1
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Liu J, Cui L, Shi X, Yan J, Wang Y, Ni Y, He J, Wang X. Generation of DNAzyme in Bacterial Cells by a Bacterial Retron System. ACS Synth Biol 2024; 13:300-309. [PMID: 38171507 DOI: 10.1021/acssynbio.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DNAzymes are catalytically active single-stranded DNAs in which DNAzyme 10-23 (Dz 10-23) consists of a catalytic core and a substrate-binding arm that reduces gene expression through sequence-specific mRNA cleavage. However, the in vivo application of Dz 10-23 depends on exogenous delivery, which leads to its inability to be synthesized and stabilized in vivo, thus limiting its application. As a unique reverse transcription system, the bacterial retron system can synthesize single-stranded DNA in vivo using ncRNA msr/msd as a template. The objective of this work is to reduce target gene expression using Dz 10-23 generated in vivo by the retron system. In this regard, we successfully generated Dz 10-23 by cloning the Dz 10-23 coding sequence into the retron msd gene and tested its ability to reduce specific gene expression by examining the mRNA levels of cfp encoding cyan fluorescence protein and other functional genes such as mreB and ftsZ. We found that Dz had different repressive effects when targeting different mRNA regions, and in general, the repressive effect was stronger when targeting downstream of mRNAs. Our results also suggested that the reduction effect was due to cleavage of the substrate mRNA by Dz 10-23 rather than the antisense effect of the substrate-binding arm. Therefore, this study not only provided a retron-based method for the intracellular generation of Dz 10-23 but also demonstrated that Dz 10-23 could reduce gene expression by cleaving target mRNAs in cells. We believe that this new strategy would have great potential in the regulation of gene expression.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lina Cui
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xinyu Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jiahao Yan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yifei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuyang Ni
- College of Life Sciences, Shangrao Normal University, Shangrao 334001, PR China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xun Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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2
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Montserrat Pagès A, Hertog M, Nicolaï B, Spasic D, Lammertyn J. Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme. Int J Mol Sci 2023; 24:13686. [PMID: 37761982 PMCID: PMC10531344 DOI: 10.3390/ijms241813686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
DNA-based enzymes, or DNAzymes, are single-stranded DNA sequences with the ability to catalyze various chemical reactions, including the cleavage of the bond between two RNA nucleotides. Lately, an increasing interest has been observed in these RNA-cleaving DNAzymes in the biosensing and therapeutic fields for signal generation and the modulation of gene expression, respectively. Additionally, multiple efforts have been made to study the effects of the reaction environment and the sequence of the catalytic core on the conversion of the substrate into product. However, most of these studies have only reported alterations of the general reaction course, but only a few have focused on how each individual reaction step is affected. In this work, we present for the first time a mathematical model that describes and predicts the reaction of the 10-23 RNA-cleaving DNAzyme. Furthermore, the model has been employed to study the effect of temperature, magnesium cations and shorter substrate-binding arms of the DNAzyme on the different kinetic rate constants, broadening the range of conditions in which the model can be exploited. In conclusion, this work depicts the prospects of such mathematical models to study and anticipate the course of a reaction given a particular environment.
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Affiliation(s)
- Aida Montserrat Pagès
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Maarten Hertog
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Bart Nicolaï
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
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3
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Liu H, Li Y, Du S, Wang C, Li Y, Cao R, Shi W, Liu S, He J. Studies on the Effect of Lipofectamine and Cell-Penetrating Peptide on the Properties of 10-23 DNAzyme. Molecules 2023; 28:molecules28093942. [PMID: 37175352 PMCID: PMC10179765 DOI: 10.3390/molecules28093942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Cationic polymeric materials and cell-penetrating peptides (CPPs) were often used as the delivery vectors in the evaluation of nucleic acid therapeutics. 10-23 DNAzyme is a kind of potential antisense therapeutics by catalytic cleavage of the disease-related RNAs. Here, lipofectamine 2000 and Tat peptide were evaluated for their effect on the catalytic activity of 10-23 DNAzyme, with the observed rate constant, thermal stability, CD spectra, and PAGE analysis, with a duplex DNA mimicking DNAzyme-substrate as a control. It was shown that the cationic carriers had a negative effect on the catalytic performance of the 10-23 DNAzyme. Significantly, the destabilizing effect of the cationic carriers on the duplex formation was noteworthy, as a duplex formation is an essential prerequisite in the silencing mechanisms of antisense and RNAi.
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Affiliation(s)
- Huanhuan Liu
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Chenhong Wang
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Yuexiang Li
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Ruiyuan Cao
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Weiguo Shi
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Shihui Liu
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
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4
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Nguyen K, Malik TN, Chaput JC. Chemical evolution of an autonomous DNAzyme with allele-specific gene silencing activity. Nat Commun 2023; 14:2413. [PMID: 37105964 PMCID: PMC10140269 DOI: 10.1038/s41467-023-38100-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
Low activity has been the primary obstacle impeding the use of DNA enzymes (DNAzymes) as gene silencing agents in clinical applications. Here we describe the chemical evolution of a DNAzyme with strong catalytic activity under near physiological conditions. The enzyme achieves ~65 turnovers in 30 minutes, a feat only previously witnessed by the unmodified parent sequence under forcing conditions of elevated Mg2+ and pH. Structural constraints imposed by the chemical modifications drive catalysis toward a highly preferred UGUD motif (cut site underlined) that was validated by positive and negative predictions. Biochemical assays support an autonomous RNA cleavage mechanism independent of RNase H1 engagement. Consistent with its strong catalytic activity, the enzyme exhibits persistent allele-specific knock-down of an endogenous mRNA encoding an undruggable oncogenic KRAS target. Together, these results demonstrate that chemical evolution offers a powerful approach for discovering new chemotype combinations that can imbue DNAzymes with the physicochemical properties necessary to support therapeutic applications.
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Affiliation(s)
- Kim Nguyen
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697-3958, USA
| | - Turnee N Malik
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697-3958, USA
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697-3958, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697-3958, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697-3958, USA.
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA, 92697-3958, USA.
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5
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8-17 DNAzyme Silencing Gene Expression in Cells via Cleavage and Antisense. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010286. [PMID: 36615479 PMCID: PMC9821912 DOI: 10.3390/molecules28010286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Gene silencing is an important biological strategy for studying gene functions, exploring disease mechanisms and developing therapeutics. 8-17 DNAzyme is of great potential for gene silencing, due to its higher RNA-cleaving activity. However, it is not generally used in practice, due to its divalent cation dependence and poor understanding of its cellular mechanisms. To address these issues, we have explored its activity in vitro and in cells and found that it can cleave RNA substrates under the simulated physiological conditions, and its gene-silencing activity is additionally enhanced by its RNase H compatibility, offering both cleavage and antisense activities in cells. Further, chemical modifications can facilitate its stability, substrate binding affinity and gene-silencing activity. Our research results suggest that this DNAzyme can demonstrate high levels of activities for both actions in cells, making it a useful tool for exploring biomedical applications.
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6
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Taylor AI, Wan CJK, Donde MJ, Peak-Chew SY, Holliger P. A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Nat Chem 2022; 14:1295-1305. [PMID: 36064973 PMCID: PMC7613789 DOI: 10.1038/s41557-022-01021-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/08/2022] [Indexed: 11/07/2022]
Abstract
Nucleic-acid catalysts (ribozymes, DNA- and XNAzymes) cleave target (m)RNAs with high specificity but have shown limited efficacy in clinical applications. Here we report on the in vitro evolution and engineering of a highly specific modular RNA endonuclease XNAzyme, FR6_1, composed of 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid (FANA). FR6_1 overcomes the activity limitations of previous DNA- and XNAzymes and can be retargeted to cleave highly structured full-length (>5 kb) BRAF and KRAS mRNAs at physiological Mg2+ concentrations with allelic selectivity for tumour-associated (BRAF V600E and KRAS G12D) mutations. Phosphorothioate-FANA modification enhances FR6_1 biostability and enables rapid KRAS mRNA knockdown in cultured human adenocarcinoma cells with a G12D-allele-specific component provided by in vivo XNAzyme cleavage activity. These results provide a starting point for the development of improved gene-silencing agents based on FANA or other XNA chemistries.
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Affiliation(s)
- Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK.
| | | | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
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7
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On gene silencing by the X10-23 DNAzyme. Nat Chem 2022; 14:855-858. [DOI: 10.1038/s41557-022-00990-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/21/2022] [Indexed: 11/08/2022]
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8
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Steger G, Victor J. Design of a DNAzyme : Prediction of mRNA Regions Accessible to a DNAzyme. Methods Mol Biol 2022; 2439:47-63. [PMID: 35226314 DOI: 10.1007/978-1-0716-2047-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The efficiency of RNA-cleaving DNAzymes depends on a large extent on complex formation with their RNA targets. We describe available prediction tools that should help in the design of efficient DNAzymes and show some experimental methods to test the predictions. The main example is for a 10-23 DNAzyme, but the procedure works as well for the 8-17 DNAzyme family.
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Affiliation(s)
- Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
| | - Julian Victor
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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9
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Time-resolved structural analysis of an RNA-cleaving DNA catalyst. Nature 2022; 601:144-149. [PMID: 34949858 DOI: 10.1038/s41586-021-04225-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 11/06/2021] [Indexed: 11/08/2022]
Abstract
The 10-23 DNAzyme is one of the most prominent catalytically active DNA sequences1,2. Its ability to cleave a wide range of RNA targets with high selectivity entails a substantial therapeutic and biotechnological potential2. However, the high expectations have not yet been met, a fact that coincides with the lack of high-resolution and time-resolved information about its mode of action3. Here we provide high-resolution NMR characterization of all apparent states of the prototypic 10-23 DNAzyme and present a comprehensive survey of the kinetics and dynamics of its catalytic function. The determined structure and identified metal-ion-binding sites of the precatalytic DNAzyme-RNA complex reveal that the basis of the DNA-mediated catalysis is an interplay among three factors: an unexpected, yet exciting molecular architecture; distinct conformational plasticity; and dynamic modulation by metal ions. We further identify previously hidden rate-limiting transient intermediate states in the DNA-mediated catalytic process via real-time NMR measurements. Using a rationally selected single-atom replacement, we could considerably enhance the performance of the DNAzyme, demonstrating that the acquired knowledge of the molecular structure, its plasticity and the occurrence of long-lived intermediate states constitutes a valuable starting point for the rational design of next-generation DNAzymes.
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10
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Abstract
Studying the catalytic behavior of biocatalysts under different conditions including temperature, buffer conditions, and cofactor concentrations is an important tool to understand their reaction mechanism. We describe two protocols that allow for the investigation of the catalysis of RNA-cleaving DNAzymes. The techniques include the use of FRET-labeled RNA substrates for studying the RNA-cleavage reaction in real-time under high throughput as well as RNA substrates labeled with a fluorescein molecule at the 5' end for gel-based assays. Both methods allow for an accurate determination of rate constants given a reaction model.
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Affiliation(s)
- Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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11
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Kirchgässler N, Rosenbach H, Span I. Stability and Activity of the 10-23 DNAzyme Under Molecular Crowding Conditions. Methods Mol Biol 2022; 2439:79-89. [PMID: 35226316 DOI: 10.1007/978-1-0716-2047-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
DNAzymes are biocatalysts that have been selected in vitro and their function inside cells (in vivo) is extremely low. Thus, almost all studies have been carried out in diluted solutions (in vitro). The cellular presence of molecules such as amino acids, polypeptides, alcohols, and sugars introduces forces that modify the kinetics and thermodynamics of DNAzyme-mediated catalysis. The crowded intracellular environment referred to as molecular crowding can be mimicked by adding high concentrations of natural or synthetic macromolecules to the reaction conditions. Here, we investigate the activity of the 10-23 DNAzyme and the stability of the DNAzyme:RNA complex under molecular crowding conditions. Therefore, we use a Förster resonance energy transfer (FRET)-based activity assay in combination with denaturing urea polyacrylamide gel electrophoresis and circular dichroism (CD) spectroscopy.
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Affiliation(s)
- Nina Kirchgässler
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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12
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Borggräfe J, Etzkorn M. Solution NMR Spectroscopy as a Tool to Study DNAzyme Structure and Function. Methods Mol Biol 2022; 2439:131-151. [PMID: 35226320 DOI: 10.1007/978-1-0716-2047-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Catalytically active DNA oligomers (or DNAzymes) offer a broad spectrum of functions as well as applications. Although known for over two decades, the DNAzyme's mode-of-actions are still poorly understood, mainly due to lack of high-resolution structural insights. Due to their molecular size, structural flexibility, and dynamic interactions with metal-ion cofactors, solution nuclear magnetic resonance spectroscopy (NMR) can serve as optimal tool to obtain mechanistic insights of DNAzymes. In this respect, nearly all states of the DNAzyme and its substrate during the catalytic cycle are accessible. The instructions and protocols provided in the following may assist the initial steps of an NMR-based characterization of DNAzymes. To reduce the initial setup requirements and foster exciting new research projects, the discussed approaches focus on experiments that do not require cost-intensive isotope labeling strategies.
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Affiliation(s)
- Jan Borggräfe
- Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Manuel Etzkorn
- Institute of Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany.
- Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany.
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13
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RNA-cleaving DNAzymes as a diagnostic and therapeutic agent against antimicrobial resistant bacteria. Curr Genet 2021; 68:27-38. [PMID: 34505182 DOI: 10.1007/s00294-021-01212-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The development of nucleic-acid-based antimicrobials such as RNA-cleaving DNAzyme (RCD), a short catalytically active nucleic acid, is a promising alternative to the current antibiotics. The current rapid spread of antimicrobial resistance (AMR) in bacteria renders some antibiotics useless against bacterial infection, thus creating the need for alternative antimicrobials such as DNAzymes. This review summarizes recent advances in the use of RCD as a diagnostic and therapeutic agent against AMR. Firstly, the recent diagnostic application of RCD for the detection of bacterial cells and the associated resistant gene(s) is discussed. The next section summarises the therapeutic application of RCD in AMR bacterial infections which includes direct targeting of the resistant genes and indirect targeting of AMR-associated genes. Finally, this review extends the discussion to challenges of utilizing RCD in real-life applications, and the potential of combining both diagnostic and therapeutic applications of RCD into a single agent as a theranostic agent.
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14
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Rosenbach H, Borggräfe J, Victor J, Wuebben C, Schiemann O, Hoyer W, Steger G, Etzkorn M, Span I. Influence of monovalent metal ions on metal binding and catalytic activity of the 10-23 DNAzyme. Biol Chem 2020; 402:99-111. [PMID: 33544488 DOI: 10.1515/hsz-2020-0207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/13/2020] [Indexed: 11/15/2022]
Abstract
Deoxyribozymes (DNAzymes) are single-stranded DNA molecules that catalyze a broad range of chemical reactions. The 10-23 DNAzyme catalyzes the cleavage of RNA strands and can be designed to cleave essentially any target RNA, which makes it particularly interesting for therapeutic and biosensing applications. The activity of this DNAzyme in vitro is considerably higher than in cells, which was suggested to be a result of the low intracellular concentration of bioavailable divalent cations. While the interaction of the 10-23 DNAzyme with divalent metal ions was studied extensively, the influence of monovalent metal ions on its activity remains poorly understood. Here, we characterize the influence of monovalent and divalent cations on the 10-23 DNAzyme utilizing functional and biophysical techniques. Our results show that Na+ and K+ affect the binding of divalent metal ions to the DNAzyme:RNA complex and considerably modulate the reaction rates of RNA cleavage. We observe an opposite effect of high levels of Na+ and K+ concentrations on Mg2+- and Mn2+-induced reactions, revealing a different interplay of these metals in catalysis. Based on these findings, we propose a model for the interaction of metal ions with the DNAzyme:RNA complex.
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Affiliation(s)
- Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany
| | - Jan Borggräfe
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany.,Institute for Biological Information Processing: Structural Biochemistry (IBI-7), Research Center Jülich, Wilhelm-Johnen-Str., D-52428Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52425Jülich, Germany
| | - Julian Victor
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, D-53115Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, D-53115Bonn, Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany.,Institute for Biological Information Processing: Structural Biochemistry (IBI-7), Research Center Jülich, Wilhelm-Johnen-Str., D-52428Jülich, Germany
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany.,Institute for Biological Information Processing: Structural Biochemistry (IBI-7), Research Center Jülich, Wilhelm-Johnen-Str., D-52428Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, 52425Jülich, Germany
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225Düsseldorf, Germany
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15
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Rosenbach H, Victor J, Etzkorn M, Steger G, Riesner D, Span I. Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity. Molecules 2020; 25:E3100. [PMID: 32646019 PMCID: PMC7412337 DOI: 10.3390/molecules25133100] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/25/2020] [Accepted: 07/03/2020] [Indexed: 12/17/2022] Open
Abstract
Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications.
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Affiliation(s)
- Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Julian Victor
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Manuel Etzkorn
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Detlev Riesner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany; (H.R.); (J.V.); (M.E.); (G.S.); (D.R.)
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Frańska M, Michalak A, Ławniczak Ł. Gas-phase hydration of Mg 2+ complexes with deprotonated uracil, thymine, uridine, and thymidine. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4504. [PMID: 31970857 DOI: 10.1002/jms.4504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
The gas-phase hydration of Mg2+ complexes with deprotonated uracil (U), thymine (T), uridine (Ur , uracil riboside), and thymidine (Tdr , thymine deoxyriboside) was studied. The aim of the work was to analyze the hydration of product ions (eg, [2U-H+Mg]+ ) formed as a result of the collision induced dissociation of the respective parent ion (eg, [3Ur -H+Mg]+ ). The efficiency of gas-phase hydration of the ions [2U-H+Mg]+ and [2T-H+Mg]+ was similar. However, the efficiency of gas-phase hydration of the ion [U+Ur -H+Mg]+ was much higher than that of gas-phase hydration of the ion [T+Tdr -H+Mg]+ . On the basis of the mass spectra obtained and the performed molecular modelling, it was concluded that in the ion [T+Tdr -H+Mg]+ , we deal with a steric hindrance due to the presence of a sugar moiety, which affects water attachment. In the ion [U+Ur -H+Mg]+ , the position of the sugar moiety does not affect water attachment.
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Affiliation(s)
- Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Anna Michalak
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Łukasz Ławniczak
- Institute of Chemical Technology and Engineering, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
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