1
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Lee M, Kim M, Lee M, Kim S, Park N. Nanosized DNA Hydrogel Functionalized with a DNAzyme Tetrahedron for Highly Efficient Gene Silencing. Biomacromolecules 2024; 25:4913-4924. [PMID: 38963792 DOI: 10.1021/acs.biomac.4c00356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
DNAzymes are DNA oligonucleotides that have catalytic activity without the assistance of protein enzymes. In particular, RNA-cleaving DNAzymes were considered as ideal candidates for gene therapy due to their unique characteristics. Nevertheless, efforts to use DNAzyme as a gene therapeutic agent are limited by issues such as their low physiological stability in serum and intracellular delivery efficiency. In this study, we developed a nanosized synthetic DNA hydrogel functionalized with a DNAzyme tetrahedron (TDz Dgel) to overcome these limitations. We observed remarkable improvement in the gene-silencing effect as well as intracellular uptake without the support of gene transfection reagents using TDz Dgel. The improved catalytic activity of the DNAzyme resulted from the combination of the cell-penetrating DNA tetrahedron structure and high stability of DNA hydrogel. We envision that this approach will become a convenient and efficient strategy for gene-silencing therapy using DNAzyme in the future.
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Affiliation(s)
- Minhyuk Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Minchul Kim
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
| | - Minjae Lee
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
| | - Sungjee Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
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2
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Xia L, Du L, Hou X, Zhou R, Cheng N, Chen J. Protein-Controlled Split DNAzyme to Enhance Catalytic Activity: Design and Performance. Anal Chem 2024. [PMID: 39010288 DOI: 10.1021/acs.analchem.3c05909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
In this study, we utilized proteins to control the assembly of split DNAzyme to establish protein-controlled split DNAzymes (Pc SD), with the aim of enhancing its catalytic activity. To achieve this, simultaneous recognition of protein by affinity ligands at both ends of split DNAzyme fragments induced an increased local concentration of each split fragment, leading to reassembly of the split catalytic core with a rigid conformation and higher affinity to its cofactor. As a result, under protein control, Pc SD exhibits unexpected cleavage efficiency compared to free split DNAzyme. To further explore the catalytic features, we then systematically positioned split sites within the catalytic core of three popular DNAzyme-based Pc SDs, thus revealing the important nucleic acids that influence Pc SDs activity. Based on the excellent analytical performance of Pc SD for streptavidin (with a LOD of 0.1 pM in buffer),we equipped Pc SD with antibodies as rapid diagnostic tools for inpatient care (AFP as biomarker) with a minimized workflow (with a LOD of 2 pM in 5% human serum). The results of this study offer fundamental insights into external factors for boosting DNAzyme catalysis and will be promising for applications that utilize split DNAzymes.
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Affiliation(s)
- Lingying Xia
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
- Biliary Surgical Department of West China Hospital, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Lijie Du
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Xiandeng Hou
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Rongxing Zhou
- Biliary Surgical Department of West China Hospital, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Nansheng Cheng
- Biliary Surgical Department of West China Hospital, Sichuan University, Sichuan, Chengdu 610064, PR China
| | - Junbo Chen
- Analytical & Testing Center, Sichuan University, Sichuan, Chengdu 610064, PR China
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3
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Zhang Z, Wei W, Chen S, Yang J, Song D, Chen Y, Zhao Z, Chen J, Wang F, Wang J, Li Z, Liang Y, Yu H. Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity. J Am Chem Soc 2024; 146:7052-7062. [PMID: 38427585 DOI: 10.1021/jacs.4c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10-23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA-RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a kobs of 3.76 min-1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.
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Affiliation(s)
- Ze Zhang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Siqi Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jintao Yang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zerun Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jiawen Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Fulong Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jiahuan Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
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4
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Moreira L, Guimarães NM, Santos RS, Loureiro JA, Pereira MC, Azevedo NF. Promising strategies employing nucleic acids as antimicrobial drugs. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102122. [PMID: 38333674 PMCID: PMC10850860 DOI: 10.1016/j.omtn.2024.102122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Antimicrobial resistance (AMR) is a growing concern because it causes microorganisms to develop resistance to drugs commonly used to treat infections. This results in increased difficulty in treating infections, leading to higher mortality rates and significant economic effects. Investing in new antimicrobial agents is, therefore, necessary to prevent and control AMR. Antimicrobial nucleic acids have arisen as potential key players in novel therapies for AMR infections. They have been designed to serve as antimicrobials and to act as adjuvants to conventional antibiotics or to inhibit virulent mechanisms. This new category of antimicrobial drugs consists of antisense oligonucleotides and oligomers, DNAzymes, and transcription factor decoys, differing in terms of structure, target molecules, and mechanisms of action. They are synthesized using nucleic acid analogs to enhance their resistance to nucleases. Because bacterial envelopes are generally impermeable to oligonucleotides, delivery into the cytoplasm typically requires the assistance of nanocarriers, which can affect their therapeutic potency. Given that numerous factors contribute to the success of these antimicrobial drugs, this review aims to provide a summary of the key advancements in the use of oligonucleotides for treating bacterial infections. Their mechanisms of action and the impact of factors such as nucleic acid design, target sequence, and nanocarriers on the antimicrobial potency are discussed.
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Affiliation(s)
- Luís Moreira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno M. Guimarães
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Rita S. Santos
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana A. Loureiro
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Maria C. Pereira
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE–Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE–Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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5
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Nedorezova DD, Dubovichenko MV, Kalnin AJ, Nour MAY, Eldeeb AA, Ashmarova AI, Kurbanov GF, Kolpashchikov DM. Cleaving Folded RNA with DNAzyme Agents. Chembiochem 2024; 25:e202300637. [PMID: 37870555 DOI: 10.1002/cbic.202300637] [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: 09/17/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
Cleavage of biological mRNA by DNAzymes (Dz) has been proposed as a variation of oligonucleotide gene therapy (OGT). The design of Dz-based OGT agents includes computational prediction of two RNA-binding arms with low affinity (melting temperatures (Tm ) close to the reaction temperature of 37 °C) to avoid product inhibition and maintain high specificity. However, RNA cleavage might be limited by the RNA binding step especially if the RNA is folded in secondary structures. This calls for the need for two high-affinity RNA-binding arms. In this study, we optimized 10-23 Dz-based OGT agents for cleavage of three RNA targets with different folding energies under multiple turnover conditions in 2 mM Mg2+ at 37 °C. Unexpectedly, one optimized Dz had each RNA-binding arm with a Tm ≥60 °C, without suffering from product inhibition or low selectivity. This phenomenon was explained by the folding of the RNA cleavage products into stable secondary structures. This result suggests that Dz with long (high affinity) RNA-binding arms should not be excluded from the candidate pool for OGT agents. Rather, analysis of the cleavage products' folding should be included in Dz selection algorithms. The Dz optimization workflow should include testing with folded rather than linear RNA substrates.
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Affiliation(s)
- Daria D Nedorezova
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Mikhail V Dubovichenko
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Arseniy J Kalnin
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Moustapha A Y Nour
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Ahmed A Eldeeb
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Anna I Ashmarova
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Gabdulla F Kurbanov
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
| | - Dmitry M Kolpashchikov
- Laboratory of molecular robotics and biosensor systems, Laboratory of Frontier nucleic acid technologies in gene therapy of cancer, SCAMT Institute, ITMO University, St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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6
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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7
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Zhu X, Xu J, Ling G, Zhang P. Tunable metal-organic frameworks assist in catalyzing DNAzymes with amplification platforms for biomedical applications. Chem Soc Rev 2023; 52:7549-7578. [PMID: 37817667 DOI: 10.1039/d3cs00386h] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Various binding modes of tunable metal organic frameworks (MOFs) and functional DNAzymes (Dzs) synergistically catalyze the emergence of abundant functional nanoplatforms. Given their serial variability in formation, structural designability, and functional controllability, Dzs@MOFs tend to be excellent building blocks for the precise "intelligent" manufacture of functional materials. To present a clear outline of this new field, this review systematically summarizes the progress of Dz integration into MOFs (MOFs@Dzs) through different methods, including various surface infiltration, pore encapsulation, covalent binding, and biomimetic mineralization methods. Atomic-level and time-resolved catalytic mechanisms for biosensing and imaging are made possible by the complex interplay of the distinct molecular structure of Dzs@MOF, conformational flexibility, and dynamic regulation of metal ions. Exploiting the precision of DNAzymes, MOFs@Dzs constructed a combined nanotherapy platform to guide intracellular drug synthesis, photodynamic therapy, catalytic therapy, and immunotherapy to enhance gene therapy in different ways, solving the problems of intracellular delivery inefficiency and insufficient supply of cofactors. MOFs@Dzs nanostructures have become excellent candidates for biosensing, bioimaging, amplification delivery, and targeted cancer gene therapy while emphasizing major advancements and seminal endeavors in the fields of biosensing (nucleic acid, protein, enzyme activity, small molecules, and cancer cells), biological imaging, and targeted cancer gene delivery and gene therapy. Overall, based on the results demonstrated to date, we discuss the challenges that the emerging MOFs@Dzs might encounter in practical future applications and briefly look forward to their bright prospects in other fields.
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Affiliation(s)
- Xiaoguang Zhu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Jiaqi Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Guixia Ling
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
| | - Peng Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang 110016, China.
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8
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Xiao L, Zhao Y, Yang M, Luan G, Du T, Deng S, Jia X. A promising nucleic acid therapy drug: DNAzymes and its delivery system. Front Mol Biosci 2023; 10:1270101. [PMID: 37753371 PMCID: PMC10518456 DOI: 10.3389/fmolb.2023.1270101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Based on the development of nucleic acid therapeutic drugs, DNAzymes obtained through in vitro selection technology in 1994 are gradually being sought. DNAzymes are single-stranded DNA molecules with catalytic function, which specifically cleave RNA under the action of metal ions. Various in vivo and in vitro models have recently demonstrated that DNAzymes can target related genes in cancer, cardiovascular disease, bacterial and viral infection, and central nervous system disease. Compared with other nucleic acid therapy drugs, DNAzymes have gained more attention due to their excellent cutting efficiency, high stability, and low cost. Here, We first briefly reviewed the development and characteristics of DNAzymes, then discussed disease-targeting inhibition model of DNAzymes, hoping to provide new insights and ways for disease treatment. Finally, DNAzymes were still subject to some restrictions in practical applications, including low cell uptake efficiency, nuclease degradation and interference from other biological matrices. We discussed the latest delivery strategy of DNAzymes, among which lipid nanoparticles have recently received widespread attention due to the successful delivery of the COVID-19 mRNA vaccine, which provides the possibility for the subsequent clinical application of DNAzymes. In addition, the future development of DNAzymes was prospected.
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Affiliation(s)
- Lang Xiao
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Yan Zhao
- Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Meng Yang
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ting Du
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Shanshan Deng
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xu Jia
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
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9
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Su J, Sun C, Du J, Xing X, Wang F, Dong H. RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy. Adv Healthc Mater 2023; 12:e2300367. [PMID: 37084038 DOI: 10.1002/adhm.202300367] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Indexed: 04/22/2023]
Abstract
Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.
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Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Fang Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
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10
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Chiba K, Yamaguchi T, Obika S. Development of 8-17 XNAzymes that are functional in cells. Chem Sci 2023; 14:7620-7629. [PMID: 37476720 PMCID: PMC10355097 DOI: 10.1039/d3sc01928d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
DNA enzymes (DNAzymes), which cleave target RNA with high specificity, have been widely investigated as potential oligonucleotide-based therapeutics. Recently, xeno-nucleic acid (XNA)-modified DNAzymes (XNAzymes), exhibiting cleavage activity in cultured cells, have been developed. However, a versatile approach to modify XNAzymes that function in cells has not yet been established. Here, we report an X-ray crystal structure-based approach to modify 8-17 DNAzymes; this approach enables us to effectively locate suitable XNAs to modify. Our approach, combined with a modification strategy used in designing antisense oligonucleotides, rationally designed 8-17 XNAzyme ("X8-17") that achieved high potency in terms of RNA cleavage and biostability against nucleases. X8-17, modified with 2'-O-methyl RNA, locked nucleic acid and phosphorothioate, successfully induced endogenous MALAT-1 and SRB1 RNA knockdown in cells. This approach may help in developing XNAzyme-based novel therapeutic agents.
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Affiliation(s)
- Kosuke Chiba
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita Osaka 565-0871 Japan
- National Institutes of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi Ibaraki Osaka 567-0085 Japan
- Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University 1-1 Yamadaoka Suita Osaka 565-0871 Japan
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11
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Cramer ER, Starcovic SA, Avey RM, Kaya AI, Robart AR. Structure of a 10-23 deoxyribozyme exhibiting a homodimer conformation. Commun Chem 2023; 6:119. [PMID: 37301907 DOI: 10.1038/s42004-023-00924-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/06/2023] [Indexed: 06/12/2023] Open
Abstract
Deoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing chemical reactions. The RNA-cleaving 10-23 DNAzyme was the first DNAzyme to be evolved and possesses clinical and biotechnical applications as a biosensor and a knockdown agent. DNAzymes do not require the recruitment of other components to cleave RNA and can turnover, thus they have a distinct advantage over other knockdown methods (siRNA, CRISPR, morpholinos). Despite this, a lack of structural and mechanistic information has hindered the optimization and application of the 10-23 DNAzyme. Here, we report a 2.7 Å crystal structure of the RNA-cleaving 10-23 DNAzyme in a homodimer conformation. Although proper coordination of the DNAzyme to substrate is observed along with intriguing patterns of bound magnesium ions, the dimer conformation likely does not capture the true catalytic form of the 10-23 DNAzyme.
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Affiliation(s)
- Evan R Cramer
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, 20506, USA
| | - Sarah A Starcovic
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, 20506, USA
| | - Rebekah M Avey
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, 20506, USA
| | - Ali I Kaya
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Aaron R Robart
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV, 20506, USA.
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12
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Cramer E, Starcovic S, Avey R, Kaya A, Robart A. Structure of a 10-23 Deoxyribozyme Exhibiting a Homodimer Conformation. RESEARCH SQUARE 2023:rs.3.rs-2252941. [PMID: 37398199 PMCID: PMC10312968 DOI: 10.21203/rs.3.rs-2252941/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Deoxyribozymes (DNAzymes) are in vitro evolved DNA sequences capable of catalyzing chemical reactions. The RNA cleaving 10-23 DNAzyme was the first DNAzyme to be evolved and possesses clinical and biotechnical applications as a biosensor and a knockdown agent. DNAzymes do not require the recruitment of other components to cleave RNA and can turnover, thus they have a distinct advantage over other knockdown methods (siRNA, CRISPR, morpholinos). Despite this, a lack of structural and mechanistic information has hindered the optimization and application of the 10-23 DNAzyme. Here, we report a 2.7 Å crystal structure of the RNA cleaving 10-23 DNAzyme in a homodimer conformation. Although proper coordination of the DNAzyme to substrate is observed along with intriguing patterns of bound magnesium ions, the dimer conformation likely does not capture the true catalytic form of the 10-23 DNAzyme.
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13
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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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14
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Larcher LM, Pitout IL, Keegan NP, Veedu RN, Fletcher S. DNAzymes: Expanding the Potential of Nucleic Acid Therapeutics. Nucleic Acid Ther 2023. [PMID: 37093127 DOI: 10.1089/nat.2022.0066] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Nucleic acids drugs have been proven in the clinic as a powerful modality to treat inherited and acquired diseases. However, key challenges including drug stability, renal clearance, cellular uptake, and movement across biological barriers (foremost the blood-brain barrier) limit the translation and clinical efficacy of nucleic acid-based therapies, both systemically and in the central nervous system. In this study we provide an overview of an emerging class of nucleic acid therapeutic, called DNAzymes. In particular, we review the use of chemical modifications and carrier molecules for the stabilization and/or delivery of DNAzymes in cell and animal models. Although this review focuses on DNAzymes, the strategies described are broadly applicable to most nucleic acid technologies. This review should serve as a general guide for selecting chemical modifications to improve the therapeutic performance of DNAzymes.
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Affiliation(s)
- Leon M Larcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
| | - Ianthe L Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
| | - Niall P Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
- Discovery, PYC Therapeutics, Nedlands, Australia
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
- Precision Nucleic Acid Therapeutics, Perron Institute for Neurological and Translational Science, Perth, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Australia
- Discovery, PYC Therapeutics, Nedlands, Australia
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15
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Yi D, Zhao H, Zhao J, Li L. Modular Engineering of DNAzyme-Based Sensors for Spatioselective Imaging of Metal Ions in Mitochondria. J Am Chem Soc 2023; 145:1678-1685. [PMID: 36573341 DOI: 10.1021/jacs.2c11081] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNAzyme-based sensors remain at the forefront of metal-ion imaging efforts, but most lack the subcellular precision necessary to their applications in specific organelles. Here, we seek to overcome this limitation by presenting a DNAzyme-based biosensor technology for spatiotemporally controlled imaging of metal ions in mitochondria. A DNA nanodevice was constructed by integrating an optically activatable DNAzyme sensor and an upconversion nanoparticle with an organelle-targeting signal. We exemplify that this approach allows for mitochondria-specific imaging of Zn2+ in living cells in a near-infrared light-controlled manner. Based on this, the system is used for the monitoring of mitochondrial Zn2+ during drug treatment in a cellular model of ischemia insult. Furthermore, the DNA nanodevice is employed to assess dynamic Zn2+ change and pharmacological interventions in an injury cell model of Zn2+ toxicity. This method paves the way for engineering of DNAzyme sensors to investigate the pathophysiological roles of metal ions at the subcellular level.
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Affiliation(s)
- Deyu Yi
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hengzhi Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China.,College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Wang B, Wang M, Peng F, Fu X, Wen M, Shi Y, Chen M, Ke G, Zhang XB. Construction and Application of DNAzyme-based Nanodevices. Chem Res Chin Univ 2023; 39:42-60. [PMID: 36687211 PMCID: PMC9841151 DOI: 10.1007/s40242-023-2334-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Menghui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiaoyi Fu
- Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, 310022 P. R. China
| | - Mei Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Yuyan Shi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Mei Chen
- College of Materials Science and Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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17
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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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18
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Li Y, Wei L, Cheng A, Wang M, Ou X, Mao S, Tian B, Yang Q, Wu Y, Zhang S, Huang J, Gao Q, Sun D, Zhao X, Jia R, Liu M, Zhu D, Chen S, Yu Y, Zhang L, Pan L. Specific DNAzymes cleave the 300-618 nt of 5'UTR to inhibit DHAV-1 translation and replication. Front Microbiol 2022; 13:1064612. [PMID: 36578574 PMCID: PMC9791187 DOI: 10.3389/fmicb.2022.1064612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
DNAzymes effectively inhibit the expression of viral genes. Duck hepatitis A virus type-1 (DHAV-1) genomic RNA carries an internal ribosome entry site (IRES). The IRES initiates the translation of DHAV-1 via a mechanism that differs from that of cap-dependent translation. Therefore, it is an attractive target for the treatment of DHAV-1. In this study, we designed 6 DNAzymes (Dzs) specifically targeting 300-618 nt sequence in the DHAV-1 5'untranslated region (UTR; a predicted IRES-like element). In the presence of divalent metal ions, three designed DNAzymes (DZ369, DZ454, and DZ514) efficiently cleaved the 300-618 nt sequence of the DHAV-1 5'UTR RNA. The activity of the Dzs was particularly dependent on Mg2+ ions. Subsequently, the translation inhibitory activity of these Dzs was determined by western blotting experiments. The Dzs effectively inhibited the translation mediated by the 300-618 nt of DHAV-1 5'UTR in duck embryo fibroblasts (DEFs). Importantly, DZ454 showed the strongest inhibitory effect, and its inhibition was time and dose dependent. However, none of the Dzs showed significant inhibition of cap-dependent translation. These results suggest that these Dzs show specificity for target RNA. Moreover, DZ454 inhibited the replication of DHAV-1. In conclusion, the designed DNAzymes can be used as inhibitors of DHAV-1 RNA translation and replication, providing new insights useful for the development of anti-DHAV-1 drugs.
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Affiliation(s)
- Yanglin Li
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Wei
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,*Correspondence: Mingshu Wang,
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Leichang Pan
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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19
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Wang Q, Wang Z, He Y, Xiong B, Li Y, Wang F. Chemical and structural modification of RNA-cleaving DNAzymes for efficient biosensing and biomedical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Nedorezova DD, Dubovichenko MV, Belyaeva EP, Grigorieva ED, Peresadina AV, Kolpashchikov DM. Specificity of oligonucleotide gene therapy (OGT) agents. Theranostics 2022; 12:7132-7157. [PMID: 36276652 PMCID: PMC9576606 DOI: 10.7150/thno.77830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/11/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotide gene therapy (OGT) agents (e. g. antisense, deoxyribozymes, siRNA and CRISPR/Cas) are promising therapeutic tools. Despite extensive efforts, only few OGT drugs have been approved for clinical use. Besides the problem of efficient delivery to targeted cells, hybridization specificity is a potential limitation of OGT agents. To ensure tight binding, a typical OGT agent hybridizes to the stretch of 15-25 nucleotides of a unique targeted sequence. However, hybrids of such lengths tolerate one or more mismatches under physiological conditions, the problem known as the affinity/specificity dilemma. Here, we assess the scale of this problem by analyzing OGT hybridization-dependent off-target effects (HD OTE) in vitro, in animal models and clinical studies. All OGT agents except deoxyribozymes exhibit HD OTE in vitro, with most thorough evidence of poor specificity reported for siRNA and CRISPR/Cas9. Notably, siRNA suppress non-targeted genes due to (1) the partial complementarity to mRNA 3'-untranslated regions (3'-UTR), and (2) the antisense activity of the sense strand. CRISPR/Cas9 system can cause hundreds of non-intended dsDNA breaks due to low specificity of the guide RNA, which can limit therapeutic applications of CRISPR/Cas9 by ex-vivo formats. Contribution of this effects to the observed in vivo toxicity of OGT agents is unclear and requires further investigation. Locked or peptide nucleic acids improve OGT nuclease resistance but not specificity. Approaches that use RNA marker dependent (conditional) activation of OGT agents may improve specificity but require additional validation in cell culture and in vivo.
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Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Mikhail V. Dubovichenko
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina P. Belyaeva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Ekaterina D. Grigorieva
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Arina V. Peresadina
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, International Institute SCAMT, ITMO University, 9 Lomonosov Str., St. Petersburg, 191002, Russian Federation
- Chemistry Department, University of Central Florida, Orlando, FL 32816-2366, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
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21
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Aliev TA, Timralieva AA, Kurakina TA, Katsuba KE, Egorycheva YA, Dubovichenko MV, Kutyrev MA, Shilovskikh VV, Orekhov N, Kondratyuk N, Semenov SN, Kolpashchikov DM, Skorb EV. Designed assembly and disassembly of DNA in supramolecular structure: From ion regulated nuclear formation and machine learning recognition to running DNA cascade. NANO SELECT 2022. [DOI: 10.1002/nano.202200092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | - Nikita Orekhov
- Moscow Institute of Physics and Technology Moscow Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences Moscow Russia
- Bauman Moscow State Technical University Moscow Russia
| | - Nikolay Kondratyuk
- Moscow Institute of Physics and Technology Moscow Russia
- Joint Institute for High Temperatures of the Russian Academy of Sciences Moscow Russia
- National Research University Higher School of Economics Moscow Russia
| | - Sergey N. Semenov
- Department of Molecular Chemistry and Materials Science Weizmann Institute of Science Rehovot Israel
| | - Dmitry M. Kolpashchikov
- ITMO University Saint Petersburg Russia
- University of Central Florida Chemistry Department Orlando Florida USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando Florida USA
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22
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Lopez A, Liu J. Probing metal-dependent G-quadruplexes using the intrinsic fluorescence of DNA. Chem Commun (Camb) 2022; 58:10225-10228. [PMID: 36001027 DOI: 10.1039/d2cc03967b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
K+ enhanced the intrinsic fluorescence of a series of G-quadruplex DNAs, while Pb2+ quenched the fluorescence. The metals showed interesting quadruplex binding kinetics with various DNA sequences.
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Affiliation(s)
- Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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23
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Depaix A, Grudzien-Nogalska E, Fedorczyk B, Kiledjian M, Jemielity J, Kowalska J. Preparation of RNAs with non-canonical 5' ends using novel di- and trinucleotide reagents for co-transcriptional capping. Front Mol Biosci 2022; 9:854170. [PMID: 36060251 PMCID: PMC9437278 DOI: 10.3389/fmolb.2022.854170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022] Open
Abstract
Many eukaryotic and some bacterial RNAs are modified at the 5' end by the addition of cap structures. In addition to the classic 7-methylguanosine 5' cap in eukaryotic mRNA, several non-canonical caps have recently been identified, including NAD-linked, FAD-linked, and UDP-glucose-linked RNAs. However, studies of the biochemical properties of these caps are impaired by the limited access to in vitro transcribed RNA probes of high quality, as the typical capping efficiencies with NAD or FAD dinucleotides achieved in the presence of T7 polymerase rarely exceed 50%, and pyrimidine derivatives are not incorporated because of promoter sequence limitations. To address this issue, we developed a series of di- and trinucleotide capping reagents and in vitro transcription conditions to provide straightforward access to unconventionally capped RNAs with improved 5'-end homogeneity. We show that because of the transcription start site flexibility of T7 polymerase, R1ppApG-type structures (where R1 is either nicotinamide riboside or riboflavin) are efficiently incorporated into RNA during transcription from dsDNA templates containing both φ 6.5 and φ 2.5 promoters and enable high capping efficiencies (∼90%). Moreover, uridine-initiated RNAs are accessible by transcription from templates containing the φ 6.5 promoter performed in the presence of R2ppUpG-type initiating nucleotides (where R2 is a sugar or phosphate moiety). We successfully employed this strategy to obtain several nucleotide-sugar-capped and uncapped RNAs. The capping reagents developed herein provide easy access to chemical probes to elucidate the biological roles of non-canonical RNA 5' capping.
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Affiliation(s)
- Anaïs Depaix
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Ewa Grudzien-Nogalska
- Department of Cell Biology and Neuroscience, Rutgers University, New York, NJ, United States
| | | | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, New York, NJ, United States
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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24
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Li Y, Du S, Jin H, He J. A combination of the modified catalytic core and conjugation of 3'-inverted deoxythymidine for a more efficient and nuclease-resistant 10-23 DNAzyme. Bioorg Med Chem Lett 2022; 62:128633. [PMID: 35189319 DOI: 10.1016/j.bmcl.2022.128633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 11/02/2022]
Abstract
10-23 DNAzyme is a catalytic DNA molecule capable of cleaving complementary RNA. Its high cleavage efficiency is being pursued by chemical modifications, for realizing its genetic therapeutics potential. The most efficient and nuclease-resistant DNAzyme was obtained in this study combined two modifications - 7-aminopropyl-8-aza-7-deaza-2'-deoxyadenosine (residue 1) at A9 and 3'-inverted deoxythymidine residue (iT) at 3'-end. Moreover, this combinatorial modification could be a universal approach for designing efficient and enzyme-resistant 10-23 DNAzyme against other RNA targets, and the catalytic core-modification could be further combined with other recognition arm modifications for practical applications as genetic therapeutics and biosensor tools.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University, Beijing 100191, China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
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25
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Structure and mechanism of the methyltransferase ribozyme MTR1. Nat Chem Biol 2022; 18:547-555. [PMID: 35301481 PMCID: PMC7612680 DOI: 10.1038/s41589-022-00976-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022]
Abstract
RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the site-specific synthesis of 1-methyladenosine (m1A) in RNA, using O6-methylguanine (m6G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 Å, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m1A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.
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26
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Huang Z, Wang X, Wu Z, Jiang JH. Recent Advances on DNAzyme-Based Sensing. Chem Asian J 2022; 17:e202101414. [PMID: 35156764 DOI: 10.1002/asia.202101414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/09/2022] [Indexed: 11/08/2022]
Abstract
DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.
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Affiliation(s)
- Zhimei Huang
- Hunan University, College of Chemistry and Chemical Engineering, CHINA
| | - Xiangnan Wang
- Hunan University of Technology and Business, College of Science, CHINA
| | - Zhenkun Wu
- Hunan University, State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics and College of Chemistry and Chemical Engineering, South of Lushan Road, 410082, Changsha, CHINA
| | - Jian-Hui Jiang
- Hunan University, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering, CHINA
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27
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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: 52] [Impact Index Per Article: 26.0] [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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28
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Jung J, Kim SY, Kim SK. Single-molecule study of the effects of temperature, pH, and RNA base on the stepwise enzyme kinetics of 10–23 deoxyribozyme. RSC Adv 2022; 12:14883-14887. [PMID: 35702195 PMCID: PMC9113834 DOI: 10.1039/d2ra02131e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
We investigated how the stepwise enzyme kinetics of 10–23 deoxyribozyme was affected by temperature, pH, and RNA residue of the substrate at the single-molecule level. A deoxyribozyme-substrate system was employed to temporally categorize a single-turnover reaction into four distinct steps: binding, cleavage, dissociation of one of the cleaved fragments, and dissociation of the other fragment. The dwell time of each step was measured as the temperature was varied from 26 to 34 °C, to which the transition state theory was applied to obtain the enthalpy and entropy of activation for individual steps. In addition, we found that only the cleavage step was significantly affected by pH, indicating that it involves deprotonation of a single proton. We also found that different RNA residues specifically affect the cleavage step and cause the dwell time to change by as much as 5 times. We investigated how the stepwise enzyme kinetics of 10–23 deoxyribozyme was affected by temperature, pH, and RNA residue of the substrate at the single-molecule level.![]()
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Affiliation(s)
- Jiwon Jung
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Seon Yong Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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29
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Liczner C, Duke K, Juneau G, Egli M, Wilds CJ. Beyond ribose and phosphate: Selected nucleic acid modifications for structure-function investigations and therapeutic applications. Beilstein J Org Chem 2021; 17:908-931. [PMID: 33981365 PMCID: PMC8093555 DOI: 10.3762/bjoc.17.76] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Over the past 25 years, the acceleration of achievements in the development of oligonucleotide-based therapeutics has resulted in numerous new drugs making it to the market for the treatment of various diseases. Oligonucleotides with alterations to their scaffold, prepared with modified nucleosides and solid-phase synthesis, have yielded molecules with interesting biophysical properties that bind to their targets and are tolerated by the cellular machinery to elicit a therapeutic outcome. Structural techniques, such as crystallography, have provided insights to rationalize numerous properties including binding affinity, nuclease stability, and trends observed in the gene silencing. In this review, we discuss the chemistry, biophysical, and structural properties of a number of chemically modified oligonucleotides that have been explored for gene silencing.
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Affiliation(s)
- Christopher Liczner
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Kieran Duke
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Martin Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
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30
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31
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Wang Y, Nguyen K, Spitale RC, Chaput JC. A biologically stable DNAzyme that efficiently silences gene expression in cells. Nat Chem 2021; 13:319-326. [DOI: 10.1038/s41557-021-00645-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 11/09/2022]
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32
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Xiong H, Veedu RN, Diermeier SD. Recent Advances in Oligonucleotide Therapeutics in Oncology. Int J Mol Sci 2021; 22:3295. [PMID: 33804856 PMCID: PMC8036554 DOI: 10.3390/ijms22073295] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 02/08/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide. Conventional therapies, including surgery, radiation, and chemotherapy have achieved increased survival rates for many types of cancer over the past decades. However, cancer recurrence and/or metastasis to distant organs remain major challenges, resulting in a large, unmet clinical need. Oligonucleotide therapeutics, which include antisense oligonucleotides, small interfering RNAs, and aptamers, show promising clinical outcomes for disease indications such as Duchenne muscular dystrophy, familial amyloid neuropathies, and macular degeneration. While no approved oligonucleotide drug currently exists for any type of cancer, results obtained in preclinical studies and clinical trials are encouraging. Here, we provide an overview of recent developments in the field of oligonucleotide therapeutics in oncology, review current clinical trials, and discuss associated challenges.
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Affiliation(s)
- Haoyu Xiong
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth 6150, Australia;
- Perron Institute for Neurological and Translational Science, Perth 6009, Australia
| | - Sarah D. Diermeier
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand;
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33
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Hanpanich O, Saito K, Shimada N, Maruyama A. One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer. Biosens Bioelectron 2020; 165:112383. [PMID: 32729508 PMCID: PMC7836245 DOI: 10.1016/j.bios.2020.112383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
RNA detection permits early diagnosis of several infectious diseases and cancers, which prevent propagation of diseases and improve treatment efficacy. However, standard technique for RNA detection such as reverse transcription-quantitative polymerase chain reaction has complicated procedure and requires well-trained personnel and specialized lab equipment. These shortcomings limit the application for point-of-care analysis which is critical for rapid and effective disease management. The multicomponent nucleic acid enzymes (MNAzymes) are one of the promising biosensors for simple, isothermal and enzyme-free RNA detection. Herein, we demonstrate simple yet effective strategies that significantly enhance analytical performance of MNAzymes. The addition of the cationic copolymer and structural modification of MNAzyme significantly enhanced selectivity and activity of MNAzymes by 250 fold and 2,700 fold, respectively. The highly simplified RNA detection system achieved a detection limit of 73 fM target concentration without additional amplification. The robustness of MNAzyme in the presence of non-target RNA was also improved. Our finding opens up a route toward the development of an alternative rapid, sensitive, isothermal, and protein-free RNA diagnostic tool, which expected to be of great clinical significance.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ken Saito
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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34
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Huang PJ, Liu J. In vitro Selection of Chemically Modified DNAzymes. ChemistryOpen 2020; 9:1046-1059. [PMID: 33101831 PMCID: PMC7570446 DOI: 10.1002/open.202000134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn2+ and Hg2+. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu2+, Cd2+, Zn2+, and Ni2+. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2'-5' linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.
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Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for NanotechnologyUniversity of WaterlooWaterlooOntario, N2L 3G1Canada
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35
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Dellafiore M, Montserrat JM, Iribarren AM. Core modified 8-17 DNAzymes with 2'-deoxy-2'-C-methylpyrimidine nucleosides. Bioorg Chem 2020; 104:104328. [PMID: 33142406 DOI: 10.1016/j.bioorg.2020.104328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 11/28/2022]
Abstract
The catalytic core of an 8-17 DNAzyme directed against STAT 3 was modified using (2'R) and (2'S) 2'-deoxy-2'-C-methyluridine and cytidine. While 2'-deoxy-2'-C-methyluridine significantly diminished the catalytic activity, 2'-deoxy-2'-C-methylcytidine replacement was better accepted, being the kact of modified DNAzymes at 8- and 11-positions comparable to the non-modified one. When 2'-O-methyl and phosphorothioate nucleotides were tested in the binding arms together with core modified DNAzymes the kcat was affected in a non predictable way, emphasizing the fact that both chemical substitutions should be considered globally. Finally, 2'-deoxy-2'-C-methyl modified DNAzymes stability was assayed finding that the double 2'-C-methyl modification in the catalytic core enhanced 70% the stability against a T47D cell lysate compared to a non-modified control.
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Affiliation(s)
- María Dellafiore
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Javier M Montserrat
- Instituto de Ciencias, Universidad Nacional de Gral. Sarmiento, Los Polvorines, Provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Argentina.
| | - Adolfo M Iribarren
- Laboratorio de Biotransformaciones, Universidad Nacional de Quilmes, Provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Argentina.
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36
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Zhang J, Ma R, Blanchard A, Petree J, Jo H, Salaita K. Conditional Deoxyribozyme-Nanoparticle Conjugates for miRNA-Triggered Gene Regulation. ACS APPLIED MATERIALS & INTERFACES 2020; 12:37851-37861. [PMID: 32803952 PMCID: PMC8287654 DOI: 10.1021/acsami.0c07609] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
DNA-nanoparticle (NP) conjugates have been used to knockdown gene expression transiently and effectively, making them desirable tools for gene regulation therapy. Because DNA-NPs are constitutively active and are rapidly taken up by most cell types, they offer limited control in terms of tissue or cell type specificity. To take a step toward solving this issue, we incorporate toehold-mediated strand exchange, a versatile molecular programming modality, to switch the DNA-NPs from an inactive state to an active state in the presence of a specific RNA input. Because many transcripts are unique to cell subtype or disease state, this approach could one day lead to responsive nucleic acid therapeutics with enhanced specificity. As a proof of concept, we designed conditional deoxyribozyme-nanoparticles (conditional DzNPs) that knockdown tumor necrosis factor α (TNFα) mRNA upon miR-33 triggering. We demonstrate toehold-mediated strand exchange and restoration of TNFα DNAzyme activity in the presence of miR-33 trigger, with optimization of the preparation, configuration, and toehold length of conditional DzNPs. Our results indicate specific and strong ON/OFF response of conditional DzNPs to the miR-33 trigger in buffer. Furthermore, we demonstrate endogenous miR-33-triggered knockdown of TNFα mRNA in mouse macrophages, implying the potential of conditional gene regulation applications using these DzNPs.
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Affiliation(s)
- Jiahui Zhang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Rong Ma
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Aaron Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jessica Petree
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Department of Chemistry, Emory University, Atlanta, GA, USA
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37
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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: 10] [Impact Index Per Article: 2.5] [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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38
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Nie C, Chu X, Pan Q, Zhang J, Hu Y, Yi J, He M, He M, Chen T, Chu X. Engineering a Biodegradable Nanocarrier for Enhancing the Response of T98G Cells to Temozolomide. ACS APPLIED BIO MATERIALS 2020; 3:3337-3344. [PMID: 35025376 DOI: 10.1021/acsabm.0c00253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Temozolomide (TMZ), the most common DNA alkylating agent, is predominantly mediated by O6-methylguanine DNA lesions for the treatment of glioblastoma (GBM). When O6-methylguanine-DNA methyltransferase (MGMT) is present, TMZ-induced O6-methylguanine lesions are repaired, resulting in the emergence of resistance to chemotherapy. Herein, we attempted to enhance the response of T98G cells to TMZ by gene silencing of MGMT. In this work, we developed transition metal manganese (Mn)-doped mesoporous silica nanoparticles (MSNs) as a carrier system for the co-delivery of TMZ and 10-23 DNAzyme, and realized gene silencing to enhance the TMZ sensitivity in T98G cells. The intelligent theranostic platform based on manganese-doped mesoporous silica nanoparticles (Mn-MSNs) can be decomposed and release chemotherapy drugs under acidic pH and reducing conditions. Meanwhile, the produced Mn2+ could act as a cofactor of 10-23 DNAzyme to effectively cleave MGMT mRNA, knock down MGMT protein, and sensitize T98G cells to TMZ-induced apoptosis. By co-delivering TMZ and 10-23 DNAzyme employing Mn-MSNs, the concentrations of TMZ that needed to inhibit cell growth by 50% (IC50 values) decreased (by more than 3.8-fold) compared with free TMZ. This work shows that the designed platform holds great promise for advancing the treatment of drug-resistant cancer.
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Affiliation(s)
- Cunpeng Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Ximing Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Qingshan Pan
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Juan Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Yanlei Hu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jintao Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Manman He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Mengyun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Tingting Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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Begum AA, Toth I, Hussein WM, Moyle PM. Advances in Targeted Gene Delivery. Curr Drug Deliv 2020; 16:588-608. [PMID: 31142250 DOI: 10.2174/1567201816666190529072914] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/31/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
Gene therapy has the potential to treat both acquired and inherited genetic diseases. Generally, two types of gene delivery vectors are used - viral vectors and non-viral vectors. Non-viral gene delivery systems have attracted significant interest (e.g. 115 gene therapies approved for clinical trials in 2018; clinicaltrials.gov) due to their lower toxicity, lack of immunogenicity and ease of production compared to viral vectors. To achieve the goal of maximal therapeutic efficacy with minimal adverse effects, the cell-specific targeting of non-viral gene delivery systems has attracted research interest. Targeting through cell surface receptors; the enhanced permeability and retention effect, or pH differences are potential means to target genes to specific organs, tissues, or cells. As for targeting moieties, receptorspecific ligand peptides, antibodies, aptamers and affibodies have been incorporated into synthetic nonviral gene delivery vectors to fulfill the requirement of active targeting. This review provides an overview of different potential targets and targeting moieties to target specific gene delivery systems.
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Affiliation(s)
- Anjuman A Begum
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, St Lucia 4072, Australia.,School of Pharmacy, The University of Queensland, Woolloongabba, 4102, Australia
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, St Lucia 4072, Australia.,School of Pharmacy, The University of Queensland, Woolloongabba, 4102, Australia.,Institute for Molecular Bioscience (IMB), The University of Queensland, St Lucia, St Lucia 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, St Lucia 4072, Australia
| | - Peter M Moyle
- School of Pharmacy, The University of Queensland, Woolloongabba, 4102, Australia
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40
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Du S, Li Y, He J. 2'-Functional group of adenosine in 10-23 DNAzyme promotes catalytic activity. Bioorg Med Chem Lett 2020; 30:126961. [PMID: 31932223 DOI: 10.1016/j.bmcl.2020.126961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/28/2019] [Accepted: 01/04/2020] [Indexed: 10/25/2022]
Abstract
10-23 DNAzyme is an artificially selected catalytic DNA molecule. Its great potential as genetic therapeutics promoted chemical modifications for more efficient DNAzymes. Here, 10-23 DNAzyme was modified on its six deoxyadenosine residues (A5, A9, A11, A12, A15 in the catalytic domain and A0 of the recognition arm next to the cleavage site) with compound 1, an adenosine analogue with 2'-O-[N-(aminoethyl)carbamoyl]methyl group. A positive effect of compound 1 at A15 was observed (HJDS-05, kobs = 0.0111 min-1). Compared to the effect of 2'-H and 2'-OMe at A15, this result provided an approach for more efficient DNAzyme by combining 2'-substituted amino group of adenosine with A15 as the lead structure.
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Affiliation(s)
- Shanshan Du
- College of Chemical Engineering and Materials, Hebei Key Laboratory of Heterocyclic Compounds, Handan University, Handan 056005, China; State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Yang Li
- School of Life Science and Engineering, Handan University, Handan 056005, China; State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology & Toxicology, Beijing 100850, China.
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41
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Nucleic acid-cleaving catalytic DNA for sensing and therapeutics. Talanta 2020; 211:120709. [PMID: 32070594 DOI: 10.1016/j.talanta.2019.120709] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/28/2019] [Accepted: 12/31/2019] [Indexed: 12/21/2022]
Abstract
DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.
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42
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Li Y, Sun S, Tian X, Qiu JG, Jiang B, Wang LJ, Zhang CY. Dephosphorylation-directed tricyclic DNA amplification cascades for sensitive detection of protein tyrosine phosphatase. Chem Commun (Camb) 2020; 56:11581-11584. [DOI: 10.1039/d0cc04714g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A new fluorescence method is developed for the sensitive detection of protein tyrosine phosphatase based on dephosphorylation-directed tricyclic DNA amplification cascades.
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Affiliation(s)
- Yueying Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Shuli Sun
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Xiaorui Tian
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Jian-Ge Qiu
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - BingHua Jiang
- Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450000
- China
| | - Li-juan Wang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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Nedorezova DD, Fakhardo AF, Molden TA, Kolpashchikov DM. Deoxyribozyme‐Based DNA Machines for Cancer Therapy. Chembiochem 2019; 21:607-611. [DOI: 10.1002/cbic.201900525] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Daria D. Nedorezova
- Laboratory of Solution Chemistry of Advanced Materials and TechnologiesITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Anna F. Fakhardo
- Laboratory of Solution Chemistry of Advanced Materials and TechnologiesITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
| | - Tatiana A. Molden
- Chemistry DepartmentUniversity of Central Florida Orlando FL 32816-2366 USA
| | - Dmitry M. Kolpashchikov
- Chemistry DepartmentUniversity of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical SciencesUniversity of Central Florida Orlando FL 32816 USA
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Hanpanich O, Miyaguchi H, Huang H, Shimada N, Maruyama A. Cationic copolymer-chaperoned short-armed 10-23 DNAzymes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:156-169. [PMID: 31608816 DOI: 10.1080/15257770.2019.1675168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The cationic copolymer poly(L-lysine)-graft-dextran (PLL-g-Dex) has nucleic acid chaperone-like activity. The copolymer facilitates both DNA hybridization and strand exchange reactions. For these reasons, DNA-based enzyme (DNAzyme) activity is enhanced in the presence of copolymer. In this study, we evaluated activities of DNAzymes with substrate-binding arms (S-arms) of various lengths. The copolymer promoted DNAzyme reactivity and turnover efficacy, and, depending on S-arm length, maximally accelerated the reaction rate by 250-fold compared to the rate in the absence of copolymer. The copolymer permitted up to six nucleotides truncation of the S-arms having initial length of 10 and 11 nucleotides without loss of catalytic efficiency, enable tuning of the optimal temperature ranging from 30 to 55 °C. The approach might be useful for the development of DNAzyme systems targeting short or highly structured RNAs as well for improvement of DNAzyme-based nanomachines and biosensors.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitonari Miyaguchi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - He Huang
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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45
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Hanpanich O, Oyanagi T, Shimada N, Maruyama A. Cationic copolymer-chaperoned DNAzyme sensor for microRNA detection. Biomaterials 2019; 225:119535. [PMID: 31614289 DOI: 10.1016/j.biomaterials.2019.119535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 02/08/2023]
Abstract
Multi-component nucleic acid enzymes (MNAzymes) are allosteric deoxyribozymes that are activated upon binding of a specific nucleic acid effector. MNAzyme activity is limited due to an insufficient assembly of the MNAzyme and its turnover. In this work, we describe the successful improvement of MNAzyme reactivity and selectivity by addition of cationic copolymers, which exhibit nucleic acid chaperone-like activity. The copolymer allowed a 210-fold increase in signal activity and a 95-fold increase in the signal-to-background selectivity of MNAzymes constructed for microRNA (miRNA) detection. The selectivity of the MNAzyme for homologous miRNAs was demonstrated in a multiplex format in which isothermal reactions of two different MNAzymes were performed. In addition, the copolymer permitted miRNA detections even in the presence of a ribonuclease which is ubiquitous in environments, indicating the protective effect of the copolymer against ribonucleases.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Tomoya Oyanagi
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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46
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Targeting a viral DNA sequence with a deoxyribozyme in a preparative scale. Biochimie 2019; 165:161-169. [PMID: 31377192 DOI: 10.1016/j.biochi.2019.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/28/2019] [Indexed: 01/13/2023]
Abstract
Deoxyribozymes are synthetic and single stranded DNAs that are capable of catalysis of a variety of reactions, including cleavage of DNA substrates. Deoxyribozymes are usually characterized by analytical single-turnover kinetic assays, however, for many applications e.g. characterization of the reaction products, semi-preparative and preparative reactions are required. At such scales, there is a lack of comprehensive analysis and conditions that supports high amount of products in an appropriate time-scale are vaguely guessed by researchers. In this report, catalytic activity of an oxidizing DNA-cleaving deoxyribozyme, F-8(X), was comprehensively inspected in semi-preparative (10 μM substrate) scale. A 60 nucleotides long synthetic DNA sequence was selected as the target DNA for this study. The DNA sequence was originated from a single stranded DNA virus. Investigations revealed high yield in the presence of optimal concentration of oxidizing agents. The optimal conditions have been applied for scale-up of the reaction to preparative (40 μM substrate) and multi-turnover reactions to achieve highest amount of product in a cost-, time- and labor-effective manner. Such a comprehensive analysis of a deoxyribozyme's activity in semi-preparative scale provides a platform for expanded applications of DNA catalysts as a tool in chemical biology.
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47
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Nucleic acid enzymes based on functionalized nucleosides. Curr Opin Chem Biol 2019; 52:93-101. [PMID: 31307007 DOI: 10.1016/j.cbpa.2019.06.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 12/29/2022]
Abstract
Nucleic acid-based enzymes have recently joined their proteinaceous counterparts as important biocatalysts. While RNA enzymes (ribozymes) are found in nature, deoxyribozymes or DNAzymes are man-made entities. Numerous ribozymes and DNAzymes have been identified by Darwinian selection methods to catalyze a broad array of chemical transformations. Despite these important advances, practical applications involving nucleic acid enzymes are often plagued by relatively poor pharmacokinetic properties and cellular uptake, rapid degradation by nucleases and/or by the limited chemical arsenal carried by natural DNA and RNA. In this review, the two main chemical approaches for the modification of nucleic acid-based catalysts, particularly DNAzymes, are described. These methods aim at improving the functional properties of nucleic acid enzymes by mitigating some of these shortcomings. In this context, recent developments in the post-SELEX processing of existing nucleic acid catalysts as well as efforts for the selection of DNAzymes and ribozymes with modified nucleoside triphosphates are summarized.
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48
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Ali MM, Slepenkin A, Peterson E, Zhao W. A Simple DNAzyme-Based Fluorescent Assay for Klebsiella pneumoniae. Chembiochem 2019; 20:906-910. [PMID: 30521678 PMCID: PMC6692177 DOI: 10.1002/cbic.201800701] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Indexed: 11/09/2022]
Abstract
Pathogenic bacteria pose a serious threat to public health, and the rapid and cost-effective detection of such bacteria remains a major challenge. Herein, we present a DNAzyme-based fluorescent paper sensor for Klebsiella pneumoniae. The DNAzyme was generated by an in vitro selection technique to cleave a fluorogenic DNA-RNA chimeric substrate in the presence of K. pneumoniae. The DNAzyme was printed on a paper substrate in a 96-well format to serve as mix-and-read fluorescent assay that exhibits a limit of detection (LOD) 105 CFUs mL-1 . Evaluated with 20 strains of clinical bacterial isolates, the DNAzyme produced the desired fluorescence signal with the samples of K. pneumoniae, regardless of their source or drug resistance. The assay is simple to use, rapid, inexpensive, and avoids the complex procedures of sample preparation and equipment. We believe that this DNAzyme-based fluorescent assay has potential for practical applications to identify K. pneumoniae.
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Affiliation(s)
- M Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada
| | - Anatoly Slepenkin
- Department of Pathology and Laboratory Medicine, University of California, 1001 Health Sciences Road, Irvine, CA, 92697, USA
| | - Ellena Peterson
- Department of Pathology and Laboratory Medicine, University of California, 1001 Health Sciences Road, Irvine, CA, 92697, USA
| | - Weian Zhao
- Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology and, The Department of Biomedical Engineering, University of California-Irvine, 845 Health Sciences Road, Irvine, CA, 92697, USA
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49
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Abstract
Pseudouridylation is the most abundant of all RNA modifications. Pseudouridylation is dynamic and widespread among many different types of RNAs in living organisms, thus drawing a lot of recent interest from the RNA and epigenetics communities. To successfully carry out an investigation into RNA pseudouridylation, it is desirable to have a convenient and effective method capable of detection and quantification of pseudouridylation. Here, we present two such methods: one relies on pseudouridine (Ψ)-specific CMCT modification followed by reverse transcription/primer-extension (semiquantitative), and the other is based on site-specific cleavage and radiolabeling followed by nuclease digestion and TLC (quantitative). Although only semiquantitative, the CMCT and reverse transcription-based method is capable of detecting multiple Ψs (present in the same RNA molecule) in one reaction. In contrast, the second method, based on site-specific cleavage/labeling, nuclease digestion, and TLC, is quantitative, but can be used to analyze only one site at a time. These two methods can be used independently or in combination.
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Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Meemanage D DeZoysa
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA.
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50
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Liu C, Zhang S, Li X, Xue Q, Jiang W. Multi-code magnetic beads based on DNAzyme-mediated double-cycling amplification for a point-of-care assay of telomerase activity. Analyst 2019; 144:4241-4249. [DOI: 10.1039/c9an00589g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of a reliable and facile telomerase activity assay with high specificity and sensitivity is a central challenge to make telomerase testing a routine part of medical care with respect to cancer.
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Affiliation(s)
- Chunxue Liu
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Susu Zhang
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
| | - Xia Li
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
- School of Chemistry and Chemical Engineering
| | - Qingwang Xue
- Department of Chemistry
- Liaocheng University
- Liaocheng
- China
- School of Chemistry and Chemical Engineering
| | - Wei Jiang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
- P.R. China
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