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Mao X, Chen Q, Wei S, Qiu D, Zhang X, Lei J, Mergny JL, Ju H, Zhou J. Bioinspired Dual Hemin-Bonded G-Quadruplex and Histidine-Functionalized Metal-Organic Framework for Sensitive Biosensing. Anal Chem 2024. [PMID: 39116285 DOI: 10.1021/acs.analchem.4c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Biomimetic enzymes have emerged as ideal alternatives to natural enzymes, and there is considerable interest in designing biomimetic enzymes with enhanced catalytic performance to address the low activity of the current biomimetic enzymes. In this study, we proposed a meaningful strategy for constructing an efficient peroxidase-mimicking catalyst, called HhG-MOF, by anchoring histidine (H) and dual hemin-G-quadruplex DNAzyme (double hemin covalently linked to 3' and 5' terminals of G-quadruplex DNA, short as hG) to a mesoporous metal-organic framework (MOF). This design aims to mimic the microenvironment of natural peroxidase. Remarkably, taking a terbium MOF as a typical model, the initial rate of the resulting catalyst was found to be 21.1 and 4.3 times higher than that of Hh-MOF and hG-MOF, respectively. The exceptional catalytic properties of HhG-MOF can be attributed to its strong affinity for substrates. Based on the inhibitory effect of thiocholine (TCh) produced by the reaction between acetylcholinesterase (AChE) and acetylthiocholine, a facile, cost-effective, and sensitive colorimetric method was designed based on HhG-MOF for the measurement of AChE, a marker of several neurological diseases, and its inhibitor. This allowed a linear response in the 0.002 to 1 U L-1 range, with a detection limit of 0.001 U L-1. Furthermore, the prepared sensor demonstrated great selectivity and performed well in real blood samples, suggesting that it holds promise for applications in the clinical field.
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Affiliation(s)
- Xuanxiang Mao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
- Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Qianqian Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Shijiong Wei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Pal-aiseau Cedex 91128, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China
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2
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Lai R, Zeng X, Xu Q, Xu Y, Li X, Ru Y, Wang Y, Wang D, Zhou X, Shao Y. Ratiometric G-quadruplex/hemin DNAzymes with low-dosage associative substrates. Anal Chim Acta 2024; 1295:342320. [PMID: 38355221 DOI: 10.1016/j.aca.2024.342320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND G-quadruplex (G4)/hemin DNAzymes with conversion of substrates into colorimetric readouts are well recognized as convenient biocatalysis tools in sensor development. However, the previously developed colorimetric G4/hemin DNAzymes are diffusive substrate-based DNAzymes (DSBDs). The current colorimetric DSBDs have several drawbacks including high dosage (∼mM) of diffusive substrates (DSs), colorimetric product toxicity, and single colorimetric readout without tolerance to fluctuation of experimental factors and background. In addition, the usage of high-dosage DSs can smear the G4 foldings and their discard is more harmful to environment. Therefore, exploring alternative DNAzymes with potential to overcome these drawbacks of DSBDs is urgently needed. RESULTS We herein developed associative substrate-based DNAzymes (ASBDs). Cyanine dyes were selected as associative substrates (ASs) due to their binding competency with G4/hemin DNAzymes. With respect to DSBDs, ASBDs needed only low dosage (∼10 μM) of ASs to be able to cause a rapid and visible substrate conversion. In addition, since cyanine dyes are NIR dyes with high extinction coefficients and their conversion products have absorption bands at shorter wavelength. Therefore, a colorimetric ratio response can be developed to follow activities of G4/hemin DNAzymes with competency to tolerate fluctuation of experimental factors and background. In particular, herein developed ASBDs can endure somewhat concentration fluctuation of H2O2. ASBDs are able to cowork with other enzymes (for example, glucose oxidase) to realize cascade sensing. SIGNIFICANCE The developed ASBDs can operate at low dosage of substrates with a colorimetric ratio response and can overcome the drawbacks met in DSBDs. We expect that, by designing ASs with fruitful color panel in the future, our work will inspire more interesting in developing environment-benign and low-carbon G4/hemin DNAzymes and desired colorful high-performance sensors.
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Affiliation(s)
- Rong Lai
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xingli Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Ying Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xueni Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yulu Ru
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yilin Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, 321004, Zhejiang, PR China.
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Hu Z, Wang D, Zhou Q, Jie J, Su H. Complexed Photosensitizer of Hypericin with G-Quadruplex: Structure-Dependent Behavior. J Phys Chem B 2024; 128:576-584. [PMID: 38189153 DOI: 10.1021/acs.jpcb.3c07307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite the increased interest of visible-light-absorbing compound Hypericin (Hyp) in photodiagnosis, photocatalysis, and photodynamic therapy (PDT) applications, a major obstacle still exists; i.e., the photoactivity is diminished due to the facile aggregation of Hyp in aqueous environment that induces excited-state quenching. Herein, we explore the excited-state property of Hyp bound to the DNA G-quadruplex by combining multiple steady-state and time-resolved spectroscopy. We find that the aggregation-induced quenching effect can be successfully prevented by appropriate G-quadruplex binders that disperse Hyp into monomer. The binding of Hyp/G-quadruplex is selective, however, exhibiting a preferential binding toward parallel G-quadruplexes (c-kit2, C14B1, STAT3, S50, and PS2.M), over antiparallel or hybrid G-quadruplex (Tel22, TBA). The excited-state property of Hyp is highly related to the binding behavior, showing a consistent trend that the better the Hyp/G-quadruplex binding, the longer the triplet 3Hyp* lifetime and the higher the efficiency to produce 1O2. For Hyp/c-kit2, the major binding mode is 5'-end stacking, which offers protection from collisional quenching reactions and ensures a stable photocycle of 3Hyp*-O2 energy transfer forming 1O2, leading to the highest 1O2 quantum yield (0.67) with superior photostability. These findings open possibilities of developing Hyp/G-quadruplex complex as a biocompatible photosensitizer for PDT applications, etc.
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Affiliation(s)
- Zheng Hu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Danfeng Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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Cui Y, Zhang L, Liu J, Zhang T, Sugahara A, Momotake A, Yamamoto Y, Mao ZW, Tai H. Hydrogen Evolution of a Unique DNAzyme Composed of Cobalt-Protoporphyrin IX and G-Quadruplex DNA. CHEMSUSCHEM 2024; 17:e202301244. [PMID: 37681481 DOI: 10.1002/cssc.202301244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/09/2023]
Abstract
Molecular hydrogen (H2 ) is a clean and renewable fuel that has garnered significant interest in the search for alternatives to fossil fuels. Here, we constructed an artificial DNAzyme composed of cobalt-protoporphyrin IX (CoPP) and G-quadruplex DNA, possessing a unique H2 Oint ligand between the CoPP and G-quartet planes. We show for the first time that CoPP-DNAzyme catalyzes photo-induced H2 production under anaerobic conditions with a turnover number (TON) of 1229 ± 51 over 12 h at pH 6.05 and 10 °C. Compared with free-CoPP, complexation with G-quadruplex DNA resulted in a 4.7-fold increase in H2 production activity. The TON of the CoPP-DNAzyme revealed an optimal acid-base equilibrium with a pKa value of 7.60 ± 0.05, apparently originating from the equilibrium between Co(III)-H- and Co(I) states. Our results demonstrate that the H2 Oint ligand can augment and modulate the intrinsic catalytic activity of H2 production catalysts. These systems pave the way to using DNAzymes for H2 evolution in the direct conversion of solar energy to H2 from water.
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Affiliation(s)
- Yue Cui
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Li Zhang
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Jing Liu
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Taozhe Zhang
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
| | - Aya Sugahara
- Department of Chemistry, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba, 305-8571, Japan
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Hulin Tai
- Interdisciplinary Program of Biological Functional Molecules, Department of Chemistry, Yanbian University, Yanji, 133002, Jilin, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, Yanbian University Yanji, 133002, Jilin, China
- National Demonstration Centre for Experimental Chemistry Education, Yanbian University Yanji, 133002, Jilin, China
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5
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Cvjetan N, Schuler LD, Ishikawa T, Walde P. Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate. ACS OMEGA 2023; 8:42878-42899. [PMID: 38024761 PMCID: PMC10652838 DOI: 10.1021/acsomega.3c05915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Iron porphyrins play several important roles in present-day living systems and probably already existed in very early life forms. Hemin (= ferric protoporphyrin IX = ferric heme b), for example, is the prosthetic group at the active site of heme peroxidases, catalyzing the oxidation of a number of different types of reducing substrates after hemin is first oxidized by hydrogen peroxide as the oxidizing substrate of the enzyme. The active site of heme peroxidases consists of a hydrophobic pocket in which hemin is embedded noncovalently and kept in place through coordination of the iron atom to a proximal histidine side chain of the protein. It is this partially hydrophobic local environment of the enzyme which determines the efficiency with which the sequential reactions of the oxidizing and reducing substrates proceed at the active site. Free hemin, which has been separated from the protein moiety of heme peroxidases, is known to aggregate in an aqueous solution and exhibits low catalytic activity. Based on previous reports on the use of surfactant micelles to solubilize free hemin in a nonaggregated state, the peroxidase-like activity of hemin in the presence of sodium dodecyl sulfate (SDS) at concentrations below and above the critical concentration for SDS micelle formation (critical micellization concentration (cmc)) was systematically investigated. In most experiments, 3,3',5,5'-tetramethylbenzidine (TMB) was applied as a reducing substrate at pH = 7.2. The presence of SDS clearly had a positive effect on the reaction in terms of initial reaction rate and reaction yield, even at concentrations below the cmc. The highest activity correlated with the cmc value, as demonstrated for reactions at three different HEPES concentrations. The 4-(2-hydroxyethyl)-1-piperazineethanesulfonate salt (HEPES) served as a pH buffer substance and also had an accelerating effect on the reaction. At the cmc, the addition of l-histidine (l-His) resulted in a further concentration-dependent increase in the peroxidase-like activity of hemin until a maximal effect was reached at an optimal l-His concentration, probably corresponding to an ideal mono-l-His ligation to hemin. Some of the results obtained can be understood on the basis of molecular dynamics simulations, which indicated the existence of intermolecular interactions between hemin and HEPES and between hemin and SDS. Preliminary experiments with SDS/dodecanol vesicles at pH = 7.2 showed that in the presence of the vesicles, hemin exhibited similar peroxidase-like activity as in the case of SDS micelles. This supports the hypothesis that micelle- or vesicle-associated ferric or ferrous iron porphyrins may have played a role as primitive catalysts in membranous prebiotic compartment systems before cellular life emerged.
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Affiliation(s)
- Nemanja Cvjetan
- Department
of Materials, ETH-Zürich, Leopold-Ruzicka-Weg 4, 8093 Zürich, Switzerland
| | | | - Takashi Ishikawa
- Department
of Biology and Chemistry, Paul Scherrer Institute and Department of
Biology, ETH-Zürich, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland
| | - Peter Walde
- Department
of Materials, ETH-Zürich, Leopold-Ruzicka-Weg 4, 8093 Zürich, Switzerland
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6
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Wang X, Liu M, Li Y, Zhou X, Zhang Z, Dong S, Shen M, Wang M, Wang H, Liu L. Development and application of a visualization method for identification of Panax species with LAMP and a DNAzyme. Anal Biochem 2023; 679:115298. [PMID: 37619904 DOI: 10.1016/j.ab.2023.115298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/13/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Panax ginseng and Panax quinquefolium are two valuable Chinese herbal medicines that should not be mixed because they differ in drug properties and efficacy. The traditional identification method is easily affected by subjective factors and cannot effectively distinguish between ginseng products. This study aimed to develop a new chemical analysis method to visually identify P. ginseng and P. quinquefolium. In this method, a large number of sequences containing G-quadruplex were generated by loop-mediated isothermal amplification, and the combination of G-quadruplex and hemin was used to form deoxyribozyme, which catalyzed the color change of H2O2. Artificial simulation of adulteration experiments revealed that this method could detect more than 20% adulterated P. quinquefolium. Compared with the traditional identification methods, this technology was simpler and more efficient, providing a reference for developing rapid visual identification methods and reagents for P. ginseng and P. quinquefolium.
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Affiliation(s)
- Xiangjun Wang
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Moyi Liu
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Ying Li
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Xinchen Zhou
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Zhuo Zhang
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Shuhan Dong
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Mingmei Shen
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Minghui Wang
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Helin Wang
- College of Medical Technology, Beihua University, Jilin, 132000, China
| | - Limei Liu
- College of Medical Technology, Beihua University, Jilin, 132000, China.
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7
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Kamra A, Das S, Bhatt P, Solra M, Maity T, Rana S. A transient vesicular glue for amplification and temporal regulation of biocatalytic reaction networks. Chem Sci 2023; 14:9267-9282. [PMID: 37712020 PMCID: PMC10498679 DOI: 10.1039/d3sc00195d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/27/2023] [Indexed: 09/16/2023] Open
Abstract
Regulation of enzyme activity and biocatalytic cascades on compartmentalized cellular components is key to the adaptation of cellular processes such as signal transduction and metabolism in response to varying external conditions. Synthetic molecular glues have enabled enzyme inhibition and regulation of protein-protein interactions. So far, all the molecular glue systems based on covalent interactions operated under steady-state conditions. To emulate dynamic biological processes under dissipative conditions, we introduce herein a transient supramolecular glue with a controllable lifetime. The transient system uses multivalent supramolecular interactions between guanidinium group-bearing surfactants and adenosine triphosphate (ATP), resulting in bilayer vesicle structures. Unlike the conventional chemical agents for dissipative assemblies, ATP here plays the dual role of providing a structural component for the assembly as well as presenting active functional groups to "glue" enzymes on the surface. While gluing of the enzymes on the vesicles achieves augmented catalysis, oscillation of ATP concentration allows temporal control of the catalytic activities similar to the dissipative cellular nanoreactors. We further demonstrate temporal upregulation and control of complex biocatalytic reaction networks on the vesicles. Altogether, the temporal activation of biocatalytic cascades on the dissipative vesicular glue presents an adaptable and dynamic system emulating heterogeneous cellular processes, opening up avenues for effective protocell construction and therapeutic interventions.
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Affiliation(s)
- Alisha Kamra
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Sourav Das
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Preeti Bhatt
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Manju Solra
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Tanmoy Maity
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
| | - Subinoy Rana
- Materials Research Centre, Indian Institute of Science C.V. Raman Road Bangalore 560012 Karnataka India +9180-22932914
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8
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Ma J, Guan Y, Xing F, Wang Y, Li X, Yu Q, Yu X. Smartphone-based chemiluminescence detection of aflatoxin B 1 via labelled and label-free dual sensing systems. Food Chem 2023; 413:135654. [PMID: 36796268 DOI: 10.1016/j.foodchem.2023.135654] [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: 10/12/2022] [Revised: 01/24/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
To develop a sensing platform for onsite determination of AFB1 in foodstuffs, we developed smartphone-based chemiluminescence detection of AFB1 via labelled and label-free dual modes. The labelled mode was characteristic of double streptavidin-biotin mediated signal amplification, obtaining limit of detection (LOD) of 0.04 ng/mL in the linear range of 1-100 ng/mL. To reduce the complexity in the labelled system, a label-free mode based on both split aptamer and split DNAzyme was fabricated. A satisfactory LOD of 0.33 ng/mL was generated in the linear range of 1-100 ng/mL. Both labelled and label-free sensing systems achieved outstanding recovery rate in AFB1-spiked maize and peanut kernel samples. Finally, two systems were successfully integrated into smartphone-based portable device based on custom-made components and android application, achieving comparable AFB1 detection ability to a commercial microplate reader. Our systems hold huge potential for AFB1 onsite detection in food supply chain.
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Affiliation(s)
- Junning Ma
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yue Guan
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Fuguo Xing
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Wang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xu Li
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiang Yu
- Qingdao Tianxiang Foods Group Co., Ltd, Qingdao 266737, China
| | - Xiaohua Yu
- Qingdao Tianxiang Foods Group Co., Ltd, Qingdao 266737, China
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9
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Bhuyan SK, Wang L, Jinata C, Kinghorn AB, Liu M, He W, Sharma R, Tanner JA. Directed Evolution of a G-Quadruplex Peroxidase DNAzyme and Application in Proteomic DNAzyme-Aptamer Proximity Labeling. J Am Chem Soc 2023. [PMID: 37276197 DOI: 10.1021/jacs.3c02625] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNAzymes have been limited in application by their low catalytic rates. Here, we evolved a new peroxidase DNAzyme mSBDZ-X-3 through a directed evolution method based on the capture of self-biotinylated DNA catalyzed by its intrinsic peroxidase activity. The mSBDX-X-3 DNAzyme has a parallel G-quadruplex structure and has more favorable catalytic properties than all previously reported peroxidase DNAzyme variants. We applied mSBDZ-X-3 in an aptamer-coupled proximity-based labeling proteomic assay to determine the proteins that bind to cell surface cancer biomarkers EpCAM and nucleolin. Confocal microscopy, western blot analysis, and LC-MS/MS showed that the hybrid DNAzyme aptamer-coupled proximity assay-labeled proteins associated with EpCAM and nucleolin within 6-12 min in fixed cancer cells. The labeled proteins were identified by mass spectrometry. This study provides a highly efficient peroxidase DNAzyme, a methodology for selection of such variants, and a method for its application in spatial proteomics using entirely nucleic acid-based tooling.
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Affiliation(s)
- Soubhagya K Bhuyan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Lin Wang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Chandra Jinata
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mengping Liu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Weisi He
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rakesh Sharma
- Proteomics and Metabolomics Core Facility, Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
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10
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Abstract
Enzymes fold into three-dimensional structures to distribute amino acid residues for catalysis, which inspired the supramolecular approach to construct enzyme-mimicking catalysts. A key concern in the development of supramolecular strategies is the ability to confine and orient functional groups to form enzyme-like active sites in artificial materials. This review introduces the design principles and construction of supramolecular nanomaterials exhibiting catalytic functions of heme-dependent enzymes, a large class of metalloproteins, which rely on a heme cofactor and spatially configured residues to catalyze diverse reactions via a complex multistep mechanism. We focus on the structure-activity relationship of the supramolecular catalysts and their applications in materials synthesis/degradation, biosensing, and therapeutics. The heme-free catalysts that catalyze reactions achieved by hemeproteins are also briefly discussed. Towards the end of the review, we discuss the outlook on the challenges related to catalyst design and future prospective, including the development of structure-resolving techniques and design concepts, with the aim of creating enzyme-mimicking materials that possess catalytic power rivaling that of natural enzymes..
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Affiliation(s)
- Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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11
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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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12
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Iwaniuk EE, Adebayo T, Coleman S, Villaros CG, Nesterova IV. Activatable G-quadruplex based catalases for signal transduction in biosensing. Nucleic Acids Res 2023; 51:1600-1607. [PMID: 36727464 PMCID: PMC9976883 DOI: 10.1093/nar/gkad031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 02/03/2023] Open
Abstract
Discovery of oxidative catalysis with G-quadruplex•hemin constructs prompted a range of exciting developments in the field of biosensor design. Thus, G-quadruplex based DNAzymes with peroxidase activity found a niche as signal transduction modules in a wide range of analytical applications. The ability of nucleic acid scaffolds to recognise a variety of practically meaningful markers and to translate the recognition events into conformational changes powers numerous sensor design possibilities. In this work, we establish a catalase activity of G-quadruplex•hemin scaffolds. Catalase activated hydrogen peroxide decomposition generates molecular oxygen that forms bubbles. Observation of bubbles is a truly equipment free signal readout platform that is highly desirable in limited resources or do-it-yourself environments. We take a preliminary insight into a G-quadruplex structure-folding topology-catalase activity correlation and establish efficient operating conditions. Further, we demonstrate the platform's potential as a signal transduction modality for reporting on biomolecular recognition using an oligonucleotide as a proof-of-concept target. Ultimately, activatable catalases based on G-quadruplex•hemin scaffolds promise to become valuable contributors towards accessible molecular diagnostics applications.
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Affiliation(s)
- Elzbieta E Iwaniuk
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Thuwebat Adebayo
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Seth Coleman
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Caitlin G Villaros
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
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13
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Qiao L, Lang W, Sun C, Huang Y, Wu P, Cai C, Xing B. Near Infrared-II Photothermal and Colorimetric Synergistic Sensing for Intelligent Onsite Dietary Myrosinase Profiling. Anal Chem 2023; 95:3856-3863. [PMID: 36756955 DOI: 10.1021/acs.analchem.2c05474] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Myrosinase (Myr) is a type of critical β-thioglucosidase enzyme activator essential for sustaining many functional foods to perform their health-promoting functions. An accurate and reliable Myr test is meaningful for food quality and dietary nutrition assessments, whereas the currently reported methods do not guarantee specificity and have high reliance on instrumentation, which are not suitable for rapid and onsite Myr screening especially in complex systems from various sources. Herein, we present a unique NIR-II absorption-based photothermal-responsive colorimetric biosensor for anti-interference onsite Myr determination and realization of rapid visualized outputs with the aid of smartphone calculation. Typically, assisted by glucose oxidase (GOx), Myr specifically converts the sinigrin substrate into hydrogen peroxide (H2O2) that can oxidize 3,3',5,5'-tetramethylbenzidine (TMB) catalyzed by AuNPs to form a charge transfer complex (CTC) with NIR-II absorption and photothermal characters. Delightfully, such a proposed method is able to determine Myr within a wide range of 0 to 172.5 mU/mL with a detection limit down to 2.96 mU/mL. Moreover, simple, rapid, and real-time visual Myr identification in actual food-sourced samples could also be readily achieved by smartphone readout processing, with the promising advantages of anti-interference, high accuracy, and low cost as well as labor-saving and intelligence engagement, thus providing great feasibility for precise measurement in complex and dynamic dietary sample analysis. Overall, our proposed method presents a novel technology for onsite dietary Myr enzyme profiling, which is promising to be applied in the food industry for nutritional composition profiles, freshness evaluation, and quality assessment.
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Affiliation(s)
- Ling Qiao
- School of Chemistry, Chemical Engineering & Biotechnology, Nanyang Technological University, Singapore 637371, Singapore.,Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Wenchao Lang
- School of Chemistry, Chemical Engineering & Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Caixia Sun
- School of Chemistry, Chemical Engineering & Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Yining Huang
- School of Chemistry, Chemical Engineering & Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
| | - Ping Wu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P. R. China
| | - Bengang Xing
- School of Chemistry, Chemical Engineering & Biotechnology, Nanyang Technological University, Singapore 637371, Singapore
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14
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Abstract
Ferric heme b (= ferric protoporphyrin IX = hemin) is an important prosthetic group of different types of enzymes, including the intensively investigated and widely applied horseradish peroxidase (HRP). In HRP, hemin is present in monomeric form in a hydrophobic pocket containing among other amino acid side chains the two imidazoyl groups of His170 and His42. Both amino acids are important for the peroxidase activity of HRP as an axial ligand of hemin (proximal His170) and as an acid/base catalyst (distal His42). A key feature of the peroxidase mechanism of HRP is the initial formation of compound I under heterolytic cleavage of added hydrogen peroxide as a terminal oxidant. Investigations of free hemin dispersed in aqueous solution showed that different types of hemin dimers can form, depending on the experimental conditions, possibly resulting in hemin crystallization. Although it has been recognized already in the 1970s that hemin aggregation can be prevented in aqueous solution by using micelle-forming amphiphiles, it remains a challenge to prepare hemin-containing micellar and vesicular systems with peroxidase-like activities. Such systems are of interest as cheap HRP-mimicking catalysts for analytical and synthetic applications. Some of the key concepts on which research in this fascinating and interdisciplinary field is based are summarized, along with major accomplishments and possible directions for further improvement. A systematic analysis of the physico-chemical properties of hemin in aqueous micellar solutions and vesicular dispersions must be combined with a reliable evaluation of its catalytic activity. Future studies should show how well the molecular complexity around hemin in HRP can be mimicked by using micelles or vesicles. Because of the importance of heme b in virtually all biological systems and the fact that porphyrins and hemes can be obtained under potentially prebiotic conditions, ideas exist about the possible role of heme-containing micellar and vesicular systems in prebiotic times.
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15
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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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16
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Gan Z, Zhang T, An X, Tan Q, Zhen S, Hu Y, Hu X. Dual enzyme-mimicking fluorescent amino terephthalic acid/CuFe/adenosine triphosphate nanoparticles for determination of H2O2 and ascorbic acid. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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17
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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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18
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Mao X, He F, Qiu D, Wei S, Luo R, Chen Y, Zhang X, Lei J, Monchaud D, Mergny JL, Ju H, Zhou J. Efficient Biocatalytic System for Biosensing by Combining Metal-Organic Framework (MOF)-Based Nanozymes and G-Quadruplex (G4)-DNAzymes. Anal Chem 2022; 94:7295-7302. [PMID: 35549161 DOI: 10.1021/acs.analchem.2c00600] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A high catalytic efficiency associated with a robust chemical structure are among the ultimate goals when developing new biocatalytic systems for biosensing applications. To get ever closer to these goals, we report here on a combination of metal-organic framework (MOF)-based nanozymes and a G-quadruplex (G4)-based catalytic system known as G4-DNAzyme. This approach aims at combining the advantages of both partners (chiefly, the robustness of the former and the modularity of the latter). To this end, we used MIL-53(Fe) MOF and linked it covalently to a G4-forming sequence (F3TC), itself covalently linked to its cofactor hemin. The resulting complex (referred to as MIL-53(Fe)/G4-hemin) exhibited exquisite peroxidase-mimicking oxidation activity and an excellent robustness (being stored in water for weeks). These properties were exploited to devise a new biosensing system based on a cascade of reactions catalyzed by the nanozyme (ABTS oxidation) and an enzyme, the alkaline phosphatase (or ALP, ascorbic acid 2-phosphate dephosphorylation). The product of the latter poisoning the former, we thus designed a biosensor for ALP (a marker of bone diseases and cancers), with a very low limit of detection (LOD, 0.02 U L-1), which is operative in human plasma samples.
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Affiliation(s)
- Xuanxiang Mao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Fangni He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Dehui Qiu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Shijiong Wei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Rengan Luo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yun Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jianping Lei
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR 6302, UBFC, Dijon 21078, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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19
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Cvjetan N, Kissner R, Bajuk-Bogdanović D, Ćirić-Marjanović G, Walde P. Hemin-catalyzed oxidative oligomerization of p-aminodiphenylamine (PADPA) in the presence of aqueous sodium dodecylbenzenesulfonate (SDBS) micelles. RSC Adv 2022; 12:13154-13167. [PMID: 35520130 PMCID: PMC9063397 DOI: 10.1039/d2ra02198f] [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: 04/05/2022] [Accepted: 04/18/2022] [Indexed: 11/23/2022] Open
Abstract
In a previous report on the enzymatic synthesis of the conductive emeraldine salt form of polyaniline (PANI-ES) in aqueous solution using PADPA (p-aminodiphenylamine) as monomer, horseradish peroxidase isoenzyme C (HRPC) was applied as a catalyst at pH = 4.3 with H2O2 as a terminal oxidant. In that work, anionic vesicles were added to the reaction mixture for (i) guiding the reaction to obtain poly(PADPA) products that resemble PANI-ES, and for (ii) preventing product precipitation (known as the “template effect”). In the work now presented, instead of native HRPC, only its prosthetic group ferric heme b (= hemin) was utilized as a catalyst, and micelles formed from SDBS (sodium dodecylbenzenesulfonate) served as templates. For the elaborated optimal reaction conditions, complementary UV/vis/NIR, EPR, and Raman spectroscopy measurements clearly showed that the reaction mixture obtained after completion of the reaction contained PANI-ES-like products as dominating species, very similar to the products formed with HRPC as catalyst. HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonate) was found to have a positive effect on the reaction rate as compared to dihydrogenphosphate. This work is the first on the template-assisted formation of PANI-ES type products under mild, environmentally friendly conditions using hemin as a cost-effective catalyst. Polyaniline emeraldine salt-type products were synthesized under mild, environmentally friendly conditions using hemin as a cost-effective catalyst, p-aminodiphenylamine (PADPA) as a monomer, and micelles formed from SDBS as templates.![]()
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Affiliation(s)
- Nemanja Cvjetan
- Department of Materials, Laboratory for Multifunctional Materials, ETH Zürich Vladimir-Prelog-Weg 5 8093 Zürich Switzerland
| | - Reinhard Kissner
- Department of Chemistry and Applied Biosciences, Laboratory of Inorganic Chemistry Vladimir-Prelog-Weg 2 8093 Zürich Switzerland
| | - Danica Bajuk-Bogdanović
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16 11158 Belgrade Serbia
| | - Gordana Ćirić-Marjanović
- Faculty of Physical Chemistry, University of Belgrade Studentski trg 12-16 11158 Belgrade Serbia
| | - Peter Walde
- Department of Materials, Laboratory for Multifunctional Materials, ETH Zürich Vladimir-Prelog-Weg 5 8093 Zürich Switzerland
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20
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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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21
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Shokri E, Hosseini M, Boldaji MN, Shahsavar K, amiri-Sadeghan A, Nasiri N, Bahmani A, Ganjali MR, Saboury AA. A novel DNA/hemin complex with enzyme-like activity selected from a hairpin DNAs library at zero H2O2 concentration. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Controllable bisubstrate multi-colorimetric assay based on peroxidase-like nanozyme and complementary colorharmonic principle for semi-quantitative detection of H2O2 with the naked eye. Mikrochim Acta 2022; 189:81. [DOI: 10.1007/s00604-022-05169-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/27/2021] [Indexed: 11/26/2022]
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23
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Dervisevic E, Voelcker NH, Risbridger G, Tuck KL, Cadarso VJ. Colorimetric Detection of Extracellular Hydrogen Peroxide Using an Integrated Microfluidic Device. Anal Chem 2022; 94:1726-1732. [PMID: 35014786 DOI: 10.1021/acs.analchem.1c04312] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
It is well known that hydrogen peroxide (H2O2) is a signaling molecule essential for vital physiological reactions in mammalian cells, such as cell survival, intercellular communication, and cancer metabolism. However, to fully understand the function of H2O2, it is critical to monitor its intracellular and/or extracellular concentrations. Current techniques implemented to address this need require large sample volumes, expensive instrumentation, and long sample preparation and analysis times, inapplicable to inline or online monitoring. In this paper, a new integrated microfluidic device capable of overcoming these limitations is demonstrated for the colorimetric detection of extracellular hydrogen peroxide H2O2. The device contains an optical waveguide to determine absorbance changes and micromixers to enable complete mixing of reagents using a passive approach. This novel H2O2-sensing device has allowed the detection of H2O2 in the range of 0.5-60 μM with a detection limit of 167 ± 5.8 nM and a sensitivity of 13.5 ± 0.1 AU/mM. Proof of concept of the device was demonstrated by quantifying H2O2 release from benign prostatic epithelial (BPH-1) cells upon stimulation with phorbol 12-myristate 13-acetate (PMA). Results show that this integrated device can be potentially utilized to continuously monitor cell-released metabolites autonomously without constant human supervision during the process. Furthermore, this can be achieved without interfering with the cell culture conditions, as only a very small volume of conditioned media (less than 0.4 μL), and not the cells, is required.
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Affiliation(s)
- Esma Dervisevic
- Department of Mechanical and Aerospace Engineering, Monash University, Room 227, New Horizons Building, 20 Research Way, Clayton, Melbourne, Victoria 3800, Australia
| | - Nicolas H Voelcker
- Monash Institute of Pharmaceutical Sciences (MIPS), Monash University, 381 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia.,The Melbourne Centre for Nanofabrication, Victorian Node - Australian National Fabrication Facility, Clayton, Melbourne, Victoria 3800, Australia.,Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, Melbourne, Victoria 3168, Australia
| | - Gail Risbridger
- Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.,Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Melbourne, Victoria 3800, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
| | - Kellie L Tuck
- School of Chemistry, Monash University, Clayton, Melbourne, Victoria 3800, Australia
| | - Victor J Cadarso
- Department of Mechanical and Aerospace Engineering, Monash University, Room 227, New Horizons Building, 20 Research Way, Clayton, Melbourne, Victoria 3800, Australia.,The Melbourne Centre for Nanofabrication, Victorian Node - Australian National Fabrication Facility, Clayton, Melbourne, Victoria 3800, Australia.,Centre to Impact Antimicrobial Resistance─Sustainable Solutions, Monash University, Clayton, Melbourne, Victoria 3800 Australia
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24
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Mo F, Zhang M, Duan X, Lin C, Sun D, You T. Recent Advances in Nanozymes for Bacteria-Infected Wound Therapy. Int J Nanomedicine 2022; 17:5947-5990. [PMID: 36510620 PMCID: PMC9739148 DOI: 10.2147/ijn.s382796] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/05/2022] [Indexed: 12/12/2022] Open
Abstract
Bacterial-infected wounds are a serious threat to public health. Bacterial invasion can easily delay the wound healing process and even cause more serious damage. Therefore, effective new methods or drugs are needed to treat wounds. Nanozyme is an artificial enzyme that mimics the activity of a natural enzyme, and a substitute for natural enzymes by mimicking the coordination environment of the catalytic site. Due to the numerous excellent properties of nanozymes, the generation of drug-resistant bacteria can be avoided while treating bacterial infection wounds by catalyzing the sterilization mechanism of generating reactive oxygen species (ROS). Notably, there are still some defects in the nanozyme antibacterial agents, and the design direction is to realize the multifunctionalization and intelligence of a single system. In this review, we first discuss the pathophysiology of bacteria infected wound healing, the formation of bacterial infection wounds, and the strategies for treating bacterially infected wounds. In addition, the antibacterial advantages and mechanism of nanozymes for bacteria-infected wounds are also described. Importantly, a series of nanomaterials based on nanozyme synthesis for the treatment of infected wounds are emphasized. Finally, the challenges and prospects of nanozymes for treating bacterial infection wounds are proposed for future research in this field.
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Affiliation(s)
- Fayin Mo
- School of Nursing, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
- Center for Drug Research and Development, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Minjun Zhang
- School of Nursing, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Xuewei Duan
- School of Nursing, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Chuyan Lin
- School of Nursing, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Duanping Sun
- Center for Drug Research and Development, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
- Correspondence: Duanping Sun; Tianhui You, Email ;
| | - Tianhui You
- School of Nursing, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
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25
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Conzemius R, Haunold A, Barišić I. Padlock Probe-Based Generation of DNAzymes for the Colorimetric Detection of Antibiotic Resistance Genes. Int J Mol Sci 2021; 22:ijms222413654. [PMID: 34948456 PMCID: PMC8715668 DOI: 10.3390/ijms222413654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
The increasing emergence of multidrug- and pan-resistant pathogens requires rapid and cost-efficient diagnostic tools to contain their further spread in healthcare facilities and the environment. The currently established diagnostic technologies are of limited utility for efficient infection control measures because they are either cultivation-based and time-consuming or require sophisticated assays that are expensive. Furthermore, infectious diseases are unfortunately most problematic in countries with low-resource settings in their healthcare systems. In this study, we developed a cost-efficient detection technology that uses G-quadruplex DNAzymes to convert a chromogenic substrate resulting in a color change in the presence of antibiotic resistance genes. The assay is based on padlock probes capable of high-multiplex reactions and targets 27 clinically relevant antibiotic resistance genes associated with sepsis. In addition to an experimental proof-of-principle using synthetic target DNA, the assay was evaluated with multidrug-resistant clinical isolates.
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26
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Li J, Wu H, Yan Y, Yuan T, Shu Y, Gao X, Zhang L, Li S, Ding S, Cheng W. Zippered G-quadruplex/hemin DNAzyme: exceptional catalyst for universal bioanalytical applications. Nucleic Acids Res 2021; 49:13031-13044. [PMID: 34878146 PMCID: PMC8682752 DOI: 10.1093/nar/gkab1178] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/09/2021] [Accepted: 11/17/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplex (G4)/hemin DNAzyme is promising horseradish peroxidase (HRP)-mimic candidate in the biological field. However, its relatively unsatisfactory catalytic capacity limits the potential applications. Inspired by nature protease, we conducted a proximity-enhanced cofactor assembly strategy (PECA) to form an exceptional HRP mimic, namely zippered G4/hemin DNAzyme (Z-G4/H). The hybridization of short oligonucleotides induced proximity assembly of the DNA-grafted hemin (DGH) with the complementary G4 sequences (cG4s), mimicking the tight configuration of protease cofactor and apoenzyme. The detailed investigations of catalytic efficiency and mechanism verified the higher activity, more rapid catalytic rate and high environmental tolerance of the Z-G4/H than the classical G4/hemin DNAzymes (C-G4/H). Furthermore, a proximity recognition transducer has been developed based on the PECA for sensitive detection of gene rearrangement and imaging human epidermal growth factor receptor 2 protein (HER2) dimerization on cell surfaces. Our studies demonstrate the high efficiency of Z-G4/H and its universal application potential in clinical diagnostics and biomolecule interaction research. It also may offer significant opportunities and inspiration for the engineering of the protease-free mimic enzyme.
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Affiliation(s)
- Jia Li
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Taixian Yuan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yue Shu
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xin Gao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Lu Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Siqiao Li
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
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27
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Keijzer JF, Albada B. DNA-assisted site-selective protein modification. Biopolymers 2021; 113:e23483. [PMID: 34878181 PMCID: PMC9285461 DOI: 10.1002/bip.23483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/09/2022]
Abstract
Protein modification is important for various types of biomedical research, including proteomics and therapeutics. Many methodologies for protein modification exist, but not all possess the required level of efficiency and site selectivity. This review focuses on the use of DNA to achieve the desired conversions and levels of accuracy in protein modification by using DNA (i) as a template to help concentrate dilute reactants, (ii) as a guidance system to achieve selectivity by binding specific proteins, and (iii) even as catalytic entity or construct to enhance protein modification reactions.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, The Netherlands
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28
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Hagiwara S, Momotake A, Ogura T, Yanagisawa S, Suzuki A, Neya S, Yamamoto Y. Effects of Heme Electronic Structure and Local Heme Environment on Catalytic Activity of a Peroxidase-Mimicking Heme-DNAzyme. Inorg Chem 2021; 60:11206-11213. [PMID: 34289695 DOI: 10.1021/acs.inorgchem.1c01179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catalytic cycle of a peroxidase-mimicking heme-DNAzyme involves an iron(IV)oxo porphyrin π-cation radical intermediate known as compound I formed through heterolytic O-O bond cleavage of an Fe3+-bound hydroperoxo ligand (Fe-OOH) in compound 0, like that of a heme enzyme such as horseradish peroxidase (HRP). Peroxidase assaying of complexes composed of chemically modified hemes possessing various electron densities of the heme iron atom (ρFe) and parallel-stranded tetrameric G-quadruplex DNAs of oligonucleotides d(TTAGGG), d(TTAGGGT), and d(TTAGGGA) was performed to elucidate the effects of the heme electronic structure and local heme environment on the catalytic activity of the heme-DNAzyme. The study revealed that the DNAzyme activity is enhanced through an increase in the ρFe and general base catalysis of the adenine base adjacent to the heme, which are reminiscent of the "push" and "pull" mechanisms in the catalytic cycle of HRP, respectively, and that the activity of the heme-DNAzyme can be independently controlled through the heme electronic structure and local heme environment. These findings allow a deeper understanding of the structure-function relationship of the peroxidase-mimicking heme-DNAzyme.
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Affiliation(s)
- Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takashi Ogura
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Akihiro Suzuki
- Department of Material Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan.,Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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29
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Liu Q, Zhang A, Wang R, Zhang Q, Cui D. A Review on Metal- and Metal Oxide-Based Nanozymes: Properties, Mechanisms, and Applications. NANO-MICRO LETTERS 2021; 13:154. [PMID: 34241715 PMCID: PMC8271064 DOI: 10.1007/s40820-021-00674-8] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 05/31/2021] [Indexed: 05/19/2023]
Abstract
Since the ferromagnetic (Fe3O4) nanoparticles were firstly reported to exert enzyme-like activity in 2007, extensive research progress in nanozymes has been made with deep investigation of diverse nanozymes and rapid development of related nanotechnologies. As promising alternatives for natural enzymes, nanozymes have broadened the way toward clinical medicine, food safety, environmental monitoring, and chemical production. The past decade has witnessed the rapid development of metal- and metal oxide-based nanozymes owing to their remarkable physicochemical properties in parallel with low cost, high stability, and easy storage. It is widely known that the deep study of catalytic activities and mechanism sheds significant influence on the applications of nanozymes. This review digs into the characteristics and intrinsic properties of metal- and metal oxide-based nanozymes, especially emphasizing their catalytic mechanism and recent applications in biological analysis, relieving inflammation, antibacterial, and cancer therapy. We also conclude the present challenges and provide insights into the future research of nanozymes constituted of metal and metal oxide nanomaterials.
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Affiliation(s)
- Qianwen Liu
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Center for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan RD, Shanghai, 200240, People's Republic of China
- Institute of Nano Biomedicine, National Engineering Research Center for Nanotechnology, 28 Jiangchuan Easternroad, Shanghai, 200241, People's Republic of China
| | - Amin Zhang
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Center for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan RD, Shanghai, 200240, People's Republic of China.
- Institute of Nano Biomedicine, National Engineering Research Center for Nanotechnology, 28 Jiangchuan Easternroad, Shanghai, 200241, People's Republic of China.
| | - Ruhao Wang
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Center for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan RD, Shanghai, 200240, People's Republic of China
- Institute of Nano Biomedicine, National Engineering Research Center for Nanotechnology, 28 Jiangchuan Easternroad, Shanghai, 200241, People's Republic of China
| | - Qian Zhang
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Center for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan RD, Shanghai, 200240, People's Republic of China
- Institute of Nano Biomedicine, National Engineering Research Center for Nanotechnology, 28 Jiangchuan Easternroad, Shanghai, 200241, People's Republic of China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Shanghai Engineering Research Center for Intelligent Diagnosis and Treatment Instrument, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan RD, Shanghai, 200240, People's Republic of China.
- Institute of Nano Biomedicine, National Engineering Research Center for Nanotechnology, 28 Jiangchuan Easternroad, Shanghai, 200241, People's Republic of China.
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30
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The catalytic properties of DNA G-quadruplexes rely on their structural integrity. CHINESE JOURNAL OF CATALYSIS 2021. [DOI: 10.1016/s1872-2067(20)63744-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Yang H, Wang J, Li X, Zhang L, Yu H, Zhang L, Ge S, Yu J, Zhang Y. Self-Circulation Oxygen-Hydrogen Peroxide-Oxygen System for Ultrasensitive Cathode Photoelectrochemical Bioassay Using a Stacked Sealed Paper Device. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19793-19802. [PMID: 33886262 DOI: 10.1021/acsami.1c03891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this work, a self-circulation oxygen-hydrogen peroxide-oxygen (O2-H2O2-O2) system with photogenerated electrons as fuel and highly active hemin monomers as operators was engineered for ultrasensitive cathode photoelectrochemical bioassay of microRNA-141 (miRNA-141) using a stacked sealed paper device. During the circulation, the photogenerated electrons from BiVO4/Cu2O photosensitive structures assembled on a reduced graphene oxide paper electrode first reduced the electron acceptors (dissolved O2) to H2O2, which was then catalytically decomposed by hemin monomers to generate O2 again. The regenerated O2 continued to be reduced, which made O2 and H2O2 stuck in the infinite loop of O2-H2O2-O2 accompanied by the fast consumption of photogenerated electrons, generating an amplified photocurrent signal. When a target existed, a duplex-specific nuclease-induced target recycling reaction with dual trigger DNA probes as the output was performed to initiate the assembly of bridge-like DNA nanostructures, which endowed the self-circulation system with dual destruction functions as follows. (i) Reduced fuel supply: the assembled DNA bridges acting as a negatively charged barrier prevented the photogenerated electrons from participating in the O2 reduction to H2O2. (ii) Incapacitation of operators: DNA bridging induced the dimerization of hemin monomers linked on the DNA hairpins to catalytically inactive hemin dimers, leading to the abortive regeneration of O2. These destruction functions resulted in the circulation interruption and a remarkably decreased photocurrent signal. Thus, the developed cathode photoelectrochemical biosensing platform achieved ultrasensitive miRNA-141 detection with a linear range of 0.25 fM to 1 nM and a detection limit of 83 aM, and it also exhibited high accuracy, selectivity, and practicability.
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Affiliation(s)
- Hongmei Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Jiajun Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Xiao Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Letao Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Haihan Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Lina Zhang
- Shandong Provincial Key Laboratory of Preparation and Measurement of Building Materials, University of Jinan, Jinan 250022, P. R. China
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan 250022, P. R. China
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
| | - Yan Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, P. R. China
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32
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Citartan M. Aptamers as the powerhouse of dot blot assays. Talanta 2021; 232:122436. [PMID: 34074421 DOI: 10.1016/j.talanta.2021.122436] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022]
Abstract
Dot blot assays have always been associated with antibodies as the main molecular recognition element, which are widely employed in a myriad of diagnostic applications. With the rising of aptamers as the equivalent molecular recognition elements of antibodies, dot blot assays are also one of the diagnostic avenues that should be scrutinized for their amenability with aptamers as the potential surrogates of antibodies. In this review, the stepwise procedures of an aptamer-based dot blot assays are underscored before reviewing the existing aptamer-based dot blot assays developed so far. Most of the applications center on monitoring the progress of SELEX and as the validatory assays to assess the potency of aptamer candidates. For the purpose of diagnostics, the current effort is still languid and as such possible suggestions to galvanize the move to spur the aptamer-based dot blot assays to a point-of-care arena are discussed.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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33
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Ahmadi Y, Soldo R, Rathammer K, Eibler L, Barišić I. Analyzing Criteria Affecting the Functionality of G-Quadruplex-Based DNA Aptazymes as Colorimetric Biosensors and Development of Quinine-Binding Aptazymes. Anal Chem 2021; 93:5161-5169. [PMID: 33724777 DOI: 10.1021/acs.analchem.0c05052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A DNA aptazyme consists of an aptamer domain and a DNAzyme module, in which the DNAzyme activity can be regulated by the aptamer-target interaction. The complex of G-quadruplex (GQ) and hemin is a peroxidase-mimicking DNAzyme and has become increasingly popular as a reporter system for biosensing applications. The development of GQ-based aptazymes is of high interest as they can be used as label-free biosensors for the real-time detection of pathogens. Herein, we rationally designed ca. 200 GQ-based aptazyme candidates and evaluated the suitability of 14 aptamers targeting quinine, Protein A, Staphylococcus enterotoxin B, and ATP for this detection concept. As a result, six novel aptazymes were developed for the specific detection of quinine based on two quinine-binding aptamers. The rest of designed probes, however, hardly showed significant functionality. To uncover the reasons, we performed enzyme-linked oligonucleotide assays to find how the affinity of aptamers is affected once conjugated to the DNAzyme sequence or upon integration into the aptazyme probe. Furthermore, we investigated the impact of the structure-switching functionality in the parent aptamer and the effect of the reaction matrix on the efficiency of probes.
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Affiliation(s)
- Yasaman Ahmadi
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Regina Soldo
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Krista Rathammer
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Laura Eibler
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
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34
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Shumayrikh NM, Warren JJ, Bennet AJ, Sen D. A heme•DNAzyme activated by hydrogen peroxide catalytically oxidizes thioethers by direct oxygen atom transfer rather than by a Compound I-like intermediate. Nucleic Acids Res 2021; 49:1803-1815. [PMID: 33476369 PMCID: PMC7913675 DOI: 10.1093/nar/gkab007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/31/2020] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
Hemin [Fe(III)-protoporphyrin IX] is known to bind tightly to single-stranded DNA and RNA molecules that fold into G-quadruplexes (GQ). Such complexes are strongly activated for oxidative catalysis. These heme•DNAzymes and ribozymes have found broad utility in bioanalytical and medicinal chemistry and have also been shown to occur within living cells. However, how a GQ is able to activate hemin is poorly understood. Herein, we report fast kinetic measurements (using stopped-flow UV-vis spectrophotometry) to identify the H2O2-generated activated heme species within a heme•DNAzyme that is active for the oxidation of a thioether substrate, dibenzothiophene (DBT). Singular value decomposition and global fitting analysis was used to analyze the kinetic data, with the results being consistent with the heme•DNAzyme's DBT oxidation being catalyzed by the initial Fe(III)heme-H2O2 complex. Such a complex has been predicted computationally to be a powerful oxidant for thioether substrates. In the heme•DNAzyme, the DNA GQ enhances both the kinetics of formation of the active intermediate as well as the oxidation step of DBT by the active intermediate. We show, using both stopped flow spectrophotometry and EPR measurements, that a classic Compound I is not observable during the catalytic cycle for thioether sulfoxidation.
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Affiliation(s)
- Nisreen M Shumayrikh
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Andrew J Bennet
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Dipankar Sen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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35
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Stadlbauer P, Islam B, Otyepka M, Chen J, Monchaud D, Zhou J, Mergny JL, Šponer J. Insights into G-Quadruplex-Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding. J Chem Theory Comput 2021; 17:1883-1899. [PMID: 33533244 DOI: 10.1021/acs.jctc.0c01176] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics (MD) simulations to scrutinize the G4/hemin interaction. We find that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. The simulations do not support the catalytic mechanism relying on a wobbling guanine. Similarly, the catalytic role of the iron-bound water molecule is not in line with our results; however, given the simulation limitations, this observation should be considered with some caution. The simulations rather suggest tentative mechanisms in which the external G-quartet itself could be responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD technique are briefly discussed.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Barira Islam
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 8, 779 00 Olomouc, Czech Republic
| | - Jielin Chen
- 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, Dijon 21078, France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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36
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Abstract
In this review, DNA and nanomaterial based catalysts for porphyrin metalation reactions are summarized, including the selection of DNAzymes, choice of nanomaterials, their catalytic mechanisms, and applications of the reactions.
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Affiliation(s)
- Hualin Yang
- College of Life Science
- Yangtze University
- Jingzhou
- China
- Department of Chemistry
| | - Yu Zhou
- College of Life Science
- Yangtze University
- Jingzhou
- China
- College of Animal Science
| | - Juewen Liu
- Department of Chemistry
- Waterloo Institute for Nanotechnology
- University of Waterloo
- Waterloo
- Canada
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37
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Zhou W, Sun J, Li X. Low-Cost Quantitative Photothermal Genetic Detection of Pathogens on a Paper Hybrid Device Using a Thermometer. Anal Chem 2020; 92:14830-14837. [PMID: 33059447 DOI: 10.1021/acs.analchem.0c03700] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB), one of the deadliest infectious diseases, is caused by Mycobacterium tuberculosis (MTB) and remains a public health problem nowadays. Conventional MTB DNA detection methods require sophisticated infrastructure and well-trained personnel, which leads to increasing complexity and high cost for diagnostics and limits their wide accessibility in low-resource settings. To address these issues, we have developed a low-cost photothermal biosensing method for the quantitative genetic detection of pathogens such as MTB DNA on a paper hybrid device using a thermometer. First, DNA capture probes were simply immobilized on paper through a one-step surface modification process. After DNA sandwich hybridization, oligonucleotide-functionalized gold nanoparticles (AuNPs) were introduced on paper and then catalyzed the oxidation reaction of 3,3',5,5'-tetramethylbenzidine (TMB). The produced oxidized TMB, acting as a strong photothermal agent, was used for the photothermal biosensing of MTB DNA under 808 nm laser irradiation. Under optimal conditions, the on-chip quantitative detection of the target DNA was readily achieved using an inexpensive thermometer as a signal recorder. This method does not require any expensive analytical instrumentation but can achieve higher sensitivity and there are no color interference issues, compared to conventional colorimetric methods. The method was further validated by detecting genomic DNA with high specificity. To the best of our knowledge, this is the first photothermal biosensing strategy for quantitative nucleic acid analysis on microfluidics using a thermometer, which brings fresh inspirations on the development of simple, low-cost, and miniaturized photothermal diagnostic platforms for quantitative detection of a variety of diseases at the point of care.
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Affiliation(s)
- Wan Zhou
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - Jianjun Sun
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
| | - XiuJun Li
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States.,Biomedical Engineering, Border Biomedical Research Center, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States.,Environmental Science and Engineering, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968, United States
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38
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Yu Y, Zhang Q, Gao H, Yan C, Zheng X, Yang T, Zhou X, Shao Y. Metalloenzyme-mimic innate G-quadruplex DNAzymes using directly coordinated metal ions as active centers. Dalton Trans 2020; 49:13160-13166. [PMID: 32936164 DOI: 10.1039/d0dt02871a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G-quadruplex DNAs (G4s) have been reported to exhibit the DNAzyme activities by binding with some metal complexes and functional organic ligands. However, there is a challenge to develop metalloenzyme-mimic G4-based innate DNAzymes using the complexed metal ions directly serving as the active centers. This will diversify DNAzymes for developing novel devices since G4 structures are more polymorphic than the other DNA foldings. In this work, we found that the lanthanide trivalent cerium ion of Ce3+ can bind to the human telomere G4 (htG4) according to a 1 : 2 binding mode favorable for creating metalloenzymes-mimic G4 DNAzymes. This Ce3+-G4 entity exhibits a peroxidase activity towards the oxidation of the substrate of 3,3,5,5-tetramethylbenzidine (TMB) by hydrogen peroxide. The 5' G4 tetrads with the orderly arranged carbonyl oxygen atoms are believed to be the coordination sites for Ce3+ and favor the conversion between Ce3+ and Ce4+. Our work provides an alternative feasibility in developing the G4-based innate DNAzymes for variant applications.
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Affiliation(s)
- Yali Yu
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Qingqing Zhang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Heng Gao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Chenxiao Yan
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiong Zheng
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Tong Yang
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Xiaoshun Zhou
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
| | - Yong Shao
- Zhejiang Key Laboratory for Reactive Chemistry on Solid Surfaces, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China.
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39
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Keijzer JF, Albada B. Site-Specific and Trigger-Activated Modification of Proteins by Means of Catalytic Hemin/G-quadruplex DNAzyme Nanostructures. Bioconjug Chem 2020; 31:2283-2287. [PMID: 32909740 PMCID: PMC7581286 DOI: 10.1021/acs.bioconjchem.0c00422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Catalytic
nanostructures have the potency to mimic enzymatic features.
In this paper, we show that the complex between hemin and G-quadruplex
DNA efficiently catalyzes the modification of proteins with N-methyl luminol derivatives. Final conversions are reached
within 15–30 min, and LC-MS analysis of tryptic digests of
the proteins shows that the reaction proceeds with chemoselectivity
for electron-rich aromatic residues (Tyr ≫ Trp), and the site-specificity
of the modification depends on the sequence and secondary structure
folding of the G-quadruplex nanostructure. Furthermore, the modification
can be applied on proteins with different biomedical functions, and
the nanostructure can be designed to contain a regulatory element
in order to regulate protein modification by an external stimulus.
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Affiliation(s)
- Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
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40
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Cheng Y, Cheng M, Hao J, Jia G, Monchaud D, Li C. The noncovalent dimerization of a G-quadruplex/hemin DNAzyme improves its biocatalytic properties. Chem Sci 2020; 11:8846-8853. [PMID: 34123138 PMCID: PMC8163442 DOI: 10.1039/d0sc02907f] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/15/2020] [Indexed: 12/31/2022] Open
Abstract
While many protein enzymes exert their functions through multimerization, which improves both selectivity and activity, this has not yet been demonstrated for other naturally occurring catalysts. Here, we report a multimerization effect applied to catalytic DNAs (or DNAzymes) and demonstrate that the enzymatic efficiency of G-quadruplexes (GQs) in interaction with the hemin cofactor is remarkably enhanced by homodimerization. The resulting non-covalent dimeric GQ-DNAzyme system provides hemin with a structurally defined active site in which both the cofactor (hemin) and the oxidant (H2O2) are activated. This new biocatalytic system efficiently performs peroxidase- and peroxygenase-type biotransformations of a broad range of substrates, thus providing new perspectives for biotechnological application of GQs.
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Affiliation(s)
- Yu Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Jingya Hao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Guoqing Jia
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - David Monchaud
- Institut de Chimie Moléculaire de l' Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon 21078 Dijon France
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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41
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Chen Q, Gao R, Jia L. Enhancement of the peroxidase-like activity of aptamers modified gold nanoclusters by bacteria for colorimetric detection of Salmonella typhimurium. Talanta 2020; 221:121476. [PMID: 33076089 DOI: 10.1016/j.talanta.2020.121476] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022]
Abstract
A colorimetric aptasensor was developed for selective and sensitive detection of Salmonella typhimurium (S. typhimurium) based on the enhancement of bacteria for the peroxidase-like activity of dual aptamers modified bovine serum albumin stabilized-gold nanoclusters (aptamers@BSA-AuNCs). Micro-sized bacteria was found to be able to capture aptamers@BSA-AuNCs and 3,3',5,5'-tetramethylbenzidine (TMB), thus promoting the proximity of aptamers@BSA-AuNCs to TMB and greatly increasing the local concentrations of the enzyme-mimetic nanoparticles and their substrate. As a result, addition of bacteria promoted the formation of blue products in the catalytic system, which was utilized to achieve bacteria detection by colorimetry. The parameters influencing the colorimetric aptasensor were optimized by an orthogonal test. Under the selected conditions, the aptasensor exhibited a wide linear response to S. typhimurium in the concentration range of 101-106 cfu mL-1 with a detection limit as low as 1 cfu mL-1. The feasibility of the aptasensor was verified by successful detection of S. typhimurium in egg samples with recoveries in the range of 92.4%-110%.
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Affiliation(s)
- Qingmei Chen
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Ran Gao
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Li Jia
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
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42
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Effect of Distance from Catalytic Synergy Group to Iron Porphyrin Center on Activity of G-Quadruplex/Hemin DNAzyme. Molecules 2020; 25:molecules25153425. [PMID: 32731553 PMCID: PMC7435396 DOI: 10.3390/molecules25153425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 11/17/2022] Open
Abstract
G-quadruplex/Hemin (G4/Hemin) complex has been widely used in biocatalysis and analytical applications. Meanwhile, compared with natural proteinous enzyme, its low catalytic activity is still limiting its applications. Even though several methods have been developed to enhance the peroxidation efficiency, the important core of the G4 design based enhancement mechanism is still indistinct. Here, we focus the mechanism study on the two most important microdomains: the iron porphyrin center and the catalytic synergy group within the 3' flanking. These microdomains not only provide the pocket for the combination of substrate, but also offer the axial coordination for the accelerated formation of Compound I (catalytic intermediate). In order to obtain a more suitable space layout to further accelerate the catalytic process, we have used the bases within the 3' flanking to precisely regulate the distance between microdomains. Finally, the position-dependent effect on catalytic enhancement is observed. When dC is positioned at the second-position of 3' flanking, the newly obtained DNAzyme achieves an order of magnitude improvement compared to parent G4/Hemin in catalytic activity. The results highlight the influence of the distance between the catalytic synergy group and iron porphyrin center on the activity of DNAzyme, and provide insightful information for the design of highly active DNAzymes.
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43
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Cao Y, Ding P, Yang L, Li W, Luo Y, Wang J, Pei R. Investigation and improvement of catalytic activity of G-quadruplex/hemin DNAzymes using designed terminal G-tetrads with deoxyadenosine caps. Chem Sci 2020; 11:6896-6906. [PMID: 34094131 PMCID: PMC8159390 DOI: 10.1039/d0sc01905d] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
It is generally acknowledged that G-quadruplexes (G4s) acquire peroxidase activity upon interaction with hemin. Hemin has been demonstrated to bind selectively to the 3′-terminal G-tetrad of parallel G4s via end-stacking; however, the relationships between different terminal G-tetrads and the catalytic functions of G4/hemin DNAzymes are not fully understood. Herein, the oligonucleotide d(AGGGGA) and its three analogues, d(AGBrGBrGGA), d(AGBrGGGBrA) and d(AGBrGGBrGA) (GBr indicates 8-bromo-2′-deoxyguanosine), were designed. These oligonucleotides form three parallel G4s and one antiparallel G4 without loop regions. The scaffolds had terminal G-tetrads that were either anti-deoxyguanosines (anti-dGs) or syn-deoxyguanosines (syn-dGs) at different proportions. The results showed that the parallel G4 DNAzymes exhibited 2 to 5-fold higher peroxidase activities than the antiparallel G4 DNAzyme, which is due to the absence of the 3′-terminal G-tetrad in the antiparallel G4. Furthermore, the 3′-terminal G-tetrad consisting of four anti-dGs in parallel G4s was more energetically favorable and thus more preferable for hemin stacking compared with that consisting of four syn-dGs. We further investigated the influence of 3′ and 5′ deoxyadenosine (dA) caps on the enzymatic performance by adding 3′-3′ or 5′-5′ phosphodiester bonds to AG4A. Our data demonstrated that 3′ dA caps are versatile residues in promoting the interaction of G4s with hemin. Thus, by increasing the number of 3′ dA caps, the DNAzyme of 3′A5′-5′GG3′-3′GG5′-5′A3′ with two 5′-terminal G-tetrads can exhibit significantly high catalytic activity, which is comparable to that of 5′A3′-3′GG5′-5′GG3′-3′A5′ with two 3′-terminal G-tetrads. This study may provide insights into the catalytic mechanism of G4-based DNAzymes and strategies for promoting their catalytic activities. Investigation of the peroxidase activities of G4/hemin DNAzymes using designed terminal G-tetrads by eliminating the steric effect of loop regions.![]()
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Affiliation(s)
- Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Pi Ding
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Luyan Yang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China
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44
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Wang J, Cheng M, Chen J, Ju H, Monchaud D, Mergny JL, Zhou J. An oxidatively damaged G-quadruplex/hemin DNAzyme. Chem Commun (Camb) 2020; 56:1839-1842. [PMID: 31950946 DOI: 10.1039/c9cc09237d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oxidative damage of guanine to 8-oxoguanine triggers a partial and variable loss of G-quadruplex/hemin DNAzyme activity and provides clues to the mechanistic origins of DNAzyme deactivation, which originates from an interplay between decreased G-quadruplex stability, lower hemin affinity and a modification of the nature of hemin binding sites.
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Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - David Monchaud
- Institut de Chimie Moléculaire, Université de Bourgogne (ICMUB), CNRS UMR6302, UBFC Dijon 21000, France
| | - Jean-Louis Mergny
- 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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45
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LIU ZL, TAO CA, WANG JF. Progress on Applications of G-quadruplex in Biochemical Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(19)61212-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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46
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Vallabani NVS, Vinu A, Singh S, Karakoti A. Tuning the ATP-triggered pro-oxidant activity of iron oxide-based nanozyme towards an efficient antibacterial strategy. J Colloid Interface Sci 2020; 567:154-164. [PMID: 32045737 DOI: 10.1016/j.jcis.2020.01.099] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 01/28/2023]
Abstract
An alarming increase in bacterial resistance towards various types of antibiotics makes it imperative to design alternate or combinational therapies to treat stubborn bacterial infections. In this perspective, emerging tools like nanozymes, nanomaterials with biological enzyme like characteristics, are being utilised to control infections caused by bacterial pathogens. Among several nanozymes used for antibacterial applications, Fe3O4 nanoparticles (NP) received great attention due to their effective peroxidase like activity. The pH dependent peroxidase activity of Fe3O4 NP results in generation of OH radical via the unique Fenton chemistry of iron. However, their pH dependent activity is restricted to acidic environment and dramatic loss in antibacterial activity is observed at near neutral pH. Here we describe a novel strategy to overcome the pH lacunae of citrate coated Fe3O4 NP by utilizing adenosine triphosphate disodium salt (ATP) as a synergistic agent to accelerate the OH radical production and restore its antibacterial activity over a wide range of pH. This synergistic combination (30 µg/mL Fe3O4 NP and 2.5 mM ATP) shows a high bactericidal activity against both gram positive (B. subtilis) and gram negative (E. coli) bacterial strains, in presence of H2O2, at neutral pH. The synergistic effect (Fe3O4 NP + ATP) is determined from the viability assessment and membrane damage studies and is further confirmed by comparing the concentration of generated OH radicals. Over all, this study illustrates ATP assisted and OH-mediated bactericidal activity of Fe3O4 nanozyme at near neutral pH.
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Affiliation(s)
- N V Srikanth Vallabani
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India
| | - Ajayan Vinu
- Global Innovative Center for Advanced Nanomaterials (GICAN), Faculty of Engineering and Built Environment (FEBE), The University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Sanjay Singh
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India.
| | - Ajay Karakoti
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad 380009, Gujarat, India; Global Innovative Center for Advanced Nanomaterials (GICAN), Faculty of Engineering and Built Environment (FEBE), The University of Newcastle, Callaghan, New South Wales 2308, Australia.
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47
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Liu Y, Lai P, Wang J, Xing X, Xu L. A superior G-quadruplex DNAzyme through functionalized modification of the hemin cofactor. Chem Commun (Camb) 2020; 56:2427-2430. [DOI: 10.1039/c9cc09729e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemical modifications of the hemin structure through introducing new functionalities are proposed to enhance the catalytic efficiency of the hemin/G-quadruplex DNAzyme.
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Affiliation(s)
- Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou
- China
| | - Peidong Lai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou
- China
| | - Jingru Wang
- Department of Biotechnology
- College of Life Science and Technology
- Jinan University
- Guangzhou
- China
| | - Xiwen Xing
- Department of Biotechnology
- College of Life Science and Technology
- Jinan University
- Guangzhou
- China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry
- Sun Yat-Sen University
- Guangzhou
- China
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48
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Chishti B, Fouad H, Seo HK, Alothman OY, Ansari ZA, Ansari SG. ATP fosters the tuning of nanostructured CeO2 peroxidase-like activity for promising antibacterial performance. NEW J CHEM 2020. [DOI: 10.1039/c9nj05955e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recyclable nano CeO2 POD mimic records a Km reduction (∼30% and ∼19.72% for TMB and H2O2, respectively) in 900 seconds at pH 4.5. ATP boosts catalytic feasibility in nano CeO2 at physiological pH.
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Affiliation(s)
- Benazir Chishti
- Centre for Interdisciplinary Research in Basic Science
- Jamia Millia Islamia
- India
| | - H. Fouad
- Applied Medical Science Dept. Community College
- King Saud University
- Riyadh 11433
- Saudi Arabia
- Biomedical Engineering Department
| | - H. K. Seo
- School of Chemical Engineering
- Jeonbuk National University
- Jeonju 54896
- South Korea
| | - Othman Y. Alothman
- Chemical Engineering Department
- College of Engineering
- King Saud University
- Riyadh
- Saudi Arabia
| | - Z. A. Ansari
- Centre for Interdisciplinary Research in Basic Science
- Jamia Millia Islamia
- India
| | - S. G. Ansari
- Centre for Interdisciplinary Research in Basic Science
- Jamia Millia Islamia
- India
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49
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Kumari S, Mandal S, Das P. Carbon dot mediated G quadruplex nano-network formation for enhanced DNAzyme activity and easy catalyst reclamation. RSC Adv 2019; 9:41502-41510. [PMID: 35541604 PMCID: PMC9076458 DOI: 10.1039/c9ra08290e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/01/2019] [Indexed: 02/01/2023] Open
Abstract
The significant application potential of the DNAzyme activity of G-quadruplex (G4)–hemin complexes has prompted considerable research efforts to amplify their peroxidase mimicking activity to match that of their enzymatic counterparts. However, concurrent improvements in the catalytic cycle and catalyst recovery remain elusive. Herein, we report the creation of a network array of G-quadruplex (G4)–hemin complexes crosslinked by carbon quantum dots (CDs) that not only significantly improves the G-quadruplex–hemin DNAzyme activity, stability, and catalytic cycle, but also points towards easy catalyst regeneration via a semi-heterogeneous catalysis approach. 5′-phosphate terminated G-rich single-stranded DNA molecules proficient in generating intermolecular and intramolecular G-quadruplexes were covalently conjugated to anthrarufin derived CDs through phosphoramidite chemistry. The network array was achieved through K+ mediated intermolecular G-quadruplex formation that readily complexes with hemin to give the catalytic core. The presence of CDs in close vicinity ensures a favorable microenvironment that helps in amplifying the DNAzyme activity in both the intermolecular CD–G-quadruplex network assembly and the intramolecular CD–G quadruplex conjugate, while the former is necessary for easy catalyst regeneration. The CD photophysics enable the monitoring of the DNAzyme recovery and reaction progress. Enhanced DNAzyme activity of G-quadruplex–hemin complex in carbon dot crosslinked nanonetwork with access to easy catalyst regeneration.![]()
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Affiliation(s)
- Sonam Kumari
- Department of Chemistry, Indian Institute of Technology Patna Bihta Patna 801103 Bihar India
| | - Saptarshi Mandal
- Department of Chemistry, Indian Institute of Technology Patna Bihta Patna 801103 Bihar India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna Bihta Patna 801103 Bihar India
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50
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Virgilio A, Esposito V, Lejault P, Monchaud D, Galeone A. Improved performances of catalytic G-quadruplexes (G4-DNAzymes) via the chemical modifications of the DNA backbone to provide G-quadruplexes with double 3'-external G-quartets. Int J Biol Macromol 2019; 151:976-983. [PMID: 31747569 DOI: 10.1016/j.ijbiomac.2019.10.181] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/17/2022]
Abstract
Here we report on the design of a new catalytic G-quadruplex-DNA system (G4-DNAzyme) based on the modification of the DNA scaffold to provide the DNA pre-catalyst with two identical 3'-ends, known to be more catalytically proficient than the 5'-ends. To this end, we introduced a 5'-5' inversion of polarity site in the middle of the G4-forming sequences AG4A and AG6A to obtain d(3'AGG5'-5'GGA3') (or AG2-G2A) and d(3'AGGG5'-5'GGGA3') (or AG3-G3A) that fold into stable G4 whose tetramolecular nature was confirmed via nuclear magnetic resonance (NMR) and circular dichroism (CD) investigations. Both AG2-G2A and AG3-G3A display two identical external G-quartets (3'-ends) known to interact with the cofactor hemin with a high efficiency, making the resulting complex competent to perform hemoprotein-like catalysis (G4-DNAzyme). A systematic comparison of the performances of modified and unmodified G4s lends credence to the relevance of the modification exploited here (5'-5' inversion of polarity site), which represents a new chemical opportunity to improve the overall activity of catalytic G4s.
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Affiliation(s)
| | - Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Pauline Lejault
- ICMUB CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, Dijon 21078, France
| | - David Monchaud
- ICMUB CNRS UMR6302, UBFC Dijon, 9, Avenue Alain Savary, Dijon 21078, France.
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy.
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