1
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Ali M, Nair P, Capretta A, Brennan JD. In-vitro Clinical Diagnostics using RNA-Cleaving DNAzymes. Chembiochem 2024; 25:e202400085. [PMID: 38574237 DOI: 10.1002/cbic.202400085] [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: 01/30/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/06/2024]
Abstract
Over the last three decades, significant advancements have been made in the development of biosensors and bioassays that use RNA-cleaving DNAzymes (RCDs) as molecular recognition elements. While early examples of RCDs were primarily responsive to metal ions, the past decade has seen numerous RCDs reported for more clinically relevant targets such as bacteria, cancer cells, small metabolites, and protein biomarkers. Over the past 5 years several RCD-based biosensors have also been evaluated using either spiked biological matrixes or patient samples, including blood, serum, saliva, nasal mucus, sputum, urine, and faeces, which is a critical step toward regulatory approval and commercialization of such sensors. In this review, an overview of the methods used to generate RCDs and the properties of key RCDs that have been utilized for in vitro testing is first provided. Examples of RCD-based assays and sensors that have been used to test either spiked biological samples or patient samples are then presented, highlighting assay performance in different biological matrixes. A summary of current prospects and challenges for development of in vitro diagnostic tests incorporating RCDs and an overview of future directions of the field is also provided.
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Affiliation(s)
- Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Parameswaran Nair
- Division of Respirology, McMaster University, and, Firestone Institute of Respiratory Health at St. Joseph's Health Care, Hamilton, ON, L8N 4A6, Canada
| | - Alfredo Capretta
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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2
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Yin M, Zhang Y, Liang H, Liu C, Bi Y, Sun J, Guo W. Smart Free-Standing Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film-Based Sensing System Using Changes in Bending Angles as a Visual Signal Readout. Anal Chem 2024; 96:5215-5222. [PMID: 38506337 DOI: 10.1021/acs.analchem.3c05562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Stimuli-responsive DNA hydrogels have shown great potential in sensing applications due to their attractive properties such as programmable target responsiveness, excellent biocompatibility, and biodegradability. In contrast to the extensively developed DNA hydrogel sensing systems based on the stimuli-responsive hydrogel-to-solution phase transition of the hydrogel matrix, the quantitative sensing application of DNA hydrogels exhibiting smart shape deformations has rarely been explored. Moreover, bulk DNA hydrogel-based sensing systems also suffer from high material cost and slow response. Herein, free-standing bilayer polyacrylamide/DNA hybrid hydrogel films with programmable responsive properties directed by the sequence of functional DNA units have been constructed. Compared with bulk DNA hydrogels, these DNA hydrogel films with a thickness at the micrometer scale not only greatly reduce the consumption of DNA materials but also facilitate the mass transfer of biomacromolecular substances within the hydrogel network, thus favoring their sensing applications. Therefore, a target-responsive smart DNA hydrogel film-based sensor system is further demonstrated based on the large amplitude macroscopic shape deformation of the film as a visual signal readout. As a proof of concept, Pb2+ or UO22+ ion-responsive DNA units were introduced into the active layer of the bilayer hydrogel films. In the presence of Pb2+ or UO22+ ions, the occurrence of a cleavage reaction within the DNA units leads to the release of DNA segments from the hydrogel film, inducing a dramatic shape deformation of the film, and thus sensing of Pb2+ or UO22+ ions with high specificity is achieved based on measuring the bending angle changes of these smart free-standing films. These smart DNA hydrogel film sensors with target-programmable responsiveness, simple operation, and ease of storage may hold promise for future rapid on-site testing applications.
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Affiliation(s)
- Mengyuan Yin
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yaxing Zhang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hanxue Liang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chang Liu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yanhui Bi
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Juanjuan Sun
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Weiwei Guo
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Molecular Recognition and Biosensing, College of Chemistry, Nankai University, Tianjin 300071, China
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3
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Zhang Z, Wei W, Chen S, Yang J, Song D, Chen Y, Zhao Z, Chen J, Wang F, Wang J, Li Z, Liang Y, Yu H. Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity. J Am Chem Soc 2024; 146:7052-7062. [PMID: 38427585 DOI: 10.1021/jacs.4c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10-23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA-RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a kobs of 3.76 min-1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.
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Affiliation(s)
- Ze Zhang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Siqi Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jintao Yang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zerun Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jiawen Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Fulong Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jiahuan Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
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4
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Takezawa Y, Zhang H, Mori K, Hu L, Shionoya M. Ligase-mediated synthesis of Cu II-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases. Chem Sci 2024; 15:2365-2370. [PMID: 38362437 PMCID: PMC10866359 DOI: 10.1039/d3sc05042d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both hydrogen-bonded caU-A and metal-mediated caU-CuII-caU base pairs. The base sequence was logically designed based on a known RNA-cleaving DNAzyme so that the caU-modified DNAzyme (caU-DNAzyme) can form a catalytically inactive structure containing three caU-A base pairs and an active form with three caU-CuII-caU pairs. The caU-DNAzyme was synthesized by joining short caU-containing fragments with a standard DNA ligase. The activity of caU-DNAzyme was suppressed without CuII, but enhanced 21-fold with the addition of CuII. Furthermore, the DNAzyme activity was turned on and off during the reaction by the addition and removal of CuII ions. Both ligase-mediated synthesis and CuII-dependent allosteric regulation were achieved by the bifacial base pairing properties of caU. This study provides a new strategy for designing stimuli-responsive DNA molecular systems.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hanci Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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5
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Rath WH, Göstl R, Herrmann A. Mechanochemical Activation of DNAzyme by Ultrasound. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306236. [PMID: 38308193 PMCID: PMC10885644 DOI: 10.1002/advs.202306236] [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: 08/31/2023] [Revised: 01/11/2024] [Indexed: 02/04/2024]
Abstract
Controlling the activity of DNAzymes by external triggers is an important task. Here a temporal control over DNAzyme activity through a mechanochemical pathway with the help of ultrasound (US) is demonstrated. The deactivation of the DNAzyme is achieved by hybridization to a complementary strand generated through rolling circle amplification (RCA), an enzymatic polymerization process. Due to the high molar mass of the resulting polynucleic acids, shear force can be applied on the RCA strand through inertial cavitation induced by US. This exerts mechanical force and leads to the cleavage of the base pairing between RCA strand and DNAzyme, resulting in the recovery of DNAzyme activity. This is the first time that this release mechanism is applied for the activation of catalytic nucleic acids, and it has multiple advantages over other stimuli. US has higher penetration depth into tissues compared to light, and it offers a more specific stimulus than heat, which has also limited use in biological systems due to cell damage caused by hyperthermia. This approach is envisioned to improve the control over DNAzyme activity for the development of reliable and specific sensing applications.
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Affiliation(s)
- Wolfgang H. Rath
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Robert Göstl
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Andreas Herrmann
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
- DWI – Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
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6
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Takezawa Y, Hu L, Nakama T, Shionoya M. Metal-dependent activity control of a compact-sized 8-17 DNAzyme based on metal-mediated unnatural base pairing. Chem Commun (Camb) 2024; 60:288-291. [PMID: 38063055 DOI: 10.1039/d3cc05520e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
A compact 8-17 DNAzyme was modified with a CuII-meditated artificial base pair to develop a metal-responsive allosteric DNAzyme. The base sequence was rationally designed based on the reported three-dimensional structure. The activity of the modified DNAzyme was enhanced 5.1-fold by the addition of one equivalent of CuII ions, showing good metal responsiveness. Since it has been challenging to modify compactly folded DNAzymes without losing their activity, this study demonstrates the utility of the metal-mediated artificial base pairing to create stimuli-responsive functional DNAs.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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7
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Nedorezova DD, Rubel MS, Rubel AA. Multicomponent DNAzyme Nanomachines: Structure, Applications, and Prospects. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S249-S261. [PMID: 38621754 DOI: 10.1134/s0006297924140141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 04/17/2024]
Abstract
Nucleic acids (NAs) are important components of living organisms responsible for the storage and transmission of hereditary information. They form complex structures that can self-assemble and bind to various biological molecules. DNAzymes are NAs capable of performing simple chemical reactions, which makes them potentially useful elements for creating DNA nanomachines with required functions. This review focuses on multicomponent DNA-based nanomachines, in particular on DNAzymes as their main functional elements, as well as on the structure of DNAzyme nanomachines and their application in the diagnostics and treatment of diseases. The article also discusses the advantages and disadvantages of DNAzyme-based nanomachines and prospects for their future applications. The review provides information about new technologies and the possibilities of using NAs in medicine.
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8
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Tang H, Chang W, Xue H, Xu C, Li Z, Liu H, Xing C, Liu G, Liu X, Wang H, Wang J. Engineered DNA molecular machine for ultrasensitive detection of environmental lead pollution. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132306. [PMID: 37597388 DOI: 10.1016/j.jhazmat.2023.132306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/02/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Dynamic monitoring of environmental Pb2+ is of utmost importance for food safety and personal well-being. Herein, we report a novel, rapid, and practical fluorescence detection platform for Pb2+. The platform comprises two essential components: an engineered DNAzyme probe (EDP) and a responsive functionalized probe (RFP). The EDP demonstrates specific recognition of Pb2+ and the subsequent release of free DNA fragments. The released DNA fragments are then captured using the RFP to form DNA complexes, which undergo multiple cascade amplification reactions involving polymerases and nickases, resulting in the generation of a large number of fluorescence signals. These signals can detect Pb2+ at concentrations as low as 0.114 nmol/L, with a dynamic range spanning from 0.1 nmol/L to 50 nmol/L. Moreover, the platform exhibits excellent sensitivity and selectivity for Pb2+ detection. To further validate its effectiveness, we successfully quantitatively detected lead contamination in water from Chaohu Lake, and the results aligned closely with those obtained using inductively coupled plasma-mass spectrometry (ICP-MS). Moreover, this platform is suitable for detecting Pb2+ in seawater, soil, and fish samples. These findings confirm the suitability of the current detection platform for the dynamic assessment of Pb contamination in ecological environments, thereby contributing to environmental and food safety.
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Affiliation(s)
- Hehe Tang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, School of Public Health, Anhui Medical University, Hefei 230032, PR China
| | - Wei Chang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, School of Public Health, Anhui Medical University, Hefei 230032, PR China; Department of Toxicology, Key laboratory of environmental toxicology of anhui higher education institutes, School of Public Health, Anhui Medical University, Hefei 230032, PR China
| | - Huijie Xue
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, School of Public Health, Anhui Medical University, Hefei 230032, PR China
| | - Changlu Xu
- School of Dentistry, University of California, Los Angeles, USA
| | - Zhi Li
- School of Dentistry, University of California, Los Angeles, USA
| | - Hao Liu
- School of Pharmacy, Bengbu Medical College, Bengbu 233000, PR China
| | - Chao Xing
- Fujian Key Laboratory of Functional Marine Sensing Materials, Minjiang University, Fujian 350000, PR China
| | - Gang Liu
- Environmental Monitoring Station, Authority Bureau of Lake Chaohu, Chaohu 238000, PR China
| | - Xiaoyan Liu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, School of Public Health, Anhui Medical University, Hefei 230032, PR China.
| | - Hua Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, School of Public Health, Anhui Medical University, Hefei 230032, PR China; Department of Toxicology, Key laboratory of environmental toxicology of anhui higher education institutes, School of Public Health, Anhui Medical University, Hefei 230032, PR China.
| | - Jie Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, School of Pharmacy, School of Public Health, Anhui Medical University, Hefei 230032, PR China; Department of Toxicology, Key laboratory of environmental toxicology of anhui higher education institutes, School of Public Health, Anhui Medical University, Hefei 230032, PR China.
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9
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Ali MM, Mukherjee M, Radford K, Patel Z, Capretta A, Nair P, Brennan JD. A Rapid Sputum-based Lateral Flow Assay for Airway Eosinophilia using an RNA-cleaving DNAzyme Selected for Eosinophil Peroxidase. Angew Chem Int Ed Engl 2023; 62:e202307451. [PMID: 37477970 DOI: 10.1002/anie.202307451] [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: 05/26/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
The first protein-binding allosteric RNA-cleaving DNAzyme (RCD) obtained by direct in vitro selection against eosinophil peroxidase (EPX), a validated marker for airway eosinophilia, is described. The RCD has nanomolar affinity for EPX, shows high selectivity against related peroxidases and other eosinophil proteins, and is resistant to degradation by mammalian nucleases. An optimized RCD was used to develop both fluorescence and lateral flow assays, which were evaluated using 38 minimally processed patient sputum samples (23 non-eosinophilic, 15 eosinophilic), producing a clinical sensitivity of 100 % and specificity of 96 %. This RCD-based lateral flow assay should allow for rapid evaluation of airway eosinophilia as an aid for guiding asthma therapy.
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Affiliation(s)
- M Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, L8S 4K1, Hamilton, ON, Canada
| | - Manali Mukherjee
- Division of Respirology, McMaster University, Firestone Institute of Respiratory Health at St. Joseph's Health Care, L8N 4A6, Hamilton, ON, Canada
| | - Katherine Radford
- Division of Respirology, McMaster University, Firestone Institute of Respiratory Health at St. Joseph's Health Care, L8N 4A6, Hamilton, ON, Canada
| | - Zil Patel
- Division of Respirology, McMaster University, Firestone Institute of Respiratory Health at St. Joseph's Health Care, L8N 4A6, Hamilton, ON, Canada
| | - Alfredo Capretta
- Biointerfaces Institute, McMaster University, 1280 Main Street West, L8S 4K1, Hamilton, ON, Canada
| | - Parameswaran Nair
- Division of Respirology, McMaster University, Firestone Institute of Respiratory Health at St. Joseph's Health Care, L8N 4A6, Hamilton, ON, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, L8S 4K1, Hamilton, ON, Canada
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10
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Wu Y, Lewis W, Wai JL, Xiong M, Zheng J, Yang Z, Gordon C, Lu Y, New SY, Zhang XB, Lu Y. Ratiometric Detection of Zn 2+ Using DNAzyme-Based Bioluminescence Resonance Energy Transfer Sensors. CHEMISTRY (BASEL, SWITZERLAND) 2023; 5:1745-1759. [PMID: 38371491 PMCID: PMC10874629 DOI: 10.3390/chemistry5030119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
While fluorescent sensors have been developed for monitoring metal ions in health and diseases, they are limited by the requirement of an excitation light source that can lead to photobleaching and a high autofluorescence background. To address these issues, bioluminescence resonance energy transfer (BRET)-based protein or small molecule sensors have been developed; however, most of them are not highly selective nor generalizable to different metal ions. Taking advantage of the high selectivity and generalizability of DNAzymes, we report herein DNAzyme-based ratiometric sensors for Zn2+ based on BRET. The 8-17 DNAzyme was labeled with luciferase and Cy3. The proximity between luciferase and Cy3 permiQed BRET when coelenterazine, the substrate for luciferase, was introduced. Adding samples containing Zn2+ resulted in a cleavage of the substrate strand, causing dehybridization of the DNAzyme construct, thus increasing the distance between Cy3 and luciferase and changing the BRET signals. Using these sensors, we detected Zn2+ in serum samples and achieved Zn2+ detection with a smartphone camera. Moreover, since the BRET pair is not the component that determines the selectivity of the sensors, this sensing platform has the potential to be adapted for the detection of other metal ions with other metal-dependent DNAzymes.
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Affiliation(s)
- Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Whitney Lewis
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jing Luen Wai
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- School of Pharmacy, Faculty of Science and Engineering, University of No0ingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Mengyi Xiong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jiao Zheng
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Zhenglin Yang
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chloe Gordon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Ying Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
| | - Siu Yee New
- School of Pharmacy, Faculty of Science and Engineering, University of No0ingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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11
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Takezawa Y, Mori K, Huang WE, Nishiyama K, Xing T, Nakama T, Shionoya M. Metal-mediated DNA strand displacement and molecular device operations based on base-pair switching of 5-hydroxyuracil nucleobases. Nat Commun 2023; 14:4759. [PMID: 37620299 PMCID: PMC10449808 DOI: 10.1038/s41467-023-40353-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 07/13/2023] [Indexed: 08/26/2023] Open
Abstract
Rational design of self-assembled DNA nanostructures has become one of the fastest-growing research areas in molecular science. Particular attention is focused on the development of dynamic DNA nanodevices whose configuration and function are regulated by specific chemical inputs. Herein, we demonstrate the concept of metal-mediated base-pair switching to induce inter- and intramolecular DNA strand displacement in a metal-responsive manner. The 5-hydroxyuracil (UOH) nucleobase is employed as a metal-responsive unit, forming both a hydrogen-bonded UOH-A base pair and a metal-mediated UOH-GdIII-UOH base pair. Metal-mediated strand displacement reactions are demonstrated under isothermal conditions based on the base-pair switching between UOH-A and UOH-GdIII-UOH. Furthermore, metal-responsive DNA tweezers and allosteric DNAzymes are developed as typical models for DNA nanodevices simply by incorporating UOH bases into the sequence. The metal-mediated base-pair switching will become a versatile strategy for constructing stimuli-responsive DNA nanostructures, expanding the scope of dynamic DNA nanotechnology.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Wei-En Huang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kotaro Nishiyama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tong Xing
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takahiro Nakama
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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12
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Filippidou MK, Kanaris AI, Aslanidis E, Rapesi A, Tsounidi D, Ntouskas S, Skotadis E, Tsekenis G, Tsoukalas D, Tserepi A, Chatzandroulis S. Integrated Plastic Microfluidic Device for Heavy Metal Ion Detection. MICROMACHINES 2023; 14:1595. [PMID: 37630131 PMCID: PMC10456536 DOI: 10.3390/mi14081595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
The presence of heavy metal ions in soil, air and water constitutes an important global environmental threat, as these ions accumulate throughout the food chain, contributing to the rise of chronic diseases, including, amongst others, cancer and kidney failure. To date, many efforts have been made for their detection, but there is still a need for the development of sensitive, low-cost, and portable devices able to conduct on-site detection of heavy metal ions. In this work, we combine microfluidic technology and electrochemical sensing in a plastic chip for the selective detection of heavy metal ions utilizing DNAzymes immobilized in between platinum nanoparticles (PtNPs), demonstrating a reliable portable solution for water pollution monitoring. For the realization of the microfluidic-based heavy metal ion detection device, a fast and easy-to-implement fabrication method based on the photolithography of dry photosensitive layers is proposed. As a proof of concept, we demonstrate the detection of Pb2+ ions using the prototype microfluidic device.
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Affiliation(s)
- Myrto Kyriaki Filippidou
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Aris Ioannis Kanaris
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Evangelos Aslanidis
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
| | - Annita Rapesi
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece (G.T.)
| | - Dimitra Tsounidi
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece (G.T.)
| | - Sotirios Ntouskas
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Evangelos Skotadis
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
| | - George Tsekenis
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece (G.T.)
| | - Dimitris Tsoukalas
- Department of Applied Sciences, National Technical University of Athens, 15780 Zografou, Greece; (E.A.); (E.S.); (D.T.)
| | - Angeliki Tserepi
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
| | - Stavros Chatzandroulis
- Institute of Nanoscience and Nanotechnology, NCSR ‘‘Demokritos’’, 15341 Aghia Paraskevi, Greece; (M.K.F.); (A.T.)
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13
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Kan A, Ding S, Zhang N, Jiang W. A magnetic DNAzyme walker for both in-situ imaging and sensitive detection of MUC1 on living cells. Talanta 2023; 257:124374. [PMID: 36841017 DOI: 10.1016/j.talanta.2023.124374] [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: 08/26/2022] [Revised: 01/30/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Mucin 1 (MUC1) is a transmembrane glycoprotein commonly expressed in epithelial cells with stable levels and polarized distribution. Their expression levels and spatial distribution abnormally altered during oncogenesis and play tumor-promoting roles synergistically. We herein propose a magnetic DNAzyme walker (MDW) for both in-situ imaging and sensitive detection of MUC1. This MDW was constructed by modifying specially designed track strands (TSs) and walking strands (WSs) on a streptavidin magnetic bead (SA-MB). The TSs contained cleavage sites for DNAzymes and were labeled with Cy3 at free ends. The WSs contained DNAzyme sequences and were firstly blocked by hybridizing with Cy5-labeled aptamers of MUC1. The DNAzymes were unlocked upon aptamers binding to MUC1 on cells. MDWs were then transferred to a buffer suitable for DNAzyme action, where the unlocked DNAzymes cleaved multiple TSs, releasing amplified Cy3-fragments, which were separated from the uncleaved ones by magnetic separation. In-situ imaging of MUC1 were achieved by the fluorescence of Cy5 on aptamers bound to MUC1. Sensitive detection of MUC1 were achieved by the amplified fluorescence of released Cy3. In-situ imaging and walker operation for detection were triggered by the same targets at the same time, ensuring the signals are real-time correlative. Moreover, MDWs' operation was separated from cells, reducing interference between imaging and detection. The proposed MDW offers a potential approach for comprehensive analysis of MUC1 in early diagnosis and progression assessment of tumor.
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Affiliation(s)
- Ailing Kan
- Research Center of Basic Medicine, Breast Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, PR China
| | - Shengyong Ding
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Nan Zhang
- Research Center of Basic Medicine, Breast Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, PR China.
| | - Wei Jiang
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
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14
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Liu J, Bi Y, Tai W, Wei Y, Zhang Q, Liu A, Hu Q, Yu L. The development of a paper-based distance sensor for the detection of Pb 2+ assisted with the target-responsive DNA hydrogel. Talanta 2023; 257:124344. [PMID: 36801758 DOI: 10.1016/j.talanta.2023.124344] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
Due to the serious risks of lead pollution to human health, it plays a great role in constructing a simple, inexpensive, portable, and user-friendly strategy for Pb2+ detection in environmental samples. Herein, a paper-based distance sensor is developed to detect Pb2+ assisted with the target-responsive DNA hydrogel. Pb2+ can activate DNAzyme to cleave its substrate strand, which results in the hydrolysis of the DNA hydrogel. The released water molecules trapped in the hydrogel can flow along the patterned pH paper due to the capillary force. The water flow distance (WFD) is significantly influenced by the amount of water released from the collapsed DNA hydrogel triggered by the addition of various Pb2+ concentrations. In this way, Pb2+ can be quantitatively detected without using specialized instruments and labeled molecules, and the limit of detection (LOD) of Pb2+ is 3.0 nM. Additionally, the Pb2+ sensor works well in lake water and tap water. Overall, this simple, inexpensive, portable, and user-friendly method is very promising for quantitative and in-field detection of Pb2+ with excellent sensitivity and selectivity.
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Affiliation(s)
- Jinpeng Liu
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China
| | - Yanhui Bi
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, 19 Keyuan Street, Jinan, 250014, China.
| | - Wenjun Tai
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China
| | - Yong Wei
- Zhongtuo Biomedical Co., Ltd., Linyi, 276017, China
| | - Qiang Zhang
- Zhongtuo Biomedical Co., Ltd., Linyi, 276017, China
| | - Anna Liu
- Zhongtuo Biomedical Co., Ltd., Linyi, 276017, China
| | - Qiongzheng Hu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, 19 Keyuan Street, Jinan, 250014, China
| | - Li Yu
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China.
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15
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Higashi SL, Shintani Y, Ikeda M. Installing Reduction Responsiveness into Biomolecules by Introducing Nitroaryl Groups. Chemistry 2022; 28:e202201103. [DOI: 10.1002/chem.202201103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Present address: Institut für Physiologische Chemie und Pathobiochemie Universität Münster Waldeyerstraße 15 48149 Münster Germany
| | - Yuki Shintani
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
| | - Masato Ikeda
- United Graduate School of Drug Discovery and Medical Information Sciences Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Department of Life Science and Chemistry Graduate School of Natural Science and Technology Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute for Glyco-core Research (iGCORE) Gifu University 1-1 Yanagido Gifu 501-1193 Japan
- Institute of Nano-Life-Systems Institutes of Innovation for Future Society Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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16
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Wang J, Liu Z, Li Y, Yang C, Ma X, Li H, Sun C. Signal-on fluorescent sensing strategy for Pb 2+ detection based on 8-17 DNAzyme-mediated molecular beacon-type catalytic hairpin assembly circuit. Anal Bioanal Chem 2022; 414:6581-6590. [PMID: 35831535 DOI: 10.1007/s00216-022-04218-w] [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: 05/29/2022] [Revised: 06/26/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
Abstract
Based on a Pb2+-specific 8-17 DNAzyme-induced catalytic hairpin assembly (CHA), a simple signal-on fluorescence strategy for lead ion detection was established. 8-17 DNAzyme was used as the recognition element of Pb2+, which catalyzed the cleavage of the RNA base embedded in the DNA substrate strand, while releasing part of the substrate strand (S') as CHA initiator. And two hairpin probes (H1 and H2-FQ) were designed according to the sequence of S' for CHA, in which H2-FQ was labeled with the fluorophore FAM and quencher BHQ-1 as fluorescent "molecular switch" based on fluorescence resonance energy transfer (FRET). In the presence of Pb2+, the CHA reaction was triggered to form a large number of H1-H2 complexes, enabling enzyme-free isothermal amplification and a signal-on fluorescence strategy. In the concentration range of 0.5-1000 nM, the fluorescence signal increases with the increase of Pb2+ concentration. The quantitative detection limit of Pb2+ by this method is 0.5 nM, which has better detection performance compared with the FQ-labeled 8-17 DNAzyme method. The established biosensor exhibits good specificity and can be effectively used for the detection of Pb2+ in real samples of river water and grass carp. Through ingenious nucleic acid sequence design, DNAzyme and CHA reactions are integrated to realize the enzyme-free isothermal amplifications and sensitive detection of Pb2+, which holds potential versatility in food supervision and environmental monitoring.
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Affiliation(s)
- Junyang Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Zheng Liu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Ying Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Chuanyu Yang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Hongxia Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
- Chongqing Research Institute, Jilin University, Changchun, People's Republic of China.
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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