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Safarkhani M, Ahmadi S, Ipakchi H, Saeb MR, Makvandi P, Ebrahimi Warkiani M, Rabiee N, Huh Y. Advancements in Aptamer-Driven DNA Nanostructures for Precision Drug Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401617. [PMID: 38713753 PMCID: PMC11234471 DOI: 10.1002/advs.202401617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/08/2024] [Indexed: 05/09/2024]
Abstract
DNA nanostructures exhibit versatile geometries and possess sophisticated capabilities not found in other nanomaterials. They serve as customizable nanoplatforms for orchestrating the spatial arrangement of molecular components, such as biomolecules, antibodies, or synthetic nanomaterials. This is achieved by incorporating oligonucleotides into the design of the nanostructure. In the realm of drug delivery to cancer cells, there is a growing interest in active targeting assays to enhance efficacy and selectivity. The active targeting approach involves a "key-lock" mechanism where the carrier, through its ligand, recognizes specific receptors on tumor cells, facilitating the release of drugs. Various DNA nanostructures, including DNA origami, Tetrahedral, nanoflower, cruciform, nanostar, nanocentipede, and nanococklebur, can traverse the lipid layer of the cell membrane, allowing cargo delivery to the nucleus. Aptamers, easily formed in vitro, are recognized for their targeted delivery capabilities due to their high selectivity for specific targets and low immunogenicity. This review provides a comprehensive overview of recent advancements in the formation and modification of aptamer-modified DNA nanostructures within drug delivery systems.
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Affiliation(s)
- Moein Safarkhani
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
- School of Chemistry, Damghan University, Damghan, 36716-45667, Iran
| | - Sepideh Ahmadi
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
| | - Hossein Ipakchi
- Department of Chemical Engineering, McMaster University, Hamilton, L8S 4L8, Canada
| | - Mohammad Reza Saeb
- Department of Pharmaceutical Chemistry, Medical University of Gdańsk, J. Hallera 107, Gdańsk, 80-416, Poland
| | - Pooyan Makvandi
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, 324000 Quzhou, Zhejiang, China
- Centre of Research Impact and Outreach, Chitkara University, Rajpura, Punjab, 140417, India
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai, 600077, India
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia
- Institute for Biomedical Materials and Devices (IBMD), University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Navid Rabiee
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai, 600077, India
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, 6150, Australia
| | - YunSuk Huh
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon, 22212, Republic of Korea
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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Nam K, Kim YM, Choi I, Han HS, Kim T, Choi KY, Roh YH. Crystallinity-tuned ultrasoft polymeric DNA networks for controlled release of anticancer drugs. J Control Release 2023; 355:7-17. [PMID: 36706839 DOI: 10.1016/j.jconrel.2023.01.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/26/2022] [Accepted: 01/19/2023] [Indexed: 01/29/2023]
Abstract
Despite the vast interest in utilizing rolling circle amplification (RCA)-based DNA networks for bioapplications, precise control of the mechanical and physicochemical properties is highly challenging. To address this concern, we aimed to develop ultrasoft self-supporting polymerized DNA networks (pDNets) of variable crystallinities to manipulate sequence-mediated drug release efficiency. A controlled ratio of the inorganic magnesium pyrophosphate (MgPPi) crystal to the organic polymeric DNA resulted in the synthesis of pDNets of various nanoporosities. The number of crystal microstructures influencing drug localization and release pattern and the tunable mechanical properties influencing injectability and structural stability under physiological conditions were investigated. The pDNets exhibited ultrasoft properties with Young's moduli of 0.06-0.54 Pa; approximately 9-fold differences in mechanical properties were obtained by varying the degree of crystallinity. With functional DNA sequences, the developed platforms showed pH stimuli-responsive drug release profiles of the dynamic DNA structures and aptamer-specific cell target adhesion efficiency. Analyses of controlled delivery of anticancer therapeutics in vitro and in vivo revealed crystallinity-dependent antitumor efficacy without side effects. This strategy provides an effective one-pot enzymatic polymerization methodology and a favorable microenvironment for a three-dimensional DNA network based on demand-localized drug delivery.
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Affiliation(s)
- Keonwook Nam
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Young Min Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Inseok Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Hwa Seung Han
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, 679 Saimdang-ro, Gangneung 25451, South Korea
| | - Taehyung Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Ki Young Choi
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, 679 Saimdang-ro, Gangneung 25451, South Korea
| | - Young Hoon Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, South Korea.
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Self-assembled endogenous DNA nanoparticles for auto-release and expression of the eGFP gene in Bacillus subtilis. Commun Biol 2022; 5:1373. [PMID: 36517556 PMCID: PMC9751278 DOI: 10.1038/s42003-022-04233-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 11/08/2022] [Indexed: 12/23/2022] Open
Abstract
The development of DNA delivery techniques is critical to promote the wider use of deoxyribonucleic acids as cellular transporters. The present study aimed to develop a type of DNA nanoparticle (citZ-box) to automatically load and release cargo. The restriction enzyme can cleave citZ-boxes at pro-designed sites, and the enhanced green fluorescent protein gene (eGFP) can be delivered into the B. subtilis protoplasts by them. The process of eGFP expression is recorded using a confocal microscope over 4 h. Here, multiscaffold and multimodular designs are used for citZ-box assembly with a DAEDALUS module, DX_cage_design and rem (edge_length, 21), to ensure the structure was predicted as B-type DNA. Finally the citZ-box is estimated to be a 50.7 nm cube. The 3D structure of the citZ-box particle is detected to be approximately 50.3 ± 0.3 nm. DNA nanoparticles prepared as citZ-boxes have great potential as drug carriers with automatic loading and releasing abilities.
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Wang Q, Qu Y, Zhang Z, Huang H, Xu Y, Shen F, Wang L, Sun L. Injectable DNA Hydrogel-Based Local Drug Delivery and Immunotherapy. Gels 2022; 8:gels8070400. [PMID: 35877485 PMCID: PMC9320917 DOI: 10.3390/gels8070400] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 12/26/2022] Open
Abstract
Regulated drug delivery is an important direction in the field of medicine and healthcare research. In recent years, injectable hydrogels with good biocompatibility and biodegradability have attracted extensive attention due to their promising application in controlled drug release. Among them, DNA hydrogel has shown great potentials in local drug delivery and immunotherapy. DNA hydrogel is a three-dimensional network formed by cross-linking of hydrophilic DNA strands with extremely good biocompatibility. Benefiting from the special properties of DNA, including editable sequence and specificity of hybridization reactions, the mechanical properties and functions of DNA hydrogels can be precisely designed according to specific applications. In addition, other functional materials, including peptides, proteins and synthetic organic polymers can be easily integrated with DNA hydrogels, thereby enriching the functions of the hydrogels. In this review, we first summarize the types and synthesis methods of DNA hydrogels, and then review the recent research progress of injectable DNA hydrogels in local drug delivery, especially in immunotherapy. Finally, we discuss the challenges facing DNA hydrogels and future development directions.
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Affiliation(s)
- Qi Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Yanfei Qu
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Ziyi Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Hao Huang
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Yufei Xu
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
| | - Fengyun Shen
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 201240, China
- Correspondence: (F.S.); (L.S.)
| | - Lihua Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China;
| | - Lele Sun
- School of Life Sciences, Shanghai University, Shanghai 200444, China; (Q.W.); (Y.Q.); (Z.Z.); (H.H.); (Y.X.)
- Correspondence: (F.S.); (L.S.)
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Han S, Park Y, Kim H, Nam H, Ko O, Lee JB. Double Controlled Release of Therapeutic RNA Modules through Injectable DNA-RNA Hybrid Hydrogel. ACS APPLIED MATERIALS & INTERFACES 2020; 12:55554-55563. [PMID: 33259200 DOI: 10.1021/acsami.0c12506] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Advances in the DNA nanotechnology have enabled the fabrication of DNA-based hydrogels with precisely controlled structures and tunable mechanical and biological properties. Compared to DNA hydrogel, preparation of RNA-based hydrogel remains challenging due to the inherent instability of naked RNA. To overcome these limitations, we fabricated a DNA-RNA hybrid hydrogel via stepwise dual enzymatic polymerization. Multimeric short hairpin RNAs (shRNAs) were hybridized with functional DNA aptamers for targeting and mechanical properties of the hydrogel. The obtained DNA-RNA hybrid hydrogel was ultrasoft, robust, and injectable hence reconfigurable into any confined structures. As a model system, the hydrogel was able to mimic microtubule structures under physiological conditions and designed to release the functional small interfering RNA (siRNA)-aptamer complex (SAC) sequentially. In addition, we encoded restriction enzyme-responsive sites in DNA-RNA hybrid hydrogel to boost the release of SAC. This novel strategy provides an excellent platform for systematic RNA delivery through double-controlled release, SAC release from hydrogel, and subsequent release of siRNA from the SAC, which has promising potential in RNA therapy.
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Affiliation(s)
- Sangwoo Han
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Yongkuk Park
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Hyejin Kim
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Hyangsu Nam
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Ohsung Ko
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, 163 Seoulsiripdaero, Dongdaemungu, Seoul 02504, Republic of Korea
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Yuan Y, Liu T, Xiao J, Yu Q, Feng L, Niu B, Feng S, Zhang J, Wang N. DNA nano-pocket for ultra-selective uranyl extraction from seawater. Nat Commun 2020; 11:5708. [PMID: 33177515 PMCID: PMC7659010 DOI: 10.1038/s41467-020-19419-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022] Open
Abstract
Extraction of uranium from seawater is critical for the sustainable development of nuclear energy. However, the currently available uranium adsorbents are hampered by co-existing metal ion interference. DNAzymes exhibit high selectivity to specific metal ions, yet there is no DNA-based adsorbent for extraction of soluble minerals from seawater. Herein, the uranyl-binding DNA strand from the DNAzyme is polymerized into DNA-based uranium extraction hydrogel (DNA-UEH) that exhibits a high uranium adsorption capacity of 6.06 mg g−1 with 18.95 times high selectivity for uranium against vanadium in natural seawater. The uranium is found to be bound by oxygen atoms from the phosphate groups and the carbonyl groups, which formed the specific nano-pocket that empowers DNA-UEH with high selectivity and high binding affinity. This study both provides an adsorbent for uranium extraction from seawater and broadens the application of DNA for being used in recovery of high-value soluble minerals from seawater. The extraction of metals from seawater is an area of great potential; especially for the extraction of uranium. Here, the authors report on the synthesis of a DNA based uranium adsorbent with high selectivity and demonstrate the potential for the DNA based extraction of high-value soluble minerals from seawater.
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Affiliation(s)
- Yihui Yuan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Tingting Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Juanxiu Xiao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Qiuhan Yu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Lijuan Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Biye Niu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Shiwei Feng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Jiacheng Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China
| | - Ning Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, P. R. China.
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Chi Q, Yang Z, Xu K, Wang C, Liang H. DNA Nanostructure as an Efficient Drug Delivery Platform for Immunotherapy. Front Pharmacol 2020; 10:1585. [PMID: 32063844 PMCID: PMC6997790 DOI: 10.3389/fphar.2019.01585] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/06/2019] [Indexed: 12/19/2022] Open
Abstract
Immunotherapy has received increasing attention due to its low potential side effects and high specificity. For instance, cancer immunotherapy has achieved great success. CpG is a well-known and commonly used immunotherapeutic and vaccine adjuvant, but it has the disadvantage of being unstable and low in efficacy and needs to be transported through an effective nanocarrier. With perfect structural programmability, permeability, and biocompatibility, DNA nanostructures are one of the most promising candidates to deliver immune components to realize immunotherapy. However, the instability and low capability of the payload of ordinary DNA assemblies limit the relevant applications. Consequently, DNA nanostructure with a firm structure, high drug payloads is highly desirable. In the paper, the latest progress of biostable, high-payload DNA nanoassemblies of various structures, including cage-like DNA nanostructure, DNA particles, DNA polypods, and DNA hydrogel, are reviewed. Cage-like DNA structures hold drug molecules firmly inside the structure and leave a large space within the cavity. These DNA nanostructures use their unique structure to carry abundant CpG, and their biocompatibility and size advantages to enter immune cells to achieve immunotherapy for various diseases. Part of the DNA nanostructures can also achieve more effective treatment in conjunction with other functional components such as aPD1, RNA, TLR ligands.
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Affiliation(s)
- Qingjia Chi
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
- Hubei Key Laboratory of Theory and Application of Advanced Materials Mechanics, Department of Mechanics and Engineering Structure, Wuhan University of Technology, Wuhan, China
| | - Zichang Yang
- Hubei Key Laboratory of Theory and Application of Advanced Materials Mechanics, Department of Mechanics and Engineering Structure, Wuhan University of Technology, Wuhan, China
| | - Kang Xu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunli Wang
- “111” Project Laboratory of Biomechanics and Tissue Repair, Bioengineering College, Chongqing University, Chongqing, China
| | - Huaping Liang
- State Key Laboratory of Trauma, Burns and Combined Injury, Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, China
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Tan M, Takahashi N, Fujii S, Sakurai K, Kusamori K, Takahashi Y, Takakura Y, Nishikawa M. Analysis of Tertiary Structural Features of Branched DNA Nanostructures with Partially Common Sequences Using Small-Angle X-ray Scattering. ACS APPLIED BIO MATERIALS 2019; 3:308-314. [DOI: 10.1021/acsabm.9b00829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mengmeng Tan
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29, Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Natsuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29, Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shota Fujii
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
- Structural Materials Science Laboratory SPring-8 Center, RIKEN Harima Institute Research, 1-1-1 Kouto, Sayo-cho, Sayo, Hyogo 679-5148, Japan
| | - Kosuke Kusamori
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29, Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29, Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Makiya Nishikawa
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29, Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Laboratory of Biopharmaceutics, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Li J, Lin L, Yu J, Zhai S, Liu G, Tian L. Fabrication and Biomedical Applications of “Polymer-Like” Nucleic Acids Enzymatically Produced by Rolling Circle Amplification. ACS APPLIED BIO MATERIALS 2019; 2:4106-4120. [DOI: 10.1021/acsabm.9b00622] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jing Li
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Li Lin
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Jiantao Yu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Shiyao Zhai
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Guoyuan Liu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Boulevard, Nanshan District, Shenzhen, Guangdong 518055, P. R. China
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11
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Joffroy B, Uca YO, Prešern D, Doye JPK, Schmidt TL. Rolling circle amplification shows a sinusoidal template length-dependent amplification bias. Nucleic Acids Res 2019; 46:538-545. [PMID: 29237070 PMCID: PMC5778537 DOI: 10.1093/nar/gkx1238] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 11/30/2017] [Indexed: 01/29/2023] Open
Abstract
Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with integer helical turns circularize much more efficiently than those with odd helical half turns due to stronger stacking of duplex ends. Small DNA circles can serve as templates for rolling circle amplification (RCA), which is a common and extremely robust amplification mechanism for nucleic acids. We discovered a strong template length-dependent amplification efficiency bias of RCA with the same periodicity as B-DNA. However, stacking cannot explain the mechanism behind this bias as the presence of the polymerase in the bifurcation fork inhibits base stacking of ends. Instead, coarse-grained molecular dynamics simulations imply that different amplification efficiencies come from a varying fraying probability of the last two downstream base pairs. We conclude that an increased strain-promoted fraying probability can increase the polymerization rate compared to a relaxed template.
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Affiliation(s)
- Bastian Joffroy
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany
| | - Yavuz O Uca
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Thorsten L Schmidt
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany.,B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
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12
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Deng S, Yan J, Wang F, Su Y, Zhang X, Li Q, Liu G, Fan C, Pei H, Wan Y. In situ terminus-regulated DNA hydrogelation for ultrasensitive on-chip microRNA assay. Biosens Bioelectron 2019; 137:263-270. [DOI: 10.1016/j.bios.2019.04.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 02/07/2023]
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13
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Nishikawa M, Tan M, Liao W, Kusamori K. Nanostructured DNA for the delivery of therapeutic agents. Adv Drug Deliv Rev 2019; 147:29-36. [PMID: 31614168 DOI: 10.1016/j.addr.2019.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 01/16/2023]
Abstract
DNA and RNA, the nucleic acids found in every living organism, are quite crucial, because not only do they store the genetic information, but also they are used as signals through interaction with various molecules within the body. The nature of nucleic acids, especially DNA, to form double-helix makes it possible to design nucleic acid-based nanostructures with various shapes. Because the shapes as well as the physicochemical properties determine their interaction with proteins or cells, nanostructured DNAs will have different features in the interaction compared with single- or double-stranded DNA. Some of these unique features of nanostructured DNA make ways for efficient delivery of therapeutic agents to specific targets. In this review, we begin with the factors affecting the properties of nanostructured DNA, followed by summarizing the methods for the development of nanostructured DNA. Further, we discuss the characteristics of nanostructured DNA and their applications for the delivery of bioactive compounds.
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Affiliation(s)
- Makiya Nishikawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan.
| | - Mengmeng Tan
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
| | - Wenqing Liao
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Japan
| | - Kosuke Kusamori
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Japan
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14
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Song H, Zhang Y, Cheng P, Chen X, Luo Y, Xu W. A rapidly self-assembling soft-brush DNA hydrogel based on RCA products. Chem Commun (Camb) 2019; 55:5375-5378. [PMID: 30994649 DOI: 10.1039/c9cc01022j] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A rapid self-assembly strategy was developed for fabricating a novel soft-brush DNA hydrogel in one minute by introducing a pair of L-type probes into the RCA products. The L-type probes with universality achieved a controllable size and morphology of the DNA hydrogel, providing deeper insight into variability and probability in functional biomaterials.
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Affiliation(s)
- Huan Song
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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15
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Wang J, Mao S, Li HF, Lin JM. Multi-DNAzymes-functionalized gold nanoparticles for ultrasensitive chemiluminescence detection of thrombin on microchip. Anal Chim Acta 2018; 1027:76-82. [PMID: 29866272 DOI: 10.1016/j.aca.2018.04.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
Abstract
Herein, a chemiluminescence assay with dual signal amplification has been developed based on multi-DNAzymes-functionalized gold nanoparticles (AuNPs) using in situ rolling circle amplification (RCA) for ultrasensitive detection of thrombin on microchip. In this assay, AuNPs was functionalized by aptamer and multi-RCA primer for amplification, and thrombin was sandwiched between the aptamer modified on the microchannel and the aptamer linked AuNP. The further amplification was realized by in situ RCA to expand specific oligonucleotides chains on the AuNPs and produce particular multi-DNAzymes. Enhanced chemiluminescence signal was achieved by the catalytic effect of DNAzymes in the luminol-H2O2 system. The sensitivity of detection was greatly improved by the dual amplification of multi-RCA primer modified AuNPs, and RCA. The whole strategy was applied for ultrasensitive and specific detection of thrombin. The chemiluminesce assay of thrombin performed a good linear range of 1-25 pM and the limit of detection was as low as 0.55 pM. The successful determination of thrombin in real human serum sample indicated a great potential in clinical study.
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Affiliation(s)
- Junming Wang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Sifeng Mao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Hai-Fang Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.
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16
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Zinchenko A, Sergeyev VG. DNA-based materials as chemical reactors for synthesis of metal nanoparticles. POLYMER SCIENCE SERIES C 2017. [DOI: 10.1134/s1811238217010155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Droplet Microfluidics Approach for Single-DNA Molecule Amplification and Condensation into DNA-Magnesium-Pyrophosphate Particles. MICROMACHINES 2017. [PMCID: PMC6189807 DOI: 10.3390/mi8020062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein expression in vitro has broad applications in directed evolution, synthetic biology, proteomics and drug screening. However, most of the in vitro expression systems rely on relatively high DNA template concentrations to obtain sufficient amounts of proteins, making it harder to perform in vitro screens on gene libraries. Here, we report a technique for the generation of condensed DNA particles that can serve as efficient templates for in vitro gene expression. We apply droplet microfluidics to encapsulate single-DNA molecules in 3-picoliter (pL) volume droplets and convert them into 1 μm-sized DNA particles by the multiple displacement amplification reaction driven by phi29 DNA polymerase. In the presence of magnesium ions and inorganic pyrophosphate, the amplified DNA condensed into the crystalline-like particles, making it possible to purify them from the reaction mix by simple centrifugation. Using purified DNA particles, we performed an in vitro transcription-translation reaction and successfully expressed complex enzyme β-galactosidase in droplets and in the 384-well format. The yield of protein obtained from DNA particles was significantly higher than from the corresponding amount of free DNA templates, thus opening new possibilities for high throughput screening applications.
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18
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Eguchi Y, Kato T, Tanaka T, Maruyama T. A DNA–gold nanoparticle hybrid hydrogel network prepared by enzymatic reaction. Chem Commun (Camb) 2017; 53:5802-5805. [DOI: 10.1039/c7cc02435e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report a DNA–gold nanoparticle (AuNP) hydrogel in which the AuNPs crosslink enzymatically synthesized DNA.
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Affiliation(s)
- Yuka Eguchi
- Department of Chemical Science and Engineering
- Graduate School of Engineering
- Kobe University
- Kobe 657-8501
- Japan
| | - Tomoharu Kato
- Department of Chemical Science and Engineering
- Graduate School of Engineering
- Kobe University
- Kobe 657-8501
- Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering
- Graduate School of Engineering
- Kobe University
- Kobe 657-8501
- Japan
| | - Tatsuo Maruyama
- Department of Chemical Science and Engineering
- Graduate School of Engineering
- Kobe University
- Kobe 657-8501
- Japan
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19
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Hollenstein M, Damha MJ. Rolling Circle Amplification with Chemically Modified Nucleoside Triphosphates. ACTA ACUST UNITED AC 2016; 67:7.26.1-7.26.15. [PMID: 27911492 DOI: 10.1002/cpnc.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Modified nucleoside triphosphates (dN*TPs) represent facile and versatile precursors for the introduction of chemical diversity into nucleic acids. While dN*TPs have been utilized in a plethora of practical applications, very little attention has been devoted to the assessment of their compatibility with isothermal amplification strategies. In this context, rolling circle amplification (RCA) is a wide-spread enzymatic replication method in which small single-stranded DNA (ssDNA) circles serve as templates in primer extension reactions yielding very long, ssDNA products. RCA is a pivotal tool for the generation of biosensor and diagnostic devices and is currently evaluated for its usefulness to create novel drug delivery systems. This unit describes the experimental procedures for the synthesis of modified RCA products using dN*TPs bearing chemical alterations at any possible location of the nucleosidic scaffold. Two ligation methods are presented for the generation of the DNA nanocircles that serve as templates for RCA, followed by a description of the RCA method itself and an assessment of the nuclease resistance of the ensuing products. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marcel Hollenstein
- Department of Structural Biology and Chemistry, Pasteur Institute, Paris, France
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
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20
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Stoll H, Steinle H, Stang K, Kunnakattu S, Scheideler L, Neumann B, Kurz J, Degenkolbe I, Perle N, Schlensak C, Wendel HP, Avci-Adali M. Generation of Large-Scale DNA Hydrogels with Excellent Blood and Cell Compatibility. Macromol Biosci 2016; 17. [PMID: 27758025 DOI: 10.1002/mabi.201600252] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/14/2016] [Indexed: 12/27/2022]
Abstract
Hemocompatibility and cytocompatibility of biomaterials codetermine the success of tissue engineering applications. DNA, the natural component of our cells, is an auspicious biomaterial for the generation of designable scaffolds with tailorable characteristics. In this study, a combination of rolling circle amplification and multiprimed chain amplification is used to generate hydrogels at centimeter scale consisting solely of DNA. Using an in vitro rotation model and fresh human blood, the reaction of the hemostatic system on DNA hydrogels is analyzed. The measurements of hemolysis, platelets activation, and the activation of the complement, coagulation, and neutrophils using enzyme-linked immunosorbent assays demonstrate excellent hemocompatibility. In addition, the cytocompatibility of the DNA hydrogels is tested by indirect contact (agar diffusion tests) and material extract experiments with L929 murine fibroblasts according to the ISO 10993-5 specifications and no negative impact on the cell viability is detected. These results indicate the promising potential of DNA hydrogels as biomaterials for versatile applications in the field of regenerative medicine.
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Affiliation(s)
- Heidi Stoll
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Heidrun Steinle
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Katharina Stang
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Silju Kunnakattu
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Lutz Scheideler
- Section "Medical Material Science and Technology", Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Osianderstraße 2-8, 72076, Tuebingen, Germany
| | - Bernd Neumann
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Julia Kurz
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Ilka Degenkolbe
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Nadja Perle
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Christian Schlensak
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Hans Peter Wendel
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
| | - Meltem Avci-Adali
- Department of Thoracic and Cardiovascular Surgery, University Hospital Tuebingen, Calwerstraße 7/1, 72076, Tuebingen, Germany
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21
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Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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