1
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Miao Q, Ding W, Bao X, Wang S, Lin Q, Xu Y, Lu J, Lyu M, Wang S. An efficient
DNAzyme
for the fluorescence detection of
Vibrio cholerae. Food Sci Nutr 2023. [DOI: 10.1002/fsn3.3304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Affiliation(s)
- Qingzhen Miao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Wen Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Xiuli Bao
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Siyuan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Qianru Lin
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Yingying Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Jing Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Mingsheng Lyu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
| | - Shujun Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology Jiangsu Ocean University Lianyungang China
- Co‐Innovation Center of Jiangsu Marine Bio‐industry Technology Jiangsu Ocean University Lianyungang China
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2
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Huang Z, Wang X, Wu Z, Jiang JH. Recent Advances on DNAzyme-Based Sensing. Chem Asian J 2022; 17:e202101414. [PMID: 35156764 DOI: 10.1002/asia.202101414] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/09/2022] [Indexed: 11/08/2022]
Abstract
DNAzymes are functional nucleic acid with catalytic activity. Owing to the high sensitivity, excellent programmability, and flexible obtainment through in vitro selection, RNA-cleaving DNAzymes have attracted increasing interest in developing DNAzyme-based sensors. In this review, we summarize the recent advances on DNAzyme-based sensing applications. We initially conclude two general strategies to expand the library of DNAzymes, in vitro selection to discover new DNAzymes towards different targets of interest and chemical modifications to endue the existing DNAzymes with new function or properties. We then discuss the recent applications of DNAzyme-based sensors for the detection of a variety of important biomolecules both in vitro and in vivo . Finally, perspectives on the challenges and future directions in the development of DNAzyme-based sensors are provided.
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Affiliation(s)
- Zhimei Huang
- Hunan University, College of Chemistry and Chemical Engineering, CHINA
| | - Xiangnan Wang
- Hunan University of Technology and Business, College of Science, CHINA
| | - Zhenkun Wu
- Hunan University, State Key Laboratory of Chemeo/Bio-Sensing and Chemometrics and College of Chemistry and Chemical Engineering, South of Lushan Road, 410082, Changsha, CHINA
| | - Jian-Hui Jiang
- Hunan University, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering, CHINA
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3
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Yousefi H, Samani SE, Khan S, Prasad A, Shakeri A, Li Y, Filipe CDM, Didar TF. LISzyme Biosensors: DNAzymes Embedded in an Anti-biofouling Platform for Hands-free Real-Time Detection of Bacterial Contamination in Milk. ACS NANO 2022; 16:29-37. [PMID: 34872243 DOI: 10.1021/acsnano.1c05766] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nonspecific binding is a significant challenge associated with biosensors in complex food textures. To overcome this, we have developed LISzymes, which are DNAzymes incorporated in lubricant-infused surfaces (LISs). Using milk as a complex background matrix, we show that LISzyme biosensors are significantly more effective in preventing nonspecific binding compared to other commonly used "blocking" methods. The use of lubricant infusion to treat sensing surfaces results in a 4-fold increase in the signal-to-noise ratio obtained with the DNAzyme with respect to untreated surfaces, when detecting the presence of specific bacteria in milk. This is a striking improvement upon previous DNAzyme sensors. We also show that the use of LISs does not affect the DNAzyme's ability to effectively and specifically detect its target─a protein specifically produced by Escherichia coli (E. coli), in a complex sample matrix such as milk. LISzymes drastically improve DNAzyme performance, resulting in target detection associated with E. coli at concentrations as low as 250 CFU/mL in milk in less than an hour, which is currently not possible using other optical platforms. LISzymes are promising tools for the real-time monitoring of food contamination and may prove valuable within many other biosensing applications.
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Affiliation(s)
- Hanie Yousefi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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4
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Ali MM, Silva R, White D, Mohammadi S, Li Y, Capretta A, Brennan JD. A Lateral Flow Test for
Staphylococcus aureus
in Nasal Mucus Using a New DNAzyme as the Recognition Element. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- M. Monsur Ali
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Ryan Silva
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Dawn White
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Saeed Mohammadi
- Biointerfaces Institute McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 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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5
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Perrin D, Paul S, Wong AAWL, Liu LT. Selection of M2+-independent RNA-cleaving DNAzymes with Sidechains Mimicking Arginine and Lysine. Chembiochem 2021; 23:e202100600. [PMID: 34881502 DOI: 10.1002/cbic.202100600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/04/2021] [Indexed: 11/07/2022]
Abstract
Sequence-specific cleavage of RNA by nucleic acid catalysts in the absence of a divalent metal cation (M 2+ ) has remained an important goal in biomimicry with potential therapeutic applications. Given the lack of functional group diversity in canonical nucleotides, modified nucleotides with amino acid-like side chains were used to enhance self-cleavage rates at a single embedded ribonucleoside site. Previous works relied on three functional groups: an amine, a guanidine and an imidazole ensconced on three different nucleosides. However, to date, few studies have systematically addressed the necessity of all three modifications, as the value of any single modified nucleoside is contextualized at the outset of selection. Herein, we report on the use of only two modified dNTPs, excluding an imidazole, i.e. 5-(3-guanidinoallyl)-2'-dUTP (dU ga TP) and 5-aminoallyl-2'-dCTP (dC aa TP), to select in-vitro self-cleaving DNAzymes that cleave in the absence of M 2+ in a pH-independent fashion. Cleavage shows biphasic kinetics with rate constants that are significantly higher than in unmodified DNAzymes and compare favorably to certain DNAzymes involving an imidazole. This work is the first report of a M2+-independent DNAzyme with two cationic modifications; as such it shows appreciable self-cleaving activity in the absence of an imidazole modification.
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Affiliation(s)
- David Perrin
- U. British Columbia, Chemistry, 2036 Main Mall, V6T-1Z1, Vancouver, CANADA
| | - Somdeb Paul
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Antonio A W L Wong
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Leo T Liu
- The University of British Columbia, Chemistry, 2036 Main Mall, UBC, Vancouver, V6T-1Z1, Vancouver, CANADA
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6
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Ali MM, Silva R, White D, Mohammadi S, Li Y, Capretta A, Brennan JD. A Lateral Flow Test for Staphylococcus aureus in Nasal Mucus Using a New DNAzyme as the Recognition Element. Angew Chem Int Ed Engl 2021; 61:e202112346. [PMID: 34816559 DOI: 10.1002/anie.202112346] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Indexed: 12/14/2022]
Abstract
Detection of pathogenic bacteria in complex biological matrices remains a major challenge. Herein, we report the selection and optimization of a new DNAzyme for Staphylococcus aureus (SA) and the use of the DNAzyme to develop a simple lateral flow device (LFD) for detection of SA in nasal mucus. The DNAzyme was generated by in vitro selection using a crude extra/intracellular mixture derived from SA, which could be used directly for simple solution or paper-based fluorescence assays for SA. The DNAzyme was further modified to produce a DNA cleavage fragment that acted as a bridging element to bind DNA-modified gold nanoparticles to the test line of a LFD, producing a simple colorimetric dipstick test. The LFD was evaluated with nasal mucus samples spiked with SA, and demonstrated that SA detection was possible in minutes with minimal sample processing.
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Affiliation(s)
- M Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Ryan Silva
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Dawn White
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Saeed Mohammadi
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, 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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7
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Chang D, Zakaria S, Esmaeili Samani S, Chang Y, Filipe CDM, Soleymani L, Brennan JD, Liu M, Li Y. Functional Nucleic Acids for Pathogenic Bacteria Detection. Acc Chem Res 2021; 54:3540-3549. [PMID: 34478272 DOI: 10.1021/acs.accounts.1c00355] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Pathogens have long presented a significant threat to human lives, and hence the rapid detection of infectious pathogens is vital for improving human health. Current detection methods lack the means to detect infectious pathogens in a simple, rapid, and reliable manner at the time and point of need. Functional nucleic acids (FNAs) have the potential to overcome these limitations by acting as key components for point-of-care (POC) biosensors due to their distinctive advantages that include high binding affinities and specificities, excellent chemical stability, ease of synthesis and modification, and compatibility with a variety of signal-amplification and signal-transduction mechanisms.This Account summarizes the work completed in our groups toward developing FNA-based biosensors for detecting bacteria. In vitro selection has led to the isolation of many RNA-cleaving fluorogenic DNAzymes (RFDs) and DNA aptamers that can recognize infectious pathogens, including Escherichia coli, Clostridium difficile, Helicobacter pylori, and Legionella pneumophila. In most cases, a "many-against-many" approach was employed using a DNA library against a crude cellular mixture of an infectious pathogen containing diverse biomarkers as the target to isolate RFDs, with combined counter and positive selections ensuring high specificity toward the desired target. This procedure allows for the isolation of pathogen-specific FNAs without first identifying a suitable biomarker. Multiple target-specific DNA aptamers, including anti-glutamate dehydrogenase (GDH) circular aptamers, anti-degraded toxin B aptamers, and anti-RNase HII aptamers, have also been isolated for the detection of bacteria such as Clostridium difficile. The isolated FNAs have been integrated into fluorescent, colorimetric, and electrochemical biosensors using various signal transduction mechanisms. Both simple-to-use paper-based analytical devices and hand-held electrical devices with integrated FNAs have been developed for POC applications. In addition, signal-amplification strategies, including DNA catenane enabled rolling circle amplification (RCA), DNAzyme feedback RCA, and an all-DNA amplification system using a four-way junction and catalytic hairpin assembly (CHA), have been designed and applied to these systems to further increase their detection sensitivity. The use of these FNA-based biosensors to detect pathogens directly in clinical samples, such as urine, blood, and stool, has now been demonstrated with an outstanding sensitivity of as low as 10 cells per milliliter, highlighting the tremendous potential of using FNA-based sensors in clinical applications. We further describe strategies to overcome the challenges of using FNA-based biosensors in clinical applications, including strategies to improve the stability of FNAs in biological samples and prevent their nonspecific degradation from nucleases and strategies to deal with issues such as signal loss caused by nonspecific binding and biofouling. Finally, the remaining roadblocks for employing FNA-based biosensors in clinical applications are discussed.
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Affiliation(s)
| | | | | | - 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
| | | | | | | | - 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
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8
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Zheng J, Wai JL, Lake RJ, New SY, He Z, Lu Y. DNAzyme Sensor Uses Chemiluminescence Resonance Energy Transfer for Rapid, Portable, and Ratiometric Detection of Metal Ions. Anal Chem 2021; 93:10834-10840. [PMID: 34310132 PMCID: PMC9133356 DOI: 10.1021/acs.analchem.1c01077] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNAzymes have emerged as an important class of sensors for a wide variety of metal ions, with florescence DNAzyme sensors as the most widely used in different sensing and imaging applications because of their fast response time, high signal intensity, and high sensitivity. However, the requirements of an external excitation light source and its associated power increase the cost and size of the fluorometer, making it difficult to be used for portable detections. To overcome these limitations, we report herein a DNAzyme sensor that relies on chemiluminescence resonance energy transfer (CRET) without the need for external light. The sensor is constructed by combining the functional motifs from both Pb2+-dependent 8-17 DNAzyme conjugated to fluorescein (FAM) and hemin/G-quadruplex that mimics horseradish peroxidase to catalyze the oxidation of luminol by H2O2 to yield chemiluminescence. In the absence of Pb2+, the hybridization between the enzyme and substrate strands bring the FAM and hemin/G-quadruplex in close proximity, resulting in CRET. The presence of Pb2+ ions can drive the cleavage on the substrate strand, resulting in a sharp decrease in the melting temperature of hybridization and thus separation of the FAM from hemin/G-quadruplex. The liberated CRET pair causes a ratiometric increase in the donor's fluorescent signal and a decrease in the acceptor signal. Using this method, Pb2+ ions have been measured rapidly (<15 min) with a low limit of detection at 5 nM. By removing the requirement of exogenous light excitation, we have demonstrated a simple and portable detection using a smartphone, making the DNAzyme-CRET system suitable for field tests of lake water. Since DNAzymes selective for other metal ions or targets, such as bacteria, can be obtained using in vitro selection, the method reported here opens a new avenue for rapid, portable, and ratiometric detection of many targets in environmental monitoring, food safety, and medical diagnostics.
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Affiliation(s)
- Jiao Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Jing Luen Wai
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia
| | | | - Siu Yee New
- School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, 43500 Semenyih, Selangor, Malaysia
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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9
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Xu W, He W, Du Z, Zhu L, Huang K, Lu Y, Luo Y. Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications. Angew Chem Int Ed Engl 2021; 60:6890-6918. [PMID: 31729826 PMCID: PMC9205421 DOI: 10.1002/anie.201909927] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/29/2019] [Indexed: 01/01/2023]
Abstract
Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.
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Affiliation(s)
- Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Wanchong He
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana, Illinois 61801 (USA)
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, and College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083 (China)
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10
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Rothenbroker M, McConnell EM, Gu J, Urbanus ML, Samani SE, Ensminger AW, Filipe CDM, Li Y. Selection and Characterization of an RNA‐Cleaving DNAzyme Activated by
Legionella pneumophila. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Meghan Rothenbroker
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Erin M. McConnell
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | | | | | | | | | - Yingfu Li
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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11
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Rothenbroker M, McConnell EM, Gu J, Urbanus ML, Samani SE, Ensminger AW, Filipe CDM, Li Y. Selection and Characterization of an RNA‐Cleaving DNAzyme Activated by
Legionella pneumophila. Angew Chem Int Ed Engl 2021; 60:4782-4788. [DOI: 10.1002/anie.202012444] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/22/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Meghan Rothenbroker
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Erin M. McConnell
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | | | | | | | | | - Yingfu Li
- Michael G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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12
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Gong X, Li R, Wang J, Wei J, Ma K, Liu X, Wang F. A Smart Theranostic Nanocapsule for Spatiotemporally Programmable Photo‐Gene Therapy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008413] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Ruomeng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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13
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Gong X, Li R, Wang J, Wei J, Ma K, Liu X, Wang F. A Smart Theranostic Nanocapsule for Spatiotemporally Programmable Photo‐Gene Therapy. Angew Chem Int Ed Engl 2020; 59:21648-21655. [DOI: 10.1002/anie.202008413] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/17/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Xue Gong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Ruomeng Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jing Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jie Wei
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Kang Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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14
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Xu W, He W, Du Z, Zhu L, Huang K, Lu Y, Luo Y. Funktionelle Nukleinsäure‐Nanomaterialien: Entwicklung, Eigenschaften und Anwendungen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201909927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Wanchong He
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Zaihui Du
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
| | - Yi Lu
- Department of Chemistry University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Yunbo Luo
- Key Laboratory of Precision Nutrition and Food Quality Department of Nutrition and Health, and College of Food Science and Nutritional Engineering China Agricultural University Beijing 100083 China
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15
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Zhou Z, Brennan JD, Li Y. A Multi‐component All‐DNA Biosensing System Controlled by a DNAzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Zhixue Zhou
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences 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 4O3 Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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16
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Zhou Z, Brennan JD, Li Y. A Multi‐component All‐DNA Biosensing System Controlled by a DNAzyme. Angew Chem Int Ed Engl 2020; 59:10401-10405. [PMID: 32207868 DOI: 10.1002/anie.202002019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Zhixue Zhou
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences 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 4O3 Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences McMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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17
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Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020; 59:3573-3577. [PMID: 31867832 DOI: 10.1002/anie.201915675] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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18
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Huang PJ, Rochambeau D, Sleiman HF, Liu J. Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Po‐Jung Jimmy Huang
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
| | - Donatien Rochambeau
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 Sherbrooke Street West Montréal Québec H3A 0B8 Canada
| | - Juewen Liu
- Department of ChemistryWaterloo Institute for Nanotechnology University of Waterloo 200 University Avenue West Waterloo Ontario N2L 3G1 Canada
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19
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Samani SE, Chang D, McConnell EM, Rothenbroker M, Filipe CDM, Li Y. Highly Sensitive RNA-Cleaving DNAzyme Sensors from Surface-to-Surface Product Enrichment. Chembiochem 2019; 21:632-637. [PMID: 31544309 DOI: 10.1002/cbic.201900575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Indexed: 12/13/2022]
Abstract
The engineering of easy-to-use biosensors with ultra-low detection sensitivity remains a major challenge. Herein, we report a simple approach for creating such sensors through the use of an RNA-cleaving DNAzyme (RcD) and a strategy designed to concentrate its cleavage product significantly. The assay uses micron-sized beads loaded with a target-responsive RcD and a paper strip containing a microzone covered with a DNA oligonucleotide capable of capturing the cleavage product of the RcD through Watson-Crick hybridization. Placing the beads and the paper strip in a target-containing test sample allows the bead-bound RcD molecules to undergo target-induced RNA cleavage, releasing a DNA fragment that is captured by the paper strip. This strategy, though simple, is very effective in achieving high levels of detection sensitivity, being able to enrich the concentration of the cleavage product by three orders of magnitude. It is also compatible with both fluorescence-based and colorimetric reporting mechanisms. This work provides a simple platform for developing ultrasensitive biosensors that take advantage of the widely available RcDs as molecular recognition elements.
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Affiliation(s)
- Sahar Esmaeili Samani
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Meghan Rothenbroker
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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20
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Chang D, Chang T, Salena B, Li Y. An Unintentional Discovery of a Fluorogenic DNA Probe for Ribonuclease I. Chembiochem 2019; 21:464-468. [PMID: 31420934 DOI: 10.1002/cbic.201900455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Dingran Chang
- M.G. DeGroote Institute for Infectious Disease ResearchDepartment of Biochemistry and Biomedical SciencesDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Thomas Chang
- M.G. DeGroote Institute for Infectious Disease ResearchDepartment of Biochemistry and Biomedical SciencesDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno Salena
- Department of MedicineDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease ResearchDepartment of Biochemistry and Biomedical SciencesDeGroote School of MedicineMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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21
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Ali MM, Wolfe M, Tram K, Gu J, Filipe CDM, Li Y, Brennan JD. A DNAzyme‐Based Colorimetric Paper Sensor for
Helicobacter pylori. Angew Chem Int Ed Engl 2019; 58:9907-9911. [PMID: 31095864 DOI: 10.1002/anie.201901873] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/18/2019] [Indexed: 01/25/2023]
Affiliation(s)
- M. Monsur Ali
- Biointerfaces InstituteMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Michael Wolfe
- Biointerfaces InstituteMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Kha Tram
- InnovoGene Biosciences Inc. 919 Fraser Drive Burlington ON L7L 4X8 Canada
| | - Jimmy Gu
- InnovoGene Biosciences Inc. 919 Fraser Drive Burlington ON L7L 4X8 Canada
- Department of Biochemistry and Biomedical SciencesMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Carlos D. M. Filipe
- Department of Chemical EngineeringMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- InnovoGene Biosciences Inc. 919 Fraser Drive Burlington ON L7L 4X8 Canada
- Department of Biochemistry and Biomedical SciencesMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - John D. Brennan
- Biointerfaces InstituteMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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22
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Ali MM, Wolfe M, Tram K, Gu J, Filipe CDM, Li Y, Brennan JD. A DNAzyme‐Based Colorimetric Paper Sensor forHelicobacter pylori. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901873] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- M. Monsur Ali
- Biointerfaces InstituteMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Michael Wolfe
- Biointerfaces InstituteMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Kha Tram
- InnovoGene Biosciences Inc. 919 Fraser Drive Burlington ON L7L 4X8 Canada
| | - Jimmy Gu
- InnovoGene Biosciences Inc. 919 Fraser Drive Burlington ON L7L 4X8 Canada
- Department of Biochemistry and Biomedical SciencesMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Carlos D. M. Filipe
- Department of Chemical EngineeringMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- InnovoGene Biosciences Inc. 919 Fraser Drive Burlington ON L7L 4X8 Canada
- Department of Biochemistry and Biomedical SciencesMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - John D. Brennan
- Biointerfaces InstituteMcMaster University 1280 Main Street West Hamilton ON L8S 4K1 Canada
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23
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Gu L, Yan W, Wu H, Fan S, Ren W, Wang S, Lyu M, Liu J. Selection of DNAzymes for Sensing Aquatic Bacteria: Vibrio Anguillarum. Anal Chem 2019; 91:7887-7893. [DOI: 10.1021/acs.analchem.9b01707] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | - Wei Ren
- Key Laboratory of Marine Biology, Nanjing Agricultural University, Nanjing, Jiangsu 210000, P. R. China
| | | | | | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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24
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Ali MM, Slepenkin A, Peterson E, Zhao W. A Simple DNAzyme-Based Fluorescent Assay for Klebsiella pneumoniae. Chembiochem 2019; 20:906-910. [PMID: 30521678 PMCID: PMC6692177 DOI: 10.1002/cbic.201800701] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Indexed: 11/09/2022]
Abstract
Pathogenic bacteria pose a serious threat to public health, and the rapid and cost-effective detection of such bacteria remains a major challenge. Herein, we present a DNAzyme-based fluorescent paper sensor for Klebsiella pneumoniae. The DNAzyme was generated by an in vitro selection technique to cleave a fluorogenic DNA-RNA chimeric substrate in the presence of K. pneumoniae. The DNAzyme was printed on a paper substrate in a 96-well format to serve as mix-and-read fluorescent assay that exhibits a limit of detection (LOD) 105 CFUs mL-1 . Evaluated with 20 strains of clinical bacterial isolates, the DNAzyme produced the desired fluorescence signal with the samples of K. pneumoniae, regardless of their source or drug resistance. The assay is simple to use, rapid, inexpensive, and avoids the complex procedures of sample preparation and equipment. We believe that this DNAzyme-based fluorescent assay has potential for practical applications to identify K. pneumoniae.
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Affiliation(s)
- M Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4K1, Canada
| | - Anatoly Slepenkin
- Department of Pathology and Laboratory Medicine, University of California, 1001 Health Sciences Road, Irvine, CA, 92697, USA
| | - Ellena Peterson
- Department of Pathology and Laboratory Medicine, University of California, 1001 Health Sciences Road, Irvine, CA, 92697, USA
| | - Weian Zhao
- Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology and, The Department of Biomedical Engineering, University of California-Irvine, 845 Health Sciences Road, Irvine, CA, 92697, USA
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25
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Liu M, Zhang Q, Kannan B, Botton GA, Yang J, Soleymani L, Brennan JD, Li Y. Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806489] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
- School of Environmental Science and Technology; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education); Dalian University of Technology; Dalian 116024 China
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Balamurali Kannan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Gianluigi A. Botton
- Department of Materials Science and Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Jie Yang
- School of Biomedical Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - Leyla Soleymani
- School of Biomedical Engineering; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
| | - John D. Brennan
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton Ontario L8S4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton Ontario L8S4O3 Canada
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26
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Liu M, Zhang Q, Kannan B, Botton GA, Yang J, Soleymani L, Brennan JD, Li Y. Self-Assembled Functional DNA Superstructures as High-Density and Versatile Recognition Elements for Printed Paper Sensors. Angew Chem Int Ed Engl 2018; 57:12440-12443. [PMID: 30043544 DOI: 10.1002/anie.201806489] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 11/08/2022]
Abstract
Micrometer-sized functional nucleic acid (FNA) superstructures (denoted as 3D DNA) were examined as a unique class of biorecognition elements to produce highly functional bioactive paper surfaces. 3D DNA containing repeating sequences of either a DNA aptamer or DNAzyme was created from long-chain products of rolling circle amplification followed by salt aging. The resulting 3D DNA retained its original spherical shape upon inkjet printing and adhered strongly to the paper surface via physisorption. 3D DNA paper sensors showed resistance to degradation by nucleases, suppressed nonspecific protein adsorption, and provided a much higher surface density of functional DNA relative to monomeric FNAs, making such species ideally suited for development of paper-based biosensors.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada.,School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Qiang Zhang
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Balamurali Kannan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Gianluigi A Botton
- Department of Materials Science and Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Jie Yang
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - Leyla Soleymani
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S4O3, Canada
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27
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Liu M, Yin Q, McConnell EM, Chang Y, Brennan JD, Li Y. DNAzyme Feedback Amplification: Relaying Molecular Recognition to Exponential DNA Amplification. Chemistry 2018; 24:4473-4479. [PMID: 29240289 DOI: 10.1002/chem.201705338] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Indexed: 01/10/2023]
Abstract
Technologies capable of linking DNA amplification to molecular recognition are very desirable for ultrasensitive biosensing applications. We have developed a simple but powerful isothermal DNA amplification method, termed DNAzyme feedback amplification (DFA), that is capable of relaying molecular recognition to exponential DNA amplification. The method incorporates both an RNA-cleaving DNAzyme (RCD) and rolling circle amplification (RCA) carried out by a special DNA polymerase using a circular DNA template. DFA begins with a stimulus-dependent RCA reaction, producing tandemly linked RCDs in long-chain DNA products. These RCDs cleave an RNA-containing DNA sequence to form additional primers that hybridize to the circular DNA molecule, giving rise to DNA assemblies that act as the new inputs for RCA. The RCA reaction and the cleavage event keep on feeding each other autonomously, resulting in exponential growth of repetitive DNA sequences that can be easily detected. This method can be used for the detection of both nucleic acid based targets and non-nucleic acid analytes. In this article, we discuss the conceptual framework of the feedback amplification approach, the essential features of this method as well as remaining challenges and possible solutions.
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Affiliation(s)
- 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, P. R. China
| | - Qingxin Yin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, P. R. China
| | - Erin M McConnell
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - 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, P. R. China
| | - John D Brennan
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.,Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4L8, Canada
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28
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Wang J, Qin H, Wang F, Ren J, Qu X. Metal-Ion-Activated DNAzymes Used for Regulation of Telomerase Activity in Living Cells. Chemistry 2017. [DOI: 10.1002/chem.201702236] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jiasi Wang
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | - Hongshuang Qin
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Faming Wang
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology; and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
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29
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30
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Liu M, Zhang Q, Chang D, Gu J, Brennan JD, Li Y. A DNAzyme Feedback Amplification Strategy for Biosensing. Angew Chem Int Ed Engl 2017; 56:6142-6146. [PMID: 28370773 DOI: 10.1002/anie.201700054] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Qiang Zhang
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; 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 4L8 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences and Chemistry & Chemical Biology; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Biointerfaces Institute; McMaster University; 1280 Main Street West Hamilton ON L8S 4L8 Canada
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31
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Hsieh PY, Monsur Ali M, Tram K, Jahanshahi-Anbuhi S, Brown CL, Brennan JD, Filipe CDM, Li Y. RNA Protection is Effectively Achieved by Pullulan Film Formation. Chembiochem 2017; 18:502-505. [PMID: 28090736 DOI: 10.1002/cbic.201600643] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 11/05/2022]
Abstract
RNA is a functionally versatile polymer but suffers from susceptibility to spontaneous and RNase-catalyzed degradation. This vulnerability makes it difficult to preserve RNA for extended periods of time, thus limiting its use in various contexts, including practical applications as functional nucleic acids. Here we present a simple method to preserve RNA by pullulan (a complex sugar produced by Aureobasidium pullulans fungus) film formation. This strategy can markedly suppress both spontaneous and RNase degradation. Importantly, the pullulan film readily dissolves in aqueous solution, thus allowing retrieval of fully functional RNA species. In order to illustrate the advantage of this protective method in a practical application, we engineered a simple paper sensor containing a bacteria-detecting RNA-cleaving DNAzyme. This detection capability of the device was unchanged after storage at room temperature for six months.
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Affiliation(s)
- Ping-Yao Hsieh
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - M Monsur Ali
- Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Kha Tram
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Sana Jahanshahi-Anbuhi
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada)
| | - Christine L Brown
- Department of Chemical Engineering, 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
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada)
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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32
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Zhou W, Saran R, Huang PJJ, Ding J, Liu J. An Exceptionally Selective DNA Cooperatively Binding Two Ca2+Ions. Chembiochem 2017; 18:518-522. [PMID: 28087991 DOI: 10.1002/cbic.201600708] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Wenhu Zhou
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Runjhun Saran
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
| | - Jinsong Ding
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
| | - Juewen Liu
- School of Pharmaceutical Sciences; Central South University; 172 Tongzipo Road Changsha Hunan 410013 China
- Department of Chemistry; Waterloo Institute for Nanotechnology; University of Waterloo; 200 University Avenue West Waterloo ON N2L 3G1 Canada
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33
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Shen Z, Wu Z, Chang D, Zhang W, Tram K, Lee C, Kim P, Salena BJ, Li Y. A Catalytic DNA Activated by a Specific Strain of Bacterial Pathogen. Angew Chem Int Ed Engl 2015; 55:2431-4. [PMID: 26676768 PMCID: PMC5064636 DOI: 10.1002/anie.201510125] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Indexed: 11/29/2022]
Abstract
Pathogenic strains of bacteria are known to cause various infectious diseases and there is a growing demand for molecular probes that can selectively recognize them. Here we report a special DNAzyme (catalytic DNA), RFD‐CD1, that shows exquisite specificity for a pathogenic strain of Clostridium difficile (C. difficile). RFD‐CD1 was derived by an in vitro selection approach where a random‐sequence DNA library was allowed to react with an unpurified molecular mixture derived from this strain of C. difficle, coupled with a subtractive selection strategy to eliminate cross‐reactivities to unintended C. difficile strains and other bacteria species. RFD‐CD1 is activated by a truncated version of TcdC, a transcription factor, that is unique to the targeted strain of C. difficle. Our study demonstrates for the first time that in vitro selection offers an effective approach for deriving functional nucleic acid probes that are capable of achieving strain‐specific recognition of bacterial pathogens.
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Affiliation(s)
- Zhifa Shen
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Zaisheng Wu
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Wenqing Zhang
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Kha Tram
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada
| | - Christine Lee
- Department of Pathology and Molecular Medicine, St Joseph's Healthcare, McMaster University, 50 Charlton Ave E, 424 Luke Wing, Hamilton, Ontario, L8N 4A6, Canada
| | - Peter Kim
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Bruno J Salena
- Department of Medicine, McMaster University, 1280 Main St. W., Hamilton, Ontario, L8S 4K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.
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Shen Z, Wu Z, Chang D, Zhang W, Tram K, Lee C, Kim P, Salena BJ, Li Y. A Catalytic DNA Activated by a Specific Strain of Bacterial Pathogen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201510125] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhifa Shen
- Department of Biochemistry and Biomedical Sciences; Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
- School of Laboratory Medicine and Life Sciences; Wenzhou Medical University; Wenzhou Zhejiang 325035 China
| | - Zaisheng Wu
- Department of Biochemistry and Biomedical Sciences; Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences; Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Wenqing Zhang
- Department of Biochemistry and Biomedical Sciences; Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Kha Tram
- Department of Biochemistry and Biomedical Sciences; Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Christine Lee
- Department of Pathology and Molecular Medicine; St Joseph's Healthcare; McMaster University; 50 Charlton Ave E, 424 Luke Wing Hamilton Ontario L8N 4A6 Canada
| | - Peter Kim
- Department of Mathematics and Statistics; University of Guelph; Guelph Ontario N1G 2W1 Canada
| | - Bruno J. Salena
- Department of Medicine; McMaster University; 1280 Main St. W. Hamilton Ontario L8S 4K1 Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences; Michael G. DeGroote Institute for Infectious Disease Research; McMaster University; 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
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Tram K, Kanda P, Salena BJ, Huan S, Li Y. Translating Bacterial Detection by DNAzymes into a Litmus Test. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407021] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Tram K, Kanda P, Salena BJ, Huan S, Li Y. Translating Bacterial Detection by DNAzymes into a Litmus Test. Angew Chem Int Ed Engl 2014; 53:12799-802. [DOI: 10.1002/anie.201407021] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Indexed: 01/20/2023]
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Yingfu Li. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Yingfu Li. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201403018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Chemical Institute of Canada and Canadian Society for Chemistry Awards. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201209647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Preise des Chemical Institute of Canada und der Canadian Society for Chemistry. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201209647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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