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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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Wang J, Raito H, Shimada N, Maruyama A. A Cationic Copolymer Enhances Responsiveness and Robustness of DNA Circuits. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2304091. [PMID: 37340578 DOI: 10.1002/smll.202304091] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/12/2012] [Indexed: 06/22/2023]
Abstract
Toehold-mediated DNA circuits are extensively employed to construct diverse DNA nanodevices and signal amplifiers. However, operations of these circuits are slow and highly susceptive to molecular noise such as the interference from bystander DNA strands. Herein, this work investigates the effects of a series of cationic copolymers on DNA catalytic hairpin assembly, a representative toehold-mediated DNA circuit. One copolymer, poly(L -lysine)-graft-dextran, significantly enhances the reaction rate by 30-fold due to its electrostatic interaction with DNA. Moreover, the copolymer considerably alleviates the circuit's dependency on the length and GC content of toehold, thereby enhancing the robustness of circuit operation against molecular noise. The general effectiveness of poly(L -lysine)-graft-dextran is demonstrated through kinetic characterization of a DNA AND logic circuit. Therefore, use of a cationic copolymer is a versatile and efficient approach to enhance the operation rate and robustness of toehold-mediated DNA circuits, paving the way for more flexible design and broader application.
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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
| | - Hayashi Raito
- 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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3
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Nucleic acid-based fluorescent sensor systems: a review. Polym J 2022. [DOI: 10.1038/s41428-022-00623-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ma F, Wu X, Li A, Xu L, An Y, Shi L. A Balance Between Capture and Release: How Nanochaperones Regulate Refolding of Thermally Denatured Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Feihe Ma
- Key Laboratory of Functional Polymer Materials of Ministry of Education Institute of Polymer Chemistry and College of Chemistry Nankai University Tianjin 300071 P. R. China
| | - Xiaohui Wu
- Key Laboratory of Functional Polymer Materials of Ministry of Education Institute of Polymer Chemistry and College of Chemistry Nankai University Tianjin 300071 P. R. China
| | - Ang Li
- State Key Laboratory of Medicinal Chemical Biology Nankai University Tianjin 300071 P. R. China
| | - Linlin Xu
- Key Laboratory of Functional Polymer Materials of Ministry of Education Institute of Polymer Chemistry and College of Chemistry Nankai University Tianjin 300071 P. R. China
| | - Yingli An
- Key Laboratory of Functional Polymer Materials of Ministry of Education Institute of Polymer Chemistry and College of Chemistry Nankai University Tianjin 300071 P. R. China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education Institute of Polymer Chemistry and College of Chemistry Nankai University Tianjin 300071 P. R. China
- State Key Laboratory of Medicinal Chemical Biology Nankai University Tianjin 300071 P. R. China
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Ma F, Wu X, Li A, Xu L, An Y, Shi L. A Balance Between Capture and Release: How Nanochaperones Regulate Refolding of Thermally Denatured Proteins. Angew Chem Int Ed Engl 2021; 60:10865-10870. [PMID: 33595165 DOI: 10.1002/anie.202101462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 01/06/2023]
Abstract
Nanochaperones have been designed and used for regulating the (re)folding of proteins, treating protein misfolding-related diseases, and, more recently, in drug delivery. Despite various successes, a complete understanding of the working mechanisms remains elusive, which represents a challenge for the realization of their full potential. Here, we thoroughly investigated the functioning of differently charged nanochaperones that regulate the refolding of thermally denatured lysozyme. We found that the balance between the capture and release of lysozyme clients that are controlled by nanochaperones plays a key role in regulating refolding. More importantly, the findings could be applied to other enzymes with various physicochemical properties. On the basis of these results, we could recover the activity of enzymes with high efficiency either after 20 days of storage at 40 °C or heating at high temperatures for 30-60 min. Our results provide important new design strategies for nanochaperone systems to improve their properties and expand their applications.
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Affiliation(s)
- Feihe Ma
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Xiaohui Wu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Ang Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P. R. China
| | - Linlin Xu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Yingli An
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, Institute of Polymer Chemistry and College of Chemistry, Nankai University, Tianjin, 300071, P. R. China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, P. R. China
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6
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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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7
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Nishimura T, Akiyoshi K. Artificial Molecular Chaperone Systems for Proteins, Nucleic Acids, and Synthetic Molecules. Bioconjug Chem 2020; 31:1259-1267. [DOI: 10.1021/acs.bioconjchem.0c00133] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomoki Nishimura
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Rudeejaroonrung K, Hanpanich O, Saito K, Shimada N, Maruyama A. Cationic copolymer enhances 8–17 DNAzyme and MNAzyme activities. Biomater Sci 2020; 8:3812-3818. [DOI: 10.1039/d0bm00428f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cationic copolymer acts as a chaperone to facilitate multiple strand assembly and enhance nucleic acid enzyme activities.
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Affiliation(s)
| | - Orakan Hanpanich
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Ken Saito
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Naohiko Shimada
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Atsushi Maruyama
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
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