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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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2
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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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3
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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: 0] [Impact Index Per Article: 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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4
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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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5
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Wang J, Shimada N, Maruyama A. Cationic Copolymer-Augmented DNA Hybridization Chain Reaction. ACS APPLIED MATERIALS & INTERFACES 2022; 14:39396-39403. [PMID: 35975327 DOI: 10.1021/acsami.2c11548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Various DNA assembly techniques and structures have emerged with the continuous progress of DNA nanotechnology. DNA hybridization chain reaction (HCR) is a representative example owing to isothermal and enzyme-free features. However, HCR is time consuming and is inhibited by nucleases present in biological samples. Herein, we demonstrated that a cationic copolymer, poly(l-lysine)-graft-dextran (PLL-g-Dex), significantly facilitated HCR and increased its initiator sensitivity by 40-fold. PLL-g-Dex promoted the generation of HCR products with high molecular weight by accelerating the initiation and the subsequent growth steps of HCR. Moreover, PLL-g-Dex protected the HCR system from nucleases, permitting HCR in the presence of serum components. Addition of PLL-g-Dex is a universal and efficient strategy that does not require optimization of the reactor setup or DNA sequences, thus laying a solid foundation for the wider application of HCR.
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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
| | - 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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6
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Sánchez-Visedo A, Ferrero FJ, Costa-Fernández JM, Fernández-Argüelles MT. Inorganic nanoparticles coupled to nucleic acid enzymes as analytical signal amplification tools. Anal Bioanal Chem 2022; 414:5201-5215. [PMID: 35292825 PMCID: PMC8923336 DOI: 10.1007/s00216-022-03998-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Abstract
Nucleic acid enzymes (NAzymes) are a class of nucleic acid molecules with catalytic activity, which can be modulated by the presence of different species such as metal ions, genetic biomarkers, small molecules or proteins, among others. NAzymes offer several important advantages for development of novel bioanalytical strategies, resulting from their functionality as specific recognition elements and as amplified analytical signal generators, making them ideal candidates for developing highly specific bioanalytical strategies for the detection of a wide variety of targets. When coupled with the exceptional features of inorganic nanoparticles (NPs), the sensitivity of the assays can be significantly improved, allowing the detection of targets using many different detection techniques including visual readout, spectrophotometry, fluorimetry, electrochemiluminescence, voltammetry, and single-particle inductively coupled plasma-mass spectrometry. Here we provide an overview of the fundamentals of novel strategies developed to achieve analytical signal amplification based on the use of NAzymes coupled with inorganic NPs. Some representative examples of such strategies for the highly sensitive detection of different targets will be presented, including metal ions, proteins, DNA- or RNA-based biomarkers, and small molecules or microorganisms. Furthermore, future prospective challenges will be discussed.
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Affiliation(s)
- Adrián Sánchez-Visedo
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain.
| | - Francisco Javier Ferrero
- Department of Electrical, Electronic, Computers and Systems Engineering, University of Oviedo, Campus de Gijón, Sede 3, 33204, Gijon (Asturias), Spain
| | - José M Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
| | - María T Fernández-Argüelles
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo (Asturias), Spain
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7
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Amaravathi C, Geetha K, Surendrababu MS. Biopolymer-PAA and surfactant-CTAB assistant solvothermal synthesis of Mn-based MOFs: design, characterization for enhanced biological activities. INORG NANO-MET CHEM 2021. [DOI: 10.1080/24701556.2021.1953530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chinthamreddy Amaravathi
- Department of Chemistry, School of Science, GITAM Deemed to be University, Hyderabad, Telangana, India
- Department of Chemistry, CMR Technical Campus, Hyderabad, Telangana, India
| | - Karra Geetha
- Department of Biotechnology, CMR College of Pharmacy, Hyderabad, Telangana, India
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8
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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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9
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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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10
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Safdar S, Lammertyn J, Spasic D. RNA-Cleaving NAzymes: The Next Big Thing in Biosensing? Trends Biotechnol 2020; 38:1343-1359. [PMID: 32473751 DOI: 10.1016/j.tibtech.2020.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
Nucleic acid enzymes (NAzymes) are nucleic acid molecules with catalytic activity. A subset, the RNA-cleaving NAzyme, is characterized by its substrate of choice: an RNA unit. These enzymes have been used for diverse applications, including biosensor development, akin to their protein counterparts. Owing to their function as both biorecognition elements and signal generators, robust bioassays based entirely on NAzyme molecules have been developed. Additionally, unique mechanisms for integration with other biorecognition elements and signal generation methods have been explored to realize ultrasensitive, specific, and user-friendly biosensors. Furthermore, NAzyme-based bioassays have already broken into the in vitro diagnostics market, with more promise in the pipeline.
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Affiliation(s)
- Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, 3001, Leuven, Belgium
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11
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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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12
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Hanpanich O, Miyaguchi H, Huang H, Shimada N, Maruyama A. Cationic copolymer-chaperoned short-armed 10-23 DNAzymes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 39:156-169. [PMID: 31608816 DOI: 10.1080/15257770.2019.1675168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The cationic copolymer poly(L-lysine)-graft-dextran (PLL-g-Dex) has nucleic acid chaperone-like activity. The copolymer facilitates both DNA hybridization and strand exchange reactions. For these reasons, DNA-based enzyme (DNAzyme) activity is enhanced in the presence of copolymer. In this study, we evaluated activities of DNAzymes with substrate-binding arms (S-arms) of various lengths. The copolymer promoted DNAzyme reactivity and turnover efficacy, and, depending on S-arm length, maximally accelerated the reaction rate by 250-fold compared to the rate in the absence of copolymer. The copolymer permitted up to six nucleotides truncation of the S-arms having initial length of 10 and 11 nucleotides without loss of catalytic efficiency, enable tuning of the optimal temperature ranging from 30 to 55 °C. The approach might be useful for the development of DNAzyme systems targeting short or highly structured RNAs as well for improvement of DNAzyme-based nanomachines and biosensors.
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Affiliation(s)
- Orakan Hanpanich
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitonari Miyaguchi
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - He Huang
- 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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13
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Hanpanich O, Oyanagi T, Shimada N, Maruyama A. Cationic copolymer-chaperoned DNAzyme sensor for microRNA detection. Biomaterials 2019; 225:119535. [PMID: 31614289 DOI: 10.1016/j.biomaterials.2019.119535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 02/08/2023]
Abstract
Multi-component nucleic acid enzymes (MNAzymes) are allosteric deoxyribozymes that are activated upon binding of a specific nucleic acid effector. MNAzyme activity is limited due to an insufficient assembly of the MNAzyme and its turnover. In this work, we describe the successful improvement of MNAzyme reactivity and selectivity by addition of cationic copolymers, which exhibit nucleic acid chaperone-like activity. The copolymer allowed a 210-fold increase in signal activity and a 95-fold increase in the signal-to-background selectivity of MNAzymes constructed for microRNA (miRNA) detection. The selectivity of the MNAzyme for homologous miRNAs was demonstrated in a multiplex format in which isothermal reactions of two different MNAzymes were performed. In addition, the copolymer permitted miRNA detections even in the presence of a ribonuclease which is ubiquitous in environments, indicating the protective effect of the copolymer against ribonucleases.
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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
| | - Tomoya Oyanagi
- 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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14
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Targeting a viral DNA sequence with a deoxyribozyme in a preparative scale. Biochimie 2019; 165:161-169. [PMID: 31377192 DOI: 10.1016/j.biochi.2019.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/28/2019] [Indexed: 01/13/2023]
Abstract
Deoxyribozymes are synthetic and single stranded DNAs that are capable of catalysis of a variety of reactions, including cleavage of DNA substrates. Deoxyribozymes are usually characterized by analytical single-turnover kinetic assays, however, for many applications e.g. characterization of the reaction products, semi-preparative and preparative reactions are required. At such scales, there is a lack of comprehensive analysis and conditions that supports high amount of products in an appropriate time-scale are vaguely guessed by researchers. In this report, catalytic activity of an oxidizing DNA-cleaving deoxyribozyme, F-8(X), was comprehensively inspected in semi-preparative (10 μM substrate) scale. A 60 nucleotides long synthetic DNA sequence was selected as the target DNA for this study. The DNA sequence was originated from a single stranded DNA virus. Investigations revealed high yield in the presence of optimal concentration of oxidizing agents. The optimal conditions have been applied for scale-up of the reaction to preparative (40 μM substrate) and multi-turnover reactions to achieve highest amount of product in a cost-, time- and labor-effective manner. Such a comprehensive analysis of a deoxyribozyme's activity in semi-preparative scale provides a platform for expanded applications of DNA catalysts as a tool in chemical biology.
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16
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Feng M, Gu C, Sun Y, Zhang S, Tong A, Xiang Y. Enhancing Catalytic Activity of Uranyl-Dependent DNAzyme by Flexible Linker Insertion for More Sensitive Detection of Uranyl Ion. Anal Chem 2019; 91:6608-6615. [PMID: 31016961 DOI: 10.1021/acs.analchem.9b00490] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The uranyl-dependent DNAzyme 39E cleaves its nucleic acid substrate in the presence of uranyl ion (UO22+). It has been widely utilized in many sensor designs for selective and sensitive detection of UO22+ in the environment and inside live cells. In this work, by inserting a flexible linker (C3 Spacer) into one critical site (A20) of the 39E catalytic core, we successfully enhanced the original catalytic activity of 39E up to 8.1-fold at low UO22+ concentrations. Applying such a modified DNAzyme (39E-A20-C3) in a label-free fluorescent sensor for UO22+ detection achieved more than 1 order of magnitude sensitivity enhancement over using native 39E, with the UO22+ detection limit improved from 2.6 nM (0.63 ppb) to 0.19 nM (0.047 ppb), while the high selectivity to UO22+ over other metal ions was fully preserved. The method was also successfully applied for the detection of UO22+-spiked environmental water samples to demonstrate its practical usefulness.
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Affiliation(s)
- Mengli Feng
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Chunmei Gu
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Yanping Sun
- School of Chemistry and Biological Engineering , University of Science and Technology Beijing , Beijing 100083 , People's Republic of China
| | - Shuyuan Zhang
- School of Chemistry and Biological Engineering , University of Science and Technology Beijing , Beijing 100083 , People's Republic of China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education) , Tsinghua University , Beijing 100084 , People's Republic of China
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17
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Re-engineering 10-23 core DNA- and MNAzymes for applications at standard room temperature. Anal Bioanal Chem 2018; 411:205-215. [PMID: 30341659 DOI: 10.1007/s00216-018-1429-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022]
Abstract
DNA- and MNAzymes are nucleic acid-based enzymes (NAzymes), which infiltrated the otherwise protein-rich field of enzymology three decades ago. The 10-23 core NAzymes are one of the most widely used and well-characterized NAzymes, but often require elevated working temperatures or additional complex modifications for implementation at standard room temperatures. Here, we present a generally applicable method, based on thermodynamic principles governing hybridization, to re-engineer the existing 10-23 core NAzymes for use at 23 °C. To establish this, we first assessed the activity of conventional NAzymes in the presence of cleavable and non-cleavable substrate at 23 °C as well as over a temperature gradient. These tests pointed towards a non-catalytic mechanism of signal generation at 23 °C, suggesting that conventional NAzymes are not suited for use at this temperature. Following this, several novel NAzyme-substrate complexes were re-engineered from the conventional ones and screened for their performance at 23 °C. The complex with substrate and substrate-binding arms of the NAzymes shortened by four nucleotides on each terminus demonstrated efficient catalytic activity at 23 °C. This has been further validated over a dilution of enzymes or enzyme components, revealing their superior performance at 23 °C compared to the conventional 10-23 core NAzymes at their standard operating temperature of 55 °C. Finally, the proposed approach was applied to successfully re-engineer three other new MNAzymes for activity at 23 °C. As such, these re-engineered NAzymes present a remarkable addition to the field by further widening the diverse repertoire of NAzyme applications.
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Tomaru T, Suzuki Y, Kawamata I, Nomura SIM, Murata S. Stepping operation of a rotary DNA origami device. Chem Commun (Camb) 2018; 53:7716-7719. [PMID: 28548145 DOI: 10.1039/c7cc03214e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We constructed a rotary DNA origami device and tested its stepping operation on a mica substrate by sequential strand displacement with four different sets of signal DNA strands. This work paves the way for building a variety of dynamic rotary DNA nanodevices which respond to multiple signals.
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Affiliation(s)
- Takahiro Tomaru
- Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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19
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Jafari M, Rezaei M, Kalantari H, Tabarzad M, Daraei B. DNAzyme-aptamer or aptamer-DNAzyme paradigm: Biochemical approach for aflatoxin analysis. Biotechnol Appl Biochem 2017; 65:274-280. [PMID: 28326608 DOI: 10.1002/bab.1563] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/15/2017] [Indexed: 12/22/2022]
Abstract
DNAzyme and aptamer conjugations have already been used for sensitive and accurate detection of several molecules. In this study, we tested the relationship between conjugation orientation of DNAzyme and aflatoxin B1 aptamer and their subsequent peroxidase activity. Circular dichroism (CD) spectroscopy and biochemical analysis were used here to differentiate between these two conjugation patterns. Results showed that DNAzyme-aptamer has more catalytic activity and efficiency than aptamer-DNAzyme. Thereby, DNAzyme-aptamer with its superior efficiency can be used for design and development of more sensitive aflatoxin B1 DNA based biosensors.
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Affiliation(s)
- Marzieh Jafari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohsen Rezaei
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Heibatullah Kalantari
- Department of Pharmacology and Toxicology, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Daraei
- Department of Toxicology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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20
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Saito K, Shimada N, Maruyama A. Cooperative enhancement of deoxyribozyme activity by chemical modification and added cationic copolymer. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2016; 17:437-442. [PMID: 27877894 PMCID: PMC5102035 DOI: 10.1080/14686996.2016.1208627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/22/2016] [Accepted: 06/29/2016] [Indexed: 05/27/2023]
Abstract
Deoxyribozymes (DNAzymes) having RNA-cleaving activity have widely been explored as tools for therapeutic and diagnostic purposes. Both the chemical cleaving step and the turnover step should be improved for enhancing overall activity of DNAzymes. We have shown that cationic copolymer enhanced DNAzyme activity by increasing turnover efficacy. In this paper, effects of the copolymer on DNAzymes modified with locked nucleic acids (LNA) or 2'-O-methylated (2'-OMe) nucleic acids were studied. The copolymer increased activity of these chemically modified DNAzymes. More than 30-fold enhancement in multiple-turnover catalytic activity was observed with 2'-OMe-modified DNAzyme in the presence of the copolymer. DNAzyme catalytic activity was successfully enhanced by cooperation of the added copolymer and chemical modification of DNAzyme.
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Affiliation(s)
- Ken Saito
- 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
| | - Atushi Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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Gao J, Shimada N, Maruyama A. MNAzyme-catalyzed nucleic acid detection enhanced by a cationic copolymer. Biomater Sci 2015. [PMID: 26222590 DOI: 10.1039/c4bm00449c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multi-component nucleotide acid enzymes (MNAzymes) derived from RNase-mimic DNAzymes have potential as simple and accurate DNA detectors. To enhance the MNAzyme activity under multiple-turnover conditions, a cationic comb-type copolymer, PLL-g-Dex, that facilitates hybridization and strand exchange reactions of DNA was utilized. The copolymer increased the MNAzyme reaction rate by 200 times, allowing target DNA detection at picomolar concentrations at physiological temperature.
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Affiliation(s)
- Jueyuan Gao
- Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395, Japan
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