1
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Gao L, Yi K, Tan Y, Guo C, Zheng D, Shen C, Li F. Engineering Gene-Specific DNAzymes for Accessible and Multiplexed Nucleic Acid Testing. JACS AU 2024; 4:1664-1672. [PMID: 38665662 PMCID: PMC11040662 DOI: 10.1021/jacsau.4c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024]
Abstract
The accurate and timely detection of disease biomarkers at the point-of-care is essential to ensuring effective treatment and epidemiological surveillance. Here, we report the selection and engineering of RNA-cleaving DNAzymes that respond to specific genetic markers and amplify detection signals. Because the target-specific activation of gene-specific DNAzymes (gDz) is like the trans-cleavage activity of clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated (Cas) machinery, we further developed a CRISPR-like assay using RNA-cleaving DNAzyme coupled with isothermal sequence and signal amplification (CLARISSA) for nucleic acid detection in clinical samples. Building on the high sequence specificity and orthogonality of gDzs, CLARISSA is highly versatile and expandable for multiplex testing. Upon integration with an isothermal recombinase polymerase amplification, CLARISSA enabled the detection of human papillomavirus (HPV) 16 in 189 cervical samples collected from cervical cancer screening participants (n = 189) with 100% sensitivity and 97.4% specificity, respectively. A multiplexed CLARISSA further allowed the simultaneous analyses of HPV16 and HPV18 in 46 cervical samples, which returned clinical sensitivity of 96.3% for HPV16 and 83.3% for HPV18, respectively. No false positives were found throughout our tests. Besides the fluorescence readout using fluorogenic reporter probes, CLARISSA is also demonstrated to be fully compatible with a visual lateral flow readout. Because of the high sensitivity, accessibility, and multiplexity, we believe CLARISSA is an ideal CRISPR-Dx alternative for clinical diagnosis in field-based and point-of-care applications.
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Affiliation(s)
- Lu Gao
- Key
Laboratory of Green Chemistry & Technology of Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Ke Yi
- Department
of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic
and Pediatric Diseases and Birth Defects of Ministry of Education,
West China Second Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yun Tan
- Key
Laboratory of Green Chemistry & Technology of Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Chen Guo
- Key
Laboratory of Green Chemistry & Technology of Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Danxi Zheng
- Department
of Gynecology and Obstetrics, Key Laboratory of Obstetrics and Gynecologic
and Pediatric Diseases and Birth Defects of Ministry of Education,
West China Second Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Chenlan Shen
- Department
of Laboratory Medicine, Med+X Center for Manufacturing, West China
Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Feng Li
- Key
Laboratory of Green Chemistry & Technology of Ministry of Education,
College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Department
of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
- Department
of Laboratory Medicine, Med+X Center for Manufacturing, West China
Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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2
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Yan J, Ma X, Liang D, Ran M, Zheng D, Chen X, Zhou S, Sun W, Shen X, Zhang H. An autocatalytic multicomponent DNAzyme nanomachine for tumor-specific photothermal therapy sensitization in pancreatic cancer. Nat Commun 2023; 14:6905. [PMID: 37903795 PMCID: PMC10616286 DOI: 10.1038/s41467-023-42740-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
Multicomponent deoxyribozymes (MNAzymes) have great potential in gene therapy, but their ability to recognize disease tissue and further achieve synergistic gene regulation has rarely been studied. Herein, Arginylglycylaspartic acid (RGD)-modified Distearyl acylphosphatidyl ethanolamine (DSPE)-polyethylene glycol (PEG) (DSPE-PEG-RGD) micelle is prepared with a DSPE hydrophobic core to load the photothermal therapy (PTT) dye IR780 and the calcium efflux pump inhibitor curcumin. Then, the MNAzyme is distributed into the hydrophilic PEG layer and sealed with calcium phosphate through biomineralization. Moreover, RGD is attached to the outer tail of PEG for tumor targeting. The constructed nanomachine can release MNAzyme and the cofactor Ca2+ under acidic conditions and self-assemble into an active mode to cleave heat shock protein (HSP) mRNA by consuming the oncogene miRNA-21. Silencing miRNA-21 enhances the expression of the tumor suppressor gene PTEN, leading to PTT sensitization. Meanwhile, curcumin maintains high intracellular Ca2+ to further suppress HSP-chaperone ATP by disrupting mitochondrial Ca2+ homeostasis. Therefore, pancreatic cancer is triple-sensitized to IR780-mediated PTT. The in vitro and in vivo results show that the MNAzyme-based nanomachine can strongly regulate HSP and PTEN expression and lead to significant pancreatic tumor inhibition under laser irradiation.
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Affiliation(s)
- Jiaqi Yan
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Xiaodong Ma
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Danna Liang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Meixin Ran
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Dongdong Zheng
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Shanghai, 200032, PR China
| | - Xiaodong Chen
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shichong Zhou
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Shanghai, 200032, PR China
| | - Weijian Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
| | - Xian Shen
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Hongbo Zhang
- Joint Centre of Translational Medicine, Wenzhou Key Laboratory of Interdiscipline and Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
- Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland.
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
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3
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Chang T, Li G, Chang D, Amini R, Zhu X, Zhao T, Gu J, Li Z, Li Y. An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function. Angew Chem Int Ed Engl 2023; 62:e202310941. [PMID: 37648674 DOI: 10.1002/anie.202310941] [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: 07/31/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were "compelled" to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.
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Affiliation(s)
- Tianjun Chang
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Guangping Li
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Xiaoni Zhu
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Tongqian Zhao
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Zhongping Li
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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4
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Niu R, Chen X, Sun Z, Wang L, Wang Z, Zhang C, Ding D, Yang J, Wang Y, Luo Y. A smart TESTER for reliable discrimination of cancer-derived small extracellular vesicles. Anal Chim Acta 2023; 1276:341636. [PMID: 37573115 DOI: 10.1016/j.aca.2023.341636] [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: 04/19/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 08/14/2023]
Abstract
Cancer-derived small extracellular vesicles (csEVs) are crucial liquid biopsy indicators that reflect the presence and progression of many malignancies. However, reliable discrimination of csEVs remains a great challenge owing to the interference from normal sEVs (nsEVs) and low abundance in the early stages of cancer. In this work, we developed a Two-Elements Selectively Triggered csEVs Recognization (TESTER) strategy for selective identification of csEVs from the complex clinical body fluid samples. This method was based on the MNAzyme-controlled synchronous recognition to EpCAM and CD63 proteins on the membrane of csEVs. Efficient recognition to csEVs via EpCAM aptamer and CD63 aptamer prompted the release of Partzyme A and Partzyme B probes to induce a MNAzyme structure formation, resulting in the cyclic cleavage of substrate chain to produce cascade fluorescence signal amplification. The detection threshold of the developed TESTER approach for csEVs in complicated biological samples was 72 particles μL-1, accomplishing the highly sensitive and selective quantification of csEVs. At the same time, we successfully constructed a new platform for bimolecular simultaneous recognition, which provides a good idea for the construction of bimolecular-activated detection switch in the future.
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Affiliation(s)
- Ruyan Niu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing University, Chongqing, 400044, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Xiaohui Chen
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing University, Chongqing, 400044, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Zixin Sun
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Liu Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Zining Wang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Chong Zhang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing University, Chongqing, 400044, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Dan Ding
- College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Jichun Yang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China.
| | - Yongzhong Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing University, Chongqing, 400044, PR China.
| | - Yang Luo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing University, Chongqing, 400044, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China; College of Life Science and Laboratory Medicine, Kunming Medical University, Kunming, Yunnan, 650050, PR China.
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5
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Montserrat Pagès A, Hertog M, Nicolaï B, Spasic D, Lammertyn J. Unraveling the Kinetics of the 10-23 RNA-Cleaving DNAzyme. Int J Mol Sci 2023; 24:13686. [PMID: 37761982 PMCID: PMC10531344 DOI: 10.3390/ijms241813686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
DNA-based enzymes, or DNAzymes, are single-stranded DNA sequences with the ability to catalyze various chemical reactions, including the cleavage of the bond between two RNA nucleotides. Lately, an increasing interest has been observed in these RNA-cleaving DNAzymes in the biosensing and therapeutic fields for signal generation and the modulation of gene expression, respectively. Additionally, multiple efforts have been made to study the effects of the reaction environment and the sequence of the catalytic core on the conversion of the substrate into product. However, most of these studies have only reported alterations of the general reaction course, but only a few have focused on how each individual reaction step is affected. In this work, we present for the first time a mathematical model that describes and predicts the reaction of the 10-23 RNA-cleaving DNAzyme. Furthermore, the model has been employed to study the effect of temperature, magnesium cations and shorter substrate-binding arms of the DNAzyme on the different kinetic rate constants, broadening the range of conditions in which the model can be exploited. In conclusion, this work depicts the prospects of such mathematical models to study and anticipate the course of a reaction given a particular environment.
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Affiliation(s)
- Aida Montserrat Pagès
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Maarten Hertog
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Bart Nicolaï
- Department of Biosystems, Postharvest Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven—University of Leuven, 3001 Leuven, Belgium
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6
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Ashraf G, Zhong ZT, Asif M, Aziz A, Iftikhar T, Chen W, Zhao YD. State-of-the-Art Fluorescent Probes: Duplex-Specific Nuclease-Based Strategies for Early Disease Diagnostics. BIOSENSORS 2022; 12:bios12121172. [PMID: 36551139 PMCID: PMC9775407 DOI: 10.3390/bios12121172] [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: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 05/27/2023]
Abstract
Precision healthcare aims to improve patient health by integrating prevention measures with early disease detection for prompt treatments. For the delivery of preventive healthcare, cutting-edge diagnostics that enable early disease detection must be clinically adopted. Duplex-specific nuclease (DSN) is a useful tool for bioanalysis since it can precisely digest DNA contained in duplexes. DSN is commonly used in biomedical and life science applications, including the construction of cDNA libraries, detection of microRNA, and single-nucleotide polymorphism (SNP) recognition. Herein, following the comprehensive introduction to the field, we highlight the clinical applicability, multi-analyte miRNA, and SNP clinical assays for disease diagnosis through large-cohort studies using DSN-based fluorescent methods. In fluorescent platforms, the signal is produced based on the probe (dyes, TaqMan, or molecular beacon) properties in proportion to the target concentration. We outline the reported fluorescent biosensors for SNP detection in the next section. This review aims to capture current knowledge of the overlapping miRNAs and SNPs' detection that have been widely associated with the pathophysiology of cancer, cardiovascular, neural, and viral diseases. We further highlight the proficiency of DSN-based approaches in complex biological matrices or those constructed on novel nano-architectures. The outlooks on the progress in this field are discussed.
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Affiliation(s)
- Ghazala Ashraf
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zi-Tao Zhong
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Muhammad Asif
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan 430205, China
| | - Ayesha Aziz
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Tayyaba Iftikhar
- Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wei Chen
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuan-Di Zhao
- Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
- Key Laboratory of Biomedical Photonics (HUST), Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
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7
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Taylor AI, Wan CJK, Donde MJ, Peak-Chew SY, Holliger P. A modular XNAzyme cleaves long, structured RNAs under physiological conditions and enables allele-specific gene silencing. Nat Chem 2022; 14:1295-1305. [PMID: 36064973 PMCID: PMC7613789 DOI: 10.1038/s41557-022-01021-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 07/08/2022] [Indexed: 11/07/2022]
Abstract
Nucleic-acid catalysts (ribozymes, DNA- and XNAzymes) cleave target (m)RNAs with high specificity but have shown limited efficacy in clinical applications. Here we report on the in vitro evolution and engineering of a highly specific modular RNA endonuclease XNAzyme, FR6_1, composed of 2'-deoxy-2'-fluoro-β-D-arabino nucleic acid (FANA). FR6_1 overcomes the activity limitations of previous DNA- and XNAzymes and can be retargeted to cleave highly structured full-length (>5 kb) BRAF and KRAS mRNAs at physiological Mg2+ concentrations with allelic selectivity for tumour-associated (BRAF V600E and KRAS G12D) mutations. Phosphorothioate-FANA modification enhances FR6_1 biostability and enables rapid KRAS mRNA knockdown in cultured human adenocarcinoma cells with a G12D-allele-specific component provided by in vivo XNAzyme cleavage activity. These results provide a starting point for the development of improved gene-silencing agents based on FANA or other XNA chemistries.
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Affiliation(s)
- Alexander I Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK.
| | | | - Maria J Donde
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK
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8
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Del Grosso E, Franco E, Prins LJ, Ricci F. Dissipative DNA nanotechnology. Nat Chem 2022; 14:600-613. [PMID: 35668213 DOI: 10.1038/s41557-022-00957-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 04/13/2022] [Indexed: 12/11/2022]
Abstract
DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature.
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Affiliation(s)
- Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Rome, Italy
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, USA.
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padua, Padua, Italy.
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome, Tor Vergata, Rome, Italy.
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9
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Label-free detection of HPV mRNA with an artificial chaperone-enhanced MNAzyme (ACEzyme)-based electrochemical sensor. Biosens Bioelectron 2022; 221:114352. [PMID: 35690559 DOI: 10.1016/j.bios.2022.114352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022]
Abstract
Nucleic acid biosensors for point-of-care (POC) diagnostic applications are highly desirable. The ability to detect DNA and RNA in a simple, rapid, affordable and portable format leads to a range of important applications for early screening in the field of disease monitoring and management. Herein, we report the development of an isothermal, label-free electrochemical biosensor that was designed on the basis of target-driven MNAzyme cleavage activity. Hybridization with HPV mRNA, a model nucleic acid target, activated MNAzyme and initiated the cleavage of immobilized hairpin substrates, leading to changes in the electrochemical signal. Under optimal conditions, a detection limit of 2.6 pM was obtained with an incubation time of 60 min. Furthermore, an artificial chaperone-enhanced MNAzyme (ACEzyme) system was integrated to an electrochemical biosensor for the first time. The analytical performance of the biosensor was enhanced, and the detection time was significantly reduced by the addition of PLL-g-Dex, which exhibits nucleic acid chaperone-like activity. A detection limit of 0.88 pM was obtained with a threefold decrease in incubation time without prior amplification. The proposed biosensing platform shows the advantages of simple fabrication and operation, good selectivity in the presence of single-base mismatch, and excellent versatility in a complex mixture of total RNA. We believe that this isothermal, label-free, and protein-free nucleic acid analysis platform could provide foundations for the further development of a universal nucleic acid biosensing platform for clinical application.
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10
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Sánchez-Visedo A, Ferrero FJ, Costa-Fernández JM, Fernández-Argüelles MT. Inorganic nanoparticles coupled to nucleic acid enzymes as analytical signal amplification tools. Anal Bioanal Chem 2022; 414:5201-5215. [PMID: 35292825 PMCID: PMC8923336 DOI: 10.1007/s00216-022-03998-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Abstract
Nucleic acid enzymes (NAzymes) are a class of nucleic acid molecules with catalytic activity, which can be modulated by the presence of different species such as metal ions, genetic biomarkers, small molecules or proteins, among others. NAzymes offer several important advantages for development of novel bioanalytical strategies, resulting from their functionality as specific recognition elements and as amplified analytical signal generators, making them ideal candidates for developing highly specific bioanalytical strategies for the detection of a wide variety of targets. When coupled with the exceptional features of inorganic nanoparticles (NPs), the sensitivity of the assays can be significantly improved, allowing the detection of targets using many different detection techniques including visual readout, spectrophotometry, fluorimetry, electrochemiluminescence, voltammetry, and single-particle inductively coupled plasma-mass spectrometry. Here we provide an overview of the fundamentals of novel strategies developed to achieve analytical signal amplification based on the use of NAzymes coupled with inorganic NPs. Some representative examples of such strategies for the highly sensitive detection of different targets will be presented, including metal ions, proteins, DNA- or RNA-based biomarkers, and small molecules or microorganisms. Furthermore, future prospective challenges will be discussed.
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Affiliation(s)
- Adrián Sánchez-Visedo
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain.
| | - Francisco Javier Ferrero
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus de Gijón, Sede 3, 33204, Gijon (Asturias), Spain
| | - José M Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - María T Fernández-Argüelles
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
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11
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He L, Chen H, Xu J, Shao M. Primer Exchange Reaction-Synthesized DNAzyme for the Sensitive Determination of an Oral Cancer Protein Biomarker. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2029468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Libang He
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology & West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, Sichuan China
| | - Hao Chen
- School of Medicine, Tongji University, Shanghai, China
| | - Jue Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology & West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, Sichuan China
| | - Meiying Shao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology & West China School of Public Health & West China Fourth Hospital, Sichuan University, Chengdu, Sichuan China
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12
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Zhao D, Chang D, Zhang Q, Chang Y, Liu B, Sun C, Li Z, Dong C, Liu M, Li Y. Rapid and Specific Imaging of Extracellular Signaling Molecule Adenosine Triphosphate with a Self-Phosphorylating DNAzyme. J Am Chem Soc 2021; 143:15084-15090. [PMID: 34415153 DOI: 10.1021/jacs.1c04925] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Adenosine 5'-triphosphate (ATP) is a central extracellular signaling agent involved in various physiological and pathological processes. However, precise measurements of the temporal and spatial components of ATP dynamics are lacking due primarily to the limitations of available methods for ATP detection. Here, we report on the first effort to design a self-phosphorylating DNAzyme (SPDz) sensor for fluorescence imaging of ATP. In response to ATP, SPDz sensors exhibit subsecond response kinetics, extremely high specificity, and micromolar affinities. In particular, we demonstrate cell-surface-anchored SPDz sensors for fluorescence imaging of both stress-induced endogenous ATP release in astrocytes and mechanical stimulation-evoked ATP release at the single-cell level. We also validated their utility for visualizing the rapid dynamic properties of ATP signaling upon electrical stimulation in astrocytes. Thus, SPDz sensors are robust tools for monitoring ATP signaling underlying diverse cellular processes.
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Affiliation(s)
- Dan Zhao
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Bo Liu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Changsen Sun
- School of Optoelectronic Engineering and Instrumentation Science, Dalian University of Technology, Dalian, 116024, China
| | - Zhonping Li
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Chuan Dong
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S4K1, Canada
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13
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RNA-cleaving DNAzymes as a diagnostic and therapeutic agent against antimicrobial resistant bacteria. Curr Genet 2021; 68:27-38. [PMID: 34505182 DOI: 10.1007/s00294-021-01212-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
The development of nucleic-acid-based antimicrobials such as RNA-cleaving DNAzyme (RCD), a short catalytically active nucleic acid, is a promising alternative to the current antibiotics. The current rapid spread of antimicrobial resistance (AMR) in bacteria renders some antibiotics useless against bacterial infection, thus creating the need for alternative antimicrobials such as DNAzymes. This review summarizes recent advances in the use of RCD as a diagnostic and therapeutic agent against AMR. Firstly, the recent diagnostic application of RCD for the detection of bacterial cells and the associated resistant gene(s) is discussed. The next section summarises the therapeutic application of RCD in AMR bacterial infections which includes direct targeting of the resistant genes and indirect targeting of AMR-associated genes. Finally, this review extends the discussion to challenges of utilizing RCD in real-life applications, and the potential of combining both diagnostic and therapeutic applications of RCD into a single agent as a theranostic agent.
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Cozma I, McConnell EM, Brennan JD, Li Y. DNAzymes as key components of biosensing systems for the detection of biological targets. Biosens Bioelectron 2021; 177:112972. [DOI: 10.1016/j.bios.2021.112972] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/01/2021] [Accepted: 01/02/2021] [Indexed: 12/11/2022]
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15
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Ertas YN, Mahmoodi M, Shahabipour F, Jahed V, Diltemiz SE, Tutar R, Ashammakhi N. Role of biomaterials in the diagnosis, prevention, treatment, and study of corona virus disease 2019 (COVID-19). EMERGENT MATERIALS 2021; 4:35-55. [PMID: 33748672 PMCID: PMC7962632 DOI: 10.1007/s42247-021-00165-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/12/2021] [Indexed: 05/02/2023]
Abstract
Recently emerged novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting corona virus disease 2019 (COVID-19) led to urgent search for methods to prevent and treat COVID-19. Among important disciplines that were mobilized is the biomaterials science and engineering. Biomaterials offer a range of possibilities to develop disease models, protective, diagnostic, therapeutic, monitoring measures, and vaccines. Among the most important contributions made so far from this field are tissue engineering, organoids, and organ-on-a-chip systems, which have been the important frontiers in developing tissue models for viral infection studies. Also, due to low bioavailability and limited circulation time of conventional antiviral drugs, controlled and targeted drug delivery could be applied alternatively. Fortunately, at the time of writing this paper, we have two successful vaccines and new at-home detection platforms. In this paper, we aim to review recent advances of biomaterial-based platforms for protection, diagnosis, vaccination, therapeutics, and monitoring of SARS-CoV-2 and discuss challenges and possible future research directions in this field.
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Affiliation(s)
- Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Mahboobeh Mahmoodi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Fahimeh Shahabipour
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran
- Skin Research Center, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Vahid Jahed
- Biomedical Engineering Division, Faculty of Chemical Engineering, Tarbiat Modares University, Tehran, Iran
| | | | - Rumeysa Tutar
- Department of Chemistry, Faculty of Engineering, Istanbul University-Cerrahpasa, Avcilar, Istanbul, Turkey
| | - Nureddin Ashammakhi
- Department of Bioengineering, Henry Samueli School of Engineering, University of California, Los Angeles, CA USA
- Department of Biomedical Engineering, College of Engineering, Michigan State University, East Lansing, MI USA
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