nucleic acids: development of bioresponsive devices, carriers and sensors

Castillo¹,

Baeza²

2017

Biomater. Sci.

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The discovery and control of the biological roles mediated by nucleic acids have turned them into a powerful tool for the development of advanced biotechnological materials. Much is the importance of those gene-keeping biomacromolecules that even nanomaterials have succumbed to the claimed benefits of DNA and RNA. Currently, there could be found in the literature a practically intractable number of examples which report the use in combination of nanoparticles with nucleic acids, which demands boundedness. Following this premise, this revision will only cover the most recent and powerful strategies developed to exploit the possibilities of nucleic acids as biotechnological materials when in combination with mesoporous silica nanoparticles. The extensive research done on nucleic acids has significantly incremented the technological possibilities for those biomacromolecules, which could be employed in many different applications; where substrate or sequence recognition or modulation of biological pathways due to its coding role in living cells are the most promising. In the present revision, the chosen counterpart, mesoporous silica nanoparticles, also with unique properties, became a reference material for drug delivery and biomedical applications due to their high biocompatibility and porous structure suitable for hosting and delivering small molecules. Although most of revisions deal with significant advances in the use of nucleic acid and mesoporous silica nanoparticles in biotechnological applications, a rationale classification of those new generation hybrid materials is still uncovered. Along this review there will be covered promising strategies for living cell and biological sensors, DNA-based molecular gates with targeting, transfection or silencing properties which could provide a significant advance of current nanomedicine.

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“…20 The incorporation of functional groups by templated copolymerization of modified nucleoside triphosphates has also enabled researchers to expand the potential of nucleic acids as catalytically active biopolymers, moving beyond the inherent limitations of the native polymer, including metal ion dependence. 21,22 In their efforts to develop DNA enzymes that can mimic the catalytic function of ribonuclease enzymes, Joyce, Barbas, and co-workers first reported the polymerase-catalyzed incorporation of C5-imidazole-functionalized dUTP in place of thymidine within ssDNA libraries, and subsequent in vitro selection for ribonuclease activity in the presence of Zn 2+ . 23 A small 32-nt imidazole-functionalized DNA enzyme was identified from the selection, which catalyzed RNA cleavage with rates of 4 min −1 in the presence of micromolar concentrations of Zn 2+ .…”

Section: Copolymerization Of Nucleobase Modified Nucleosidementioning

confidence: 99%

Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates

2016

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Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.

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DNA Catalysis: The Chemical Repertoire of DNAzymes

Cited by 138 publications

References 220 publications

Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes

Catalytic DNA: Scope, Applications, and Biochemistry of Deoxyribozymes

Recent applications of the combination of mesoporous silica nanoparticles with nucleic acids: development of bioresponsive devices, carriers and sensors

Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates

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