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Qiu D, He F, Liu Y, Zhou Z, Yang Y, Long Z, Chen Q, Chen D, Wei S, Mao X, Zhang X, Mergny JL, Monchaud D, Ju H, Zhou J. A Cost-Effective Hemin-Based Artificial Enzyme Allows for Practical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402237. [PMID: 38924304 DOI: 10.1002/advs.202402237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/24/2024] [Indexed: 06/28/2024]
Abstract
Nanomaterials excel in mimicking the structure and function of natural enzymes while being far more interesting in terms of structural stability, functional versatility, recyclability, and large-scale preparation. Herein, the story assembles hemin, histidine analogs, and G-quadruplex DNA in a catalytically competent supramolecular assembly referred to as assembly-activated hemin enzyme (AA-heminzyme). The catalytic properties of AA-heminzyme are investigated both in silico (by molecular docking and quantum chemical calculations) and in vitro (notably through a systematic comparison with its natural counterpart horseradish peroxidase, HRP). It is found that this artificial system is not only as efficient as HRP to oxidize various substrates (with a turnover number kcat of 115 s-1) but also more practically convenient (displaying better thermal stability, recoverability, and editability) and more economically viable, with a catalytic cost amounting to <10% of that of HRP. The strategic interest of AA-heminzyme is further demonstrated for both industrial wastewater remediation and biomarker detection (notably glutathione, for which the cost is decreased by 98% as compared to commercial kits).
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Affiliation(s)
- Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Fangni He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zhaoxi Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuqin Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zhongwen Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Qianqian Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Shijiong Wei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xuanxiang Mao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, 91120, France
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, Dijon, 21078, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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Zhou W, Lai R, Cheng Y, Bao Y, Miao W, Cao X, Jia G, Li G, Li C. Insights into How NH 4+ Ions Enhance the Activity of Dimeric G-Quadruplex/Hemin DNAzyme. ACS Catal 2023. [DOI: 10.1021/acscatal.2c05905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Wenqin Zhou
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Rui Lai
- State Key Laboratory of Molecular Reaction Dynamics, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Cheng
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Yu Bao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Wenhui Miao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Xupeng Cao
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
| | - Can Li
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Catalysis, Chinese Academy of Sciences, Dalian Institute of Chemical Physics, Dalian 116023, China
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Zhang X, Qiu D, Chen J, Zhang Y, Wang J, Chen D, Liu Y, Cheng M, Monchaud D, Mergny JL, Ju H, Zhou J. Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase. J Am Chem Soc 2023; 145:4517-4526. [PMID: 36795970 DOI: 10.1021/jacs.2c11318] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number kcat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.
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Affiliation(s)
- Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Desheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
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Cao Y, Li W, Pei R. Exploring the catalytic mechanism of multivalent G-quadruplex/hemin DNAzymes by modulating the position and spatial orientation of connected G-quadruplexes. Anal Chim Acta 2022; 1221:340105. [DOI: 10.1016/j.aca.2022.340105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/06/2022] [Accepted: 06/18/2022] [Indexed: 11/15/2022]
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Adeoye RI, Okaiyeto K, Igunnu A, Oguntibeju OO. Systematic mapping of DNAzymes research from 1995 to 2019. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:384-406. [PMID: 35343361 DOI: 10.1080/15257770.2022.2052318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
DNAzymes (catalytic DNA) have gained significant diagnostic and therapeutic applications with increasing research output over the years. Functional oligonucleotides are used as molecular recognition elements within biosensors for detection of analytes and viral infections such as SARS-CoV-2. DNAzymes are also applied for silencing and regulating cancer specific genes. However, there has not been any report on systematic analysis to track research status, reveal hotspots, and map knowledge in this field. Therefore, in the present study, research articles on DNAzymes from 1995 to 2019 were extracted from Web of Science (SCI-Expanded) after which, 1037 articles were imported into Rstudio (version 3.6.2) and analysed accordingly. The highest number of articles was published in 2019 (n = 138), while the least was in 1995 (n = 1). The articles were published across 216 journals by 2344 authors with 2337 multi-author and 7 single authors. The most prolific authors were Li Y (n = 47), Liu J (n = 46), Wang L (n = 33), Willner I (n = 33) and Zhang L (n = 33). The top three most productive countries were China (n = 2018), USA (n = 447) and Canada (n = 251). The most productive institutions were Hunan University, China (n = 141), University of Illinois, USA (n = 139) and Fuzhou University, China (n = 101). Despite the increasing interest in this field, international collaborations between institutions were very low which requires immediate attention to mitigate challenges such as limited funding, access to facilities, and existing knowledge gap.
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Affiliation(s)
- Raphael Idowu Adeoye
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- Biochemistry Unit, Department of Chemistry and Biochemistry, College of Pure and Applied Sciences, Caleb University, Imota, Lagos, Nigeria
| | - Kunle Okaiyeto
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
| | - Adedoyin Igunnu
- Enzymology Unit, Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Oluwafemi Omoniyi Oguntibeju
- Phytomedicine and Phytochemistry Group, Department of Biomedical Sciences, Faculty of Health and Wellness Sciences, Cape Peninsula University of Technology, Bellville, South Africa
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Chen Y, Qiu D, Zhang X, Liu Y, Cheng M, Lei J, Mergny JL, Ju H, Zhou J. Highly Sensitive Biosensing Applications of a Magnetically Immobilizable Covalent G-Quadruplex-Hemin DNAzyme Catalytic System. Anal Chem 2022; 94:2212-2219. [PMID: 35050586 DOI: 10.1021/acs.analchem.1c04842] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
G-quadruplex/hemin (G4/hemin) DNAzymes are biosensing systems, but their application remains limited by an overall low activity and a rather high level of unwarranted background reactions. Here, these issues were addressed through the rational design of F3T-azaC-hemin, a G4-based construct in which the hemin is covalently linked to the G4 core and its binding site flanked with a nucleotide activator, here d(T-azaC). This design led to a G4-DNAzyme whose performances have been ca. 150-fold increased compared to the parent G4-based system. The utility of F3T-azaC-hemin was demonstrated here through the ultrasensitive chemiluminescent detection of miRNA-221. The limit of detection (LOD) has been decreased to the femtomolar range, making it a new and highly efficient molecular tool in the biosensing technology field.
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Affiliation(s)
- Yun Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yuan Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau cedex 91128, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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