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Takemura S, Shimada N, Maruyama A. Malachite green-derivatized cationic comb-type copolymer acts as a photoresponsive artificial chaperone. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2023; 34:2463-2482. [PMID: 37787160 DOI: 10.1080/09205063.2023.2265127] [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: 12/02/2022] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
Molecular chaperones play vital roles in various physiological reactions by regulating the folding and assembly of biomacromolecules. We have demonstrated that cationic comb-type copolymers exhibit chaperone activity for anionic biomolecules including DNA and ionic peptide via the formation of soluble interpolyelectrolyte complexes. The development of smart artificial chaperones that can be spatiotemporally controlled by a remotely guided signal would expand the functions of artificial chaperones. Herein, to enable photocontrol of chaperone activity, a cationic comb-type copolymer bearing malachite green as a photoresponsive unit was designed. We first prepared a series of carboxylic acid derivatives of malachite green identified a derivative that could be quickly and quantitatively converted to the cationic form from the nonionic form by photoirradiation. This derivative was conjugated to the cationic comb-type copolymer, poly(allylamine)-graft-poly(ethylene glycol) through a condensation reaction. Upon photoirradiation, the copolymer bearing 9 mol% malachite green enhanced the membrane disruptive activity of acidic peptide E5 and induced morphological changes in liposomes. This demonstration of photoresponsive activation of chaperoning activity of a copolymer suggests that the installation of carboxyl derivatives of malachite green will impart photoresponsiveness to various materials including biopolymers.
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Affiliation(s)
- Seiya Takemura
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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Wang J, Huang H, Hanpanich O, Shimada N, Maruyama A. Cationic copolymer and crowding agent have a cooperative effect on a Na +-dependent DNAzyme. Biomater Sci 2023; 11:7062-7066. [PMID: 37706516 DOI: 10.1039/d3bm01119d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
DNAzymes are promising agents for theranostics and biosensors. Sodium dependent DNAzymes have been developed for sensing and imaging of Na+, but these DNAzymes have low catalytic activity. Herein, we demonstrate that a molecular crowded environment containing 10 to 40 wt% PEG enhanced the catalytic activity of a Na+-dependent DNAzyme, EtNa, although dextran did not. The cationic copolymer poly(L-lysine)-graft-poly(ethylene glycol) at 0.03 wt% (0.3 g L-1) enhanced the reaction rate of EtNa by 10-fold, which is similar to the acceleration induced by 15 wt% (150 g L-1) PEG. A cooperative impact of the copolymer and crowding agent was observed: the combination resulted in an impressive 46-fold acceleration effect. Thus, the use of a cationic copolymer and a crowding agent is a promising strategy to improve the activity of Na+-dependent DNAzyme-based nanomachines, biosensors, and theranostics, especially in environments lacking divalent metal ions.
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Affiliation(s)
- Jun Wang
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - He Huang
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259 B-57, Midori, Yokohama 226-8501, Japan.
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Liu H, Li Y, Du S, Wang C, Li Y, Cao R, Shi W, Liu S, He J. Studies on the Effect of Lipofectamine and Cell-Penetrating Peptide on the Properties of 10-23 DNAzyme. Molecules 2023; 28:molecules28093942. [PMID: 37175352 PMCID: PMC10179765 DOI: 10.3390/molecules28093942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Cationic polymeric materials and cell-penetrating peptides (CPPs) were often used as the delivery vectors in the evaluation of nucleic acid therapeutics. 10-23 DNAzyme is a kind of potential antisense therapeutics by catalytic cleavage of the disease-related RNAs. Here, lipofectamine 2000 and Tat peptide were evaluated for their effect on the catalytic activity of 10-23 DNAzyme, with the observed rate constant, thermal stability, CD spectra, and PAGE analysis, with a duplex DNA mimicking DNAzyme-substrate as a control. It was shown that the cationic carriers had a negative effect on the catalytic performance of the 10-23 DNAzyme. Significantly, the destabilizing effect of the cationic carriers on the duplex formation was noteworthy, as a duplex formation is an essential prerequisite in the silencing mechanisms of antisense and RNAi.
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Affiliation(s)
- Huanhuan Liu
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Yang Li
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Shanshan Du
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Chenhong Wang
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Yuexiang Li
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Ruiyuan Cao
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Weiguo Shi
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
| | - Shihui Liu
- School of Pharmaceutical Sciences, Guizhou University, Guiyang 550025, China
| | - Junlin He
- State Key Laboratory of Toxicology and Medical Countermeasurements, Beijing Institute of Pharmacology and Toxicology, Taiping 27, Beijing 100850, China
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8-17 DNAzyme Silencing Gene Expression in Cells via Cleavage and Antisense. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010286. [PMID: 36615479 PMCID: PMC9821912 DOI: 10.3390/molecules28010286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Gene silencing is an important biological strategy for studying gene functions, exploring disease mechanisms and developing therapeutics. 8-17 DNAzyme is of great potential for gene silencing, due to its higher RNA-cleaving activity. However, it is not generally used in practice, due to its divalent cation dependence and poor understanding of its cellular mechanisms. To address these issues, we have explored its activity in vitro and in cells and found that it can cleave RNA substrates under the simulated physiological conditions, and its gene-silencing activity is additionally enhanced by its RNase H compatibility, offering both cleavage and antisense activities in cells. Further, chemical modifications can facilitate its stability, substrate binding affinity and gene-silencing activity. Our research results suggest that this DNAzyme can demonstrate high levels of activities for both actions in cells, making it a useful tool for exploring biomedical applications.
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Label-free detection of HPV mRNA with an artificial chaperone-enhanced MNAzyme (ACEzyme)-based electrochemical sensor. Biosens Bioelectron 2022; 221:114352. [PMID: 35690559 DOI: 10.1016/j.bios.2022.114352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022]
Abstract
Nucleic acid biosensors for point-of-care (POC) diagnostic applications are highly desirable. The ability to detect DNA and RNA in a simple, rapid, affordable and portable format leads to a range of important applications for early screening in the field of disease monitoring and management. Herein, we report the development of an isothermal, label-free electrochemical biosensor that was designed on the basis of target-driven MNAzyme cleavage activity. Hybridization with HPV mRNA, a model nucleic acid target, activated MNAzyme and initiated the cleavage of immobilized hairpin substrates, leading to changes in the electrochemical signal. Under optimal conditions, a detection limit of 2.6 pM was obtained with an incubation time of 60 min. Furthermore, an artificial chaperone-enhanced MNAzyme (ACEzyme) system was integrated to an electrochemical biosensor for the first time. The analytical performance of the biosensor was enhanced, and the detection time was significantly reduced by the addition of PLL-g-Dex, which exhibits nucleic acid chaperone-like activity. A detection limit of 0.88 pM was obtained with a threefold decrease in incubation time without prior amplification. The proposed biosensing platform shows the advantages of simple fabrication and operation, good selectivity in the presence of single-base mismatch, and excellent versatility in a complex mixture of total RNA. We believe that this isothermal, label-free, and protein-free nucleic acid analysis platform could provide foundations for the further development of a universal nucleic acid biosensing platform for clinical application.
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Jiang H, Ji P, Xu Y, Liu X, Kong D. Self-paired dumbbell DNA -assisted simple preparation of stable circular DNAzyme and its application in Pb 2+ sensor. Anal Chim Acta 2021; 1175:338733. [PMID: 34330440 DOI: 10.1016/j.aca.2021.338733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/23/2021] [Accepted: 06/01/2021] [Indexed: 01/20/2023]
Abstract
During its development in recent decades, DNAzyme has become a promising candidate for application in biosensor field. However, it still suffers from the problem of thermodynamic and biological instability such as nuclease digestion, which limits its applications in complex samples. Here we have presented a simple and common strategy to resolve this problem by engineering the linear DNAzyme into a circular shape DNAzyme based on the integration of substrate and enzyme parts into one single-stranded sequence. This circular DNAzyme system is indeed endowed with excellent stability due to the stable intramolecular double-stranded formation and extraordinary resistance to nuclease digestion due to the closed structure. We demonstrated that this circular DNAzyme system gained excellent stability and could active under conditions across a broader range of temperature, salt concentrations, and pH. Depending on this circular DNAzyme, combing with Terminal deoxynucleotidyl transferase (TdT)-generated G-quadruplexes, a label free colorimetric sensing platform for Pb2+ quantitation was developed, and a detection limit of 0.085 nM was achieved. Then the enzyme digestion cycle amplification was introduced to further improve the sensitivity of the sensing system, an ultralow detection limit of 0.0015 nM for this fluorescence method was achieved. Based on the two sensing platforms, ultrasensitive analysis of Pb2+ in environmental water and food samples was successfully realized. It is anticipated that this stable circular DNAzyme design will be helpful for trace detection in complex samples.
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Affiliation(s)
- Hongxin Jiang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Pingping Ji
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China
| | - Yaping Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Xiaowei Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China; Key Laboratory for Environmental Factors Control of Agro-product Quality Safety, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, PR China.
| | - Deming Kong
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, PR China
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Takenaka T, Sakamoto W, Takahashi S, Shimada N, Maruyama A. Spatially regulated activation of membrane fusogenic peptides with chaperone-like ionic copolymers. J Control Release 2021; 330:463-469. [PMID: 33359738 DOI: 10.1016/j.jconrel.2020.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/29/2022]
Abstract
Controlled or targeted membrane lysis induced by cascades of assembly and activation of biomolecules on membrane surfaces is important in programmed cell death and host defense systems. In a previous study, we reported that an ionic graft copolymer with a polycation backbone and water-soluble graft chains, poly(allylamine)-graft-dextran (PAA-g-Dex) chaperoned folding and assembly of E5, a membrane-destructive peptide derived from influenza hemagglutinin, to its increase membrane-disruptive activity. In this study, we modified the copolymer with long acyl chains, which resulted in delivery of the copolymer to membrane surfaces of liposomes and living cells. The liposomes with PAA-g-Dex functionalized with stearic acid (PAA-g-Dex-SA) on their surfaces underwent vesicle-to-sheet conversion upon addition of E5, whereas control liposomes did not. E5 also induced selective lysis of cells incubated with PAA-g-Dex-SA. The spatially specific activation of E5 on target membrane surfaces driven by self-assembly of copolymer and activation of E5 should find application in lipid-based delivery devices and cell-based therapeutics.
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Affiliation(s)
- Tomoka Takenaka
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Midori, Yokohama 226-8501, Japan
| | - Wakako Sakamoto
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Midori, Yokohama 226-8501, Japan
| | - Shutaro Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Midori, Yokohama 226-8501, Japan
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Midori, Yokohama 226-8501, Japan
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 B-57, Nagatsuta, Midori, Yokohama 226-8501, Japan.
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Hanpanich O, Saito K, Shimada N, Maruyama A. One-step isothermal RNA detection with LNA-modified MNAzymes chaperoned by cationic copolymer. Biosens Bioelectron 2020; 165:112383. [PMID: 32729508 PMCID: PMC7836245 DOI: 10.1016/j.bios.2020.112383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Abstract
RNA detection permits early diagnosis of several infectious diseases and cancers, which prevent propagation of diseases and improve treatment efficacy. However, standard technique for RNA detection such as reverse transcription-quantitative polymerase chain reaction has complicated procedure and requires well-trained personnel and specialized lab equipment. These shortcomings limit the application for point-of-care analysis which is critical for rapid and effective disease management. The multicomponent nucleic acid enzymes (MNAzymes) are one of the promising biosensors for simple, isothermal and enzyme-free RNA detection. Herein, we demonstrate simple yet effective strategies that significantly enhance analytical performance of MNAzymes. The addition of the cationic copolymer and structural modification of MNAzyme significantly enhanced selectivity and activity of MNAzymes by 250 fold and 2,700 fold, respectively. The highly simplified RNA detection system achieved a detection limit of 73 fM target concentration without additional amplification. The robustness of MNAzyme in the presence of non-target RNA was also improved. Our finding opens up a route toward the development of an alternative rapid, sensitive, isothermal, and protein-free RNA diagnostic tool, which expected to be of great clinical significance.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Ken Saito
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Naohiko Shimada
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259 B-57, Yokohama, 226-8501, Japan.
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Artificial chaperones: From materials designs to applications. Biomaterials 2020; 254:120150. [DOI: 10.1016/j.biomaterials.2020.120150] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022]
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