1
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Shen J, Duan X, Xie T, Zhang X, Cai Y, Pan J, Zhang X, Sun X. Advances in locally administered nucleic acid therapeutics. Bioact Mater 2025; 49:218-254. [PMID: 40144794 PMCID: PMC11938090 DOI: 10.1016/j.bioactmat.2025.02.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 02/13/2025] [Accepted: 02/27/2025] [Indexed: 03/28/2025] Open
Abstract
Nucleic acid drugs represent the latest generation of precision therapeutics, holding significant promise for the treatment of a wide range of intractable diseases. Delivery technology is crucial for the clinical application of nucleic acid drugs. However, extrahepatic delivery of nucleic acid drugs remains a significant challenge. Systemic administration often fails to achieve sufficient drug enrichment in target tissues. Localized administration has emerged as the predominant approach to facilitate extrahepatic delivery. While localized administration can significantly enhance drug accumulation at the injection sites, nucleic acid drugs still face biological barriers in reaching the target lesions. This review focuses on non-viral nucleic acid drug delivery techniques utilized in local administration for the treatment of extrahepatic diseases. First, the classification of nucleic acid drugs is described. Second, the current major non-viral delivery technologies for nucleic acid drugs are discussed. Third, the bio-barriers, administration approaches, and recent research advances in the local delivery of nucleic acid drugs for treating lung, brain, eye, skin, joint, and heart-related diseases are highlighted. Finally, the challenges associated with the localized therapeutic application of nucleic acid drugs are addressed.
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Affiliation(s)
- Jie Shen
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xusheng Duan
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Ting Xie
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xinrui Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yue Cai
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Junhao Pan
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xin Zhang
- State Key Laboratory of Biopharmaceutical Preparation and Delivery, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanrong Sun
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals & College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
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2
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Wang H, Huang Y, Zhou C, Gong F, Wang J, Liu H, Zhao W, Zhao Y, Gao X. QKCMP peptide carrier macromolecule structure and release system based on triangular DNA origami nanostructures: A novel strategy for promoting angiogenesis. Int J Biol Macromol 2025; 310:143457. [PMID: 40288714 DOI: 10.1016/j.ijbiomac.2025.143457] [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: 03/14/2025] [Revised: 04/16/2025] [Accepted: 04/22/2025] [Indexed: 04/29/2025]
Abstract
In recent years, the use of nanocarriers to deliver bioactive peptides has become a new strategy to promote angiogenesis. The aim of this study was to develop a QKCMP peptide delivery system based on triangular DNA origami nanostructure (tDONs) carrier to improve the bioactivity and targeting of the peptide. The main objective of this study was to design and prepare QKCMP peptide-TDOns complexes and to evaluate their angiogenesis promoting effects in vitro and in vivo. tDONs were synthesized and purified, and then QKCMP peptide was loaded into tDONs. A variety of characterization techniques were used to evaluate the physicochemical properties of the complexes, including particle size, morphology, and RNA release efficiency. The effects of QKCMP peptid-TDons on proliferation, apoptosis, migration and angiogenesis of human umbilical vein endothelial cells (HUVEC) were evaluated by CCK8, EdU, Annexin V-FITC/PI, PI staining and Transwell assay. At the same time, its promoting effect on angiogenesis was further verified in zebrafish and mouse models. The successful preparation of QKCMP peptide-TDONS showed good biocompatibility and stability. The results of in vitro experiments showed that QKCMP peptide-TDons significantly promoted HUVEC proliferation, inhibited apoptosis, and activated endothelial cell function. Zebrafish experiments showed that QKCMP peptid-TDons effectively enhanced angiogenesis and promoted rapid repair of carotid vascular endothelium in mouse models.
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Affiliation(s)
- Haifeng Wang
- Department of Neurosurgery, Ningbo Key Laboratory of Neurological Diseases and Brain Function, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China
| | - Yi Huang
- Department of Neurosurgery, Ningbo Key Laboratory of Neurological Diseases and Brain Function, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China
| | - Chenhui Zhou
- Department of Neurosurgery, Ningbo Key Laboratory of Neurological Diseases and Brain Function, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China
| | - Fanyong Gong
- Department of Neurosurgery, Ningbo Key Laboratory of Neurological Diseases and Brain Function, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China
| | - Jianyong Wang
- Department of Neurosurgery, Ningbo Key Laboratory of Neurological Diseases and Brain Function, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China
| | - Hao Liu
- Institute of Bioengineering, Biotrans Technology Co., LTD., Shanghai, China; United New Drug Research and Development Center, Biotrans Technology Co., LTD., Changsha, China
| | - Wenhui Zhao
- Psychosomatic Medical Center, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China
| | - Yuxiang Zhao
- Institute of Bioengineering, Biotrans Technology Co., LTD., Shanghai, China; United New Drug Research and Development Center, Biotrans Technology Co., LTD., Changsha, China.
| | - Xiang Gao
- Department of Neurosurgery, Ningbo Key Laboratory of Neurological Diseases and Brain Function, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China.
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3
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Qiu Y, Qiu Y, Zhou W, Lu D, Wang H, Li B, Liu B, Wang W. Advancements in functional tetrahedral DNA nanostructures for multi-biomarker biosensing: Applications in disease diagnosis, food safety, and environmental monitoring. Mater Today Bio 2025; 31:101486. [PMID: 39935897 PMCID: PMC11810847 DOI: 10.1016/j.mtbio.2025.101486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 12/29/2024] [Accepted: 01/11/2025] [Indexed: 02/13/2025] Open
Abstract
Deoxyribonucleic acid (DNA) offers the fundamental building blocks for the precisely controlled assemblies due to its inherent self-assembly and programmability. The tetrahedral DNA nanostructure (TDN) stands out as a widely utilized nanostructure, attracting attention for its high biostability, excellent biocompatibility, and versatile modification sites. The capability of DNA tetrahedron to interact with various signal outputs makes it ideal for developing functional DNA nanostructures in biosensing platforms. This review highlights recent advancements in functional tetrahedral DNA nanostructures (FTDN) for various biomarkers monitoring, including nucleic acid, protein, mycotoxin, agent, and metal ion. Additionally, it discusses the potential of FTDN in the fields of disease diagnosis, food safety, and environmental monitoring. The review also introduces the application of FTDN-based biosensors for simultaneous identification of multiple biomarkers. Finally, challenges and prospects are addressed to provide guidance for the continued development of FTDN-based biosensing platforms.
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Affiliation(s)
- Yun Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Wenchao Zhou
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Dai Lu
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
| | - Bin Liu
- College of Biology, Hunan University, Changsha, 410082, China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, Academician Atta-ur-Rahman Belt and Road Traditional Medicine Research Center, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, China
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4
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Ge Q, Qin R, Liu S, Guo Q, Han C, Chen W. Pragmatic soft-decision data readout of encoded large DNA. Brief Bioinform 2025; 26:bbaf102. [PMID: 40091194 PMCID: PMC11911122 DOI: 10.1093/bib/bbaf102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2024] [Revised: 02/06/2025] [Accepted: 02/24/2025] [Indexed: 03/19/2025] Open
Abstract
The encoded large DNA can be cloned and stored in vivo, capable of write-once and stable replication for multiple retrievals, offering potential in economic data archiving. Nanopore sequencing is advantageous in data access of large DNA due to its rapidity and long-read sequencing capability. However, the data readout is commonly limited by insertion and deletion (indel) errors and sequence assembly complexity. Here, a pragmatic soft-decision data readout is presented, achieving assembly-free sequence reconstruction, indel error correction, and ultra-low coverage data readout. Specifically, the watermark is cleverly embedded within large DNA fragments, allowing for the direct localization of raw reads via watermark alignment to avoid complex read assembly. A soft-decision forward-backward algorithm is proposed, which can identify indel errors and provide probability information to the error correction code, enabling error-free data recovery. Additionally, a minimum state transition is maintained, and a read segmentation is incorporated to achieve fast information reading. The readout assays for two circular plasmids (~51 kb) with different coding rates were demonstrated and achieved error-free recovery directly from noisy reads (error rate ~1%) at coverage of 1-4×. Simulations conducted on large-scale datasets across various error rates further confirm the scalability of the method and its robust performance under extreme conditions. This readout method enables nearly single-molecule recovery of large DNA, particularly suitable for rapid readout of DNA storage.
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Affiliation(s)
- Qi Ge
- School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Rui Qin
- School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Shuang Liu
- School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Quan Guo
- School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Changcai Han
- School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
- Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology, School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Weigang Chen
- School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
- Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology, School of Microelectronics, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
- Frontier Science Center for Synthetic Biology, Ministry of Education, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
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5
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Postigo A, Marcuello C, Verstraeten W, Sarasa S, Walther T, Lostao A, Göpfrich K, del Barrio J, Hernández-Ainsa S. Folding and Functionalizing DNA Origami: A Versatile Approach Using a Reactive Polyamine. J Am Chem Soc 2025; 147:3919-3924. [PMID: 39869392 PMCID: PMC12124716 DOI: 10.1021/jacs.4c12637] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 11/29/2024] [Accepted: 01/08/2025] [Indexed: 01/28/2025]
Abstract
DNA nanotechnology is a powerful synthetic approach to crafting diverse nanostructures through self-assembly. Chemical decoration of such nanostructures is often required to tailor their properties for specific applications. In this Letter, we introduce a pioneering method to direct the assembly and enable the functionalization of DNA nanostructures using an azide-bearing functional polyamine. We first demonstrate the successful polyamine-assisted folding of a scaffolded DNA origami nanostructure equipped with reactive azide groups. Leveraging this reactivity, we next showcase the decoration of the DNA origami via strain-promoted azide-alkyne cycloaddition with dibenzocyclooctyne-containing functional molecules. Specifically, we incorporate a fluorophore (Cy5), polyethylene glycol (PEG), and a hydrophobic phosphatidylethanolamine (PE) tag to tailor the properties of our DNA origami nanostructures. Our approach is expected to streamline and reduce the cost of chemical customization of intricate DNA nanostructures, paving the way for enhanced versatility and applicability.
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Affiliation(s)
- Alejandro Postigo
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Ed. I+D+i. Mariano Esquillor, Zaragoza50018, Spain
| | - Carlos Marcuello
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Ed. I+D+i. Mariano Esquillor, Zaragoza50018, Spain
- Laboratorio
de Microscopias Avanzadas (LMA), Universidad
de Zaragoza, Ed. I+D+i. Mariano Esquillor, 50018Zaragoza, Spain
| | - William Verstraeten
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120Heidelberg, Germany
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstr. 29, 69120Heidelberg, Germany
| | - Santiago Sarasa
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Ed. I+D+i. Mariano Esquillor, Zaragoza50018, Spain
| | - Tobias Walther
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120Heidelberg, Germany
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstr. 29, 69120Heidelberg, Germany
| | - Anabel Lostao
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Ed. I+D+i. Mariano Esquillor, Zaragoza50018, Spain
- Fundación
ARAID, Av. Ranillas 1-D, 50018Zaragoza, Spain
- Laboratorio
de Microscopias Avanzadas (LMA), Universidad
de Zaragoza, Ed. I+D+i. Mariano Esquillor, 50018Zaragoza, Spain
| | - Kerstin Göpfrich
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120Heidelberg, Germany
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstr. 29, 69120Heidelberg, Germany
| | - Jesús del Barrio
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Ed. I+D+i. Mariano Esquillor, Zaragoza50018, Spain
| | - Silvia Hernández-Ainsa
- Instituto
de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Ed. I+D+i. Mariano Esquillor, Zaragoza50018, Spain
- Fundación
ARAID, Av. Ranillas 1-D, 50018Zaragoza, Spain
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6
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Lin P, Zhang S, Komatsubara F, Konishi H, Nakata E, Morii T. Artificial Compartments Encapsulating Enzymatic Reactions: Towards the Construction of Artificial Organelles. Chempluschem 2025; 90:e202400483. [PMID: 39351818 DOI: 10.1002/cplu.202400483] [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: 07/15/2024] [Revised: 09/30/2024] [Indexed: 11/08/2024]
Abstract
Cells have used compartmentalization to implement complex biological processes involving thousands of enzyme cascade reactions. Enzymes are spatially organized into the cellular compartments to carry out specific and efficient reactions in a spatiotemporally controlled manner. These compartments are divided into membrane-bound and membraneless organelles. Mimicking such cellular compartment systems has been a challenge for years. A variety of artificial scaffolds, including liposomes, polymersomes, proteins, nucleic acids, or hybrid materials have been used to construct artificial membrane-bound or membraneless compartments. These artificial compartments may have great potential for applications in biosynthesis, drug delivery, diagnosis and therapeutics, among others. This review first summarizes the typical examples of cellular compartments. In particular, the recent studies on cellular membraneless organelles (biomolecular condensates) are reviewed. We then summarize the recent advances in the construction of artificial compartments using engineered platforms. Finally, we provide our insights into the construction of biomimetic systems and the applications of these systems. This review article provides a timely summary of the relevant perspectives for the future development of artificial compartments, the building blocks for the construction of artificial organelles or cells.
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Affiliation(s)
- Peng Lin
- Institute of Advanced Energy, Kyoto University, Uji-shi, Kyoto, 611-0011, Japan
| | - Shiwei Zhang
- Institute of Advanced Energy, Kyoto University, Uji-shi, Kyoto, 611-0011, Japan
| | - Futa Komatsubara
- Graduate School of Energy Science, Kyoto University, Yoshida-hommachi, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroaki Konishi
- Institute of Advanced Energy, Kyoto University, Uji-shi, Kyoto, 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji-shi, Kyoto, 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji-shi, Kyoto, 611-0011, Japan
- Department of Health and Nutrition, Kyoto Koka Women's University, Ukyo-ku, Kyoto, 615-0882, Japan
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7
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Nie Q, Fang X, Huang J, Xu T, Li Y, Zhang G, Li Y. The Evolution of Nucleic Acid Nanotechnology: From DNA Assembly to DNA-Encoded Library. SMALL METHODS 2025:e2401631. [PMID: 39806846 DOI: 10.1002/smtd.202401631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 12/30/2024] [Indexed: 01/16/2025]
Abstract
Deoxyribonucleic acid (DNA), a fundamental biomacromolecule in living organisms, serves as the carrier of genetic information. Beyond its role in encoding biological functions, DNA's inherent ability to hybridize through base pairing has opened new avenues for its application in biological sciences. This review introduces DNA nanotechnology and DNA-encoded library (DEL), and highlights their shared design principles related to DNA assembly. First, a foundational overview of structural DNA nanotechnology, including its design strategies and historical development is provided. Subsequently, various approaches are examined to dynamic DNA nanotechnology, from strand displacement reactions to DNA-templated polymer synthesis. Second, how the principle of DNA assembly has facilitated the development of diverse formats of self-assembly-based DEL synthesis, DNA-template reactions (DTS), and DNA template-mediated proximity induction effects are examined. These advancements are all underpinned by the unique property of DNA assembly. Finally, this review summarizes the common principles shared by DNA nanotechnology and DEL in terms of methodology and design. Additionally, the potential synergies are explored between these two technologies, envisioning future applications where they can be combined to create more versatile and exquisite functionalities.
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Affiliation(s)
- Qigui Nie
- Chongqing Fuling Hospital, Chongqing University, Chongqing, 40800, China
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
- Pharmaceutical Department, Chongqing University Three Gorges Hospital, Chongqing University, Chongqing, 404100, China
| | - Jiale Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Tingting Xu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
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8
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Ameixa J, Sala L, Kocišek J, Bald I. Radiation and DNA Origami Nanotechnology: Probing Structural Integrity at the Nanoscale. Chemphyschem 2025; 26:e202400863. [PMID: 39473163 PMCID: PMC11747590 DOI: 10.1002/cphc.202400863] [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: 09/04/2024] [Revised: 10/24/2024] [Indexed: 11/21/2024]
Abstract
DNA nanotechnology has emerged as a groundbreaking field, using DNA as a scaffold to create nanostructures with customizable properties. These DNA nanostructures hold potential across various domains, from biomedicine to studying ionizing radiation-matter interactions at the nanoscale. This review explores how the various types of radiation, covering a spectrum from electrons and photons at sub-excitation energies to ion beams with high-linear energy transfer influence the structural integrity of DNA origami nanostructures. We discuss both direct effects and those mediated by secondary species like low-energy electrons (LEEs) and reactive oxygen species (ROS). Further we discuss the possibilities for applying radiation in modulating and controlling structural changes. Based on experimental insights, we identify current challenges in characterizing the responses of DNA nanostructures to radiation and outline further areas for investigation. This review not only clarifies the complex dynamics between ionizing radiation and DNA origami but also suggests new strategies for designing DNA nanostructures optimized for applications exposed to various qualities of ionizing radiation and their resulting byproducts.
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Affiliation(s)
- João Ameixa
- Hybrid NanostructuresInstitute of ChemistryUniversity of PotsdamKarl-Liebknecht-Str. 24–25Potsdam14476Germany
- Centre of Physics and Technological Research (CEFITEC)Department of PhysicsNOVA School of Science and TechnologyUniversity NOVA of LisbonCampus de Caparica2829-516Portugal
| | - Leo Sala
- Dynamics of Molecules and Clusters DepartmentJ. Heyrovský Institute of Physical Chemistry of the CASDolejškova 3Prague182, 23Czech Republic
| | - Jaroslav Kocišek
- Dynamics of Molecules and Clusters DepartmentJ. Heyrovský Institute of Physical Chemistry of the CASDolejškova 3Prague182, 23Czech Republic
| | - Ilko Bald
- Hybrid NanostructuresInstitute of ChemistryUniversity of PotsdamKarl-Liebknecht-Str. 24–25Potsdam14476Germany
- Dynamics of Molecules and Clusters DepartmentJ. Heyrovský Institute of Physical Chemistry of the CASDolejškova 3Prague182, 23Czech Republic
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9
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Gu S, Chen B, Xu X, Han F, Chen S. 3D Nanofabrication via Directed Material Assembly: Mechanism, Method, and Future. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2025; 37:e2312915. [PMID: 39623887 PMCID: PMC11733727 DOI: 10.1002/adma.202312915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/27/2024] [Indexed: 01/16/2025]
Abstract
Fabrication of complex three-dimensional (3D) structures at nanoscale is the core of nanotechnology, as it enables the creation of various micro-/nano-devices such as micro-robots, metamaterials, sensors, photonic devices, etc. Among most 3D nanofabrication strategies, the guided material assembly, an efficient bottom-up approach capable of directly constructing designed structures from precise integration of material building blocks, possesses compelling advantages in diverse material compatibility, sufficient driving forces, facile processing steps, and nanoscale resolution. In this review, we focus on assembly-based fabrication methods capable of creating complex 3D nanostructures (instead of periodic or 2.5D-only structures). Recent advances are classified based on the different assembly mechanisms, i.e., assembly driven by chemical reactions, physical interactions, and the synergy of multiple microscopic interactions. The design principles of representative fabrication strategies with an emphasis on their respective advantages, e.g., structural design flexibility, material compatibility, resolution, or applications are analyzed. In the summary and outlook, existing challenges, as well as possible paths to solutions for future development are reviewed. We believe that with recent advances in assembly-based nanofabrication strategies, 3D nanofabrication has achieved tremendous progress in resolution, material generality, and manufacturing cost, for it to make a greater impact in the near future.
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Affiliation(s)
- Songyun Gu
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
| | - Bingxu Chen
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
| | - Xiayi Xu
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
- School of Biomedical Sciences and EngineeringGuangzhou International CampusSouth China University of TechnologyGuangzhou511442P. R. China
| | - Fei Han
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
- School of Chemistry and Chemical EngineeringHarbin Institute of TechnologyHarbin150001P. R. China
| | - Shih‐Chi Chen
- Department of Mechanical and Automation EngineeringThe Chinese University of Hong KongShatinNew TerritoriesHong Kong SAR
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10
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Shi Y, Han X, Zou S, Liu G. Nanomaterials in Organoids: From Interactions to Personalized Medicine. ACS NANO 2024; 18:33276-33292. [PMID: 39609736 DOI: 10.1021/acsnano.4c13330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2024]
Abstract
Organoids are three-dimensional models of microscopic organisms created through the self-organization of various types of stem cells. They are widely unitized in personalized medicine due to their capacity to replicate the structure and functionality of native organs. Meanwhile, nanotechnology has been integrated into diagnostic and therapeutic tools to manage an array of medical conditions, given its unique characteristics of nanoscale. Nanomaterials have demonstrated potential in developing innovative and effective organoids. With a focus on studying the interaction of nanomaterials and organoid technology in personalized medicine, this Review examines the role of nanomaterials in regulating the fate of stem cells to construct different types of organoids. It also explores the potential of nanotechnology to create 3D microenvironments for organoids. Finally, perspectives and challenges of applying nanotechnology for organoids development toward the translation of personalized medicine are discussed.
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Affiliation(s)
- Ying Shi
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xin Han
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Siyi Zou
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Guozhen Liu
- Integrated Devices and Intelligent Diagnosis (ID2) Laboratory, CUHK(SZ)-Boyalife Joint Laboratory of Regenerative Medicine Engineering, Biomedical Engineering Programme, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
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11
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Hao Z, Kong L, Ruan L, Deng Z. Recent Advances in DNA Origami-Enabled Optical Biosensors for Multi-Scenario Application. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1968. [PMID: 39683355 DOI: 10.3390/nano14231968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Revised: 12/01/2024] [Accepted: 12/04/2024] [Indexed: 12/18/2024]
Abstract
Over the past few years, significant progress has been made in DNA origami technology due to the unrivaled self-assembly properties of DNA molecules. As a highly programmable, addressable, and biocompatible nanomaterial, DNA origami has found widespread applications in biomedicine, such as cell scaffold construction, antimicrobial drug delivery, and supramolecular enzyme assembly. To expand the scope of DNA origami application scenarios, researchers have developed DNA origami structures capable of actively identifying and quantitatively reporting targets. Optical DNA origami biosensors are promising due to their fast-to-use, sensitive, and easy implementation. However, the conversion of DNA origami to optical biosensors is still in its infancy stage, and related strategies have not been systematically summarized, increasing the difficulty of guiding subsequent researchers. Therefore, this review focuses on the universal strategies that endow DNA origami with dynamic responsiveness from both de novo design and current DNA origami modification. Various applications of DNA origami biosensors are also discussed. Additionally, we highlight the advantages of DNA origami biosensors, which offer a single-molecule resolution and high signal-to-noise ratio as an alternative to traditional analytical techniques. We believe that over the next decade, researchers will continue to transform DNA origami into optical biosensors and explore their infinite possible uses.
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Affiliation(s)
- Ziao Hao
- State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Lijun Kong
- State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Longfei Ruan
- State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Zhengtao Deng
- State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Microstructures, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
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12
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Li D, Dong J, Zhou Y, Wang Q. Toward Precise Fabrication of Finite-Sized DNA Origami Superstructures. SMALL METHODS 2024:e2401629. [PMID: 39632670 DOI: 10.1002/smtd.202401629] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 11/22/2024] [Indexed: 12/07/2024]
Abstract
DNA origami enables the precise construction of 2D and 3D nanostructures with customizable shapes and the high-resolution organization of functional materials. However, the size of a single DNA origami is constrained by the length of the scaffold strand, and since its inception, scaling up the size and complexity has been a persistent pursuit. Hierarchical self-assembly of DNA origami units offers a feasible approach to overcome the limitation. Unlike periodic arrays, finite-sized DNA origami superstructures feature well-defined structural boundaries and uniform dimensions. In recent years, increasing attention has been directed toward precise control over the hierarchical self-assembly of DNA origami structures and their applications in fields such as nanophotonics, biophysics, and material science. This review summarizes the strategies for fabricating finite-sized DNA origami superstructures, including heterogeneous self-assembly, self-limited self-assembly, and templated self-assembly, along with a comparative analysis of the advantages and limitations of each approach. Subsequently, recent advancements in the application of these structures are discussed from a structure design perspective. Finally, an outlook on the current challenges and potential future directions is provided, highlighting opportunities for further research and development in this rapidly evolving field.
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Affiliation(s)
- Dongsheng Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qiangbin Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China
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13
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Yang J, Chen T, Xiang Q, Li D, Zhou W, Xu F. Target-responsive triplex aptamer nanoswitch enables label-free and ultrasensitive detection of antibody in human serum via lighting-up RNA aptamer transcriptions. Talanta 2024; 278:126455. [PMID: 38917548 DOI: 10.1016/j.talanta.2024.126455] [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: 03/22/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Accurate and sensitive monitoring of the concentration change of anti-digoxigenin (Anti-Dig) antibody is of great importance for diagnosing infectious and immunological diseases. Combining a novel triplex aptamer nanoswitch and the high signal-to-noise ratio of lighting-up RNA aptamer signal amplification, a label-free and ultrasensitive fluorescent sensing approach for detecting Anti-Dig antibodies is described. The target Anti-Dig antibodies recognize and bind with the nanoswitch to open its triplex helix stem structure to release Taq DNA polymerase and short ssDNA primer simultaneously, which activates the Taq DNA polymerase to initiate downstream strand extension of ssDNA primer to yield specific dsDNA containing RNA promoter sequence. T7 RNA polymerase recognizes and binds to these promoter sequences to initiate RNA transcription reaction to produce many RNA aptamer sequences. These aptamers can recognize and bind with Malachite Green (MG) dye specifically and produce highly amplified fluorescent signal for monitoring Anti-Dig antibodies from 50 pM to 50 nM with a detection limit down to 33 pM. The method also exhibits high selectivity for Anti-Dig antibodies and can be used to discriminate trace Anti-Dig antibodies in diluted serum samples. Our method is superior to many immunization-based Anti-Dig antibody detection methods and thus holds great potential for monitoring disease progression and efficacy.
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Affiliation(s)
- Jirong Yang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Tiantian Chen
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Qian Xiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Daxiu Li
- College Pharmacy and Biological Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Wenjiao Zhou
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China.
| | - Fengfeng Xu
- Organization Department of the Communist Party of China, Chongqing University of Technology, Chongqing, 400054, PR China.
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14
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Roozbahani GM, Colosi PL, Oravecz A, Sorokina EM, Pfeifer W, Shokri S, Wei Y, Didier P, DeLuca M, Arya G, Tora L, Lakadamyali M, Poirier MG, Castro CE. Piggybacking functionalized DNA nanostructures into live-cell nuclei. SCIENCE ADVANCES 2024; 10:eadn9423. [PMID: 38968349 PMCID: PMC11225781 DOI: 10.1126/sciadv.adn9423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/03/2024] [Indexed: 07/07/2024]
Abstract
DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing, visualizing, and controlling biomolecular processes within live cells. We present an approach to deliver DOs into live-cell nuclei. We show that these DOs do not undergo detectable structural degradation in cell culture media or cell extracts for 24 hours. To deliver DOs into the nuclei of human U2OS cells, we conjugated 30-nanometer DO nanorods with an antibody raised against a nuclear factor, specifically the largest subunit of RNA polymerase II (Pol II). We find that DOs remain structurally intact in cells for 24 hours, including inside the nucleus. We demonstrate that electroporated anti-Pol II antibody-conjugated DOs are piggybacked into nuclei and exhibit subdiffusive motion inside the nucleus. Our results establish interfacing DOs with a nuclear factor as an effective method to deliver nanodevices into live-cell nuclei.
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Affiliation(s)
- Golbarg M. Roozbahani
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - P. L. Colosi
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Attila Oravecz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch 67404, France
- Université de Strasbourg, Illkirch 67404, France
| | - Elena M. Sorokina
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wolfgang Pfeifer
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Siamak Shokri
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Yin Wei
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Pascal Didier
- Université de Strasbourg, Illkirch 67404, France
- Laboratoire de Biophotonique et Pharmacologie, Illkirch 67401, France
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch 67404, France
- Université de Strasbourg, Illkirch 67404, France
| | - Melike Lakadamyali
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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15
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Bonde S, Osmani RAM, Trivedi R, Patravale V, Angolkar M, Prasad AG, Ravikumar AA. Harnessing DNA origami's therapeutic potential for revolutionizing cardiovascular disease treatment: A comprehensive review. Int J Biol Macromol 2024; 270:132246. [PMID: 38735608 DOI: 10.1016/j.ijbiomac.2024.132246] [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: 12/05/2023] [Revised: 03/25/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
DNA origami is a cutting-edge nanotechnology approach that creates precise and detailed 2D and 3D nanostructures. The crucial feature of DNA origami is how it is created, which enables precise control over its size and shape. Biocompatibility, targetability, programmability, and stability are further advantages that make it a potentially beneficial technique for a variety of applications. The preclinical studies of sophisticated programmable nanomedicines and nanodevices that can precisely respond to particular disease-associated triggers and microenvironments have been made possible by recent developments in DNA origami. These stimuli, which are endogenous to the targeted disorders, include protein upregulation, pH, redox status, and small chemicals. Oncology has traditionally been the focus of the majority of past and current research on this subject. Therefore, in this comprehensive review, we delve into the intricate world of DNA origami, exploring its defining features and capabilities. This review covers the fundamental characteristics of DNA origami, targeting DNA origami to cells, cellular uptake, and subcellular localization. Throughout the review, we emphasised on elucidating the imperative for such a therapeutic platform, especially in addressing the complexities of cardiovascular disease (CVD). Moreover, we explore the vast potential inherent in DNA origami technology, envisioning its promising role in the realm of CVD treatment and beyond.
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Affiliation(s)
- Smita Bonde
- Department of Pharmaceutics, SSR College of Pharmacy, Silvassa 396230, UT of Dadra and Nagar Haveli, India.
| | - Riyaz Ali M Osmani
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
| | - Rashmi Trivedi
- Department of Pharmaceutics, Smt. Kishoritai Bhoyar College of Pharmacy, Kamptee, Nagpur 441002, Maharashtra, India.
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga (E), Mumbai 400019, Maharashtra, India.
| | - Mohit Angolkar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
| | - Aprameya Ganesh Prasad
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Akhila Akkihebbal Ravikumar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research (JSS AHER), Mysuru 570015, Karnataka, India.
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16
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Bai Y, Xu P, Li S, Wang D, Zhang K, Zheng D, Yue D, Zhang G, He S, Li Y, Zou H, Deng Y. Signal amplification strategy of DNA self-assembled biosensor and typical applications in pathogenic microorganism detection. Talanta 2024; 272:125759. [PMID: 38350248 DOI: 10.1016/j.talanta.2024.125759] [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: 11/05/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Biosensors have emerged as ideal analytical devices for various bio-applications owing to their low cost, convenience, and portability, which offer great potential for improving global healthcare. DNA self-assembly techniques have been enriched with the development of innovative amplification strategies, such as dispersion-to-localization of catalytic hairpin assembly, and dumbbell hybridization chain reaction, which hold great significance for building biosensors capable of realizing sensitive, rapid and multiplexed detection of pathogenic microorganisms. Here, focusing primarily on the signal amplification strategies based on DNA self-assembly, we concisely summarized the strengths and weaknesses of diverse isothermal nucleic acid amplification techniques. Subsequently, both single-layer and cascade amplification strategies based on traditional catalytic hairpin assembly and hybridization chain reaction were critically explored. Furthermore, a comprehensive overview of the recent advances in DNA self-assembled biosensors for the detection of pathogenic microorganisms is presented to summarize methods for biorecognition and signal amplification. Finally, a brief discussion is provided about the current challenges and future directions of DNA self-assembled biosensors.
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Affiliation(s)
- Yuxin Bai
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Pingyao Xu
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongming Zheng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Daifan Yue
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Guiji Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shuya He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Yan Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China.
| | - Haimin Zou
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
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17
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Kosara S, Singh R, Bhatia D. Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives. NANOSCALE ADVANCES 2024; 6:386-401. [PMID: 38235105 PMCID: PMC10790967 DOI: 10.1039/d3na00692a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.
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Affiliation(s)
- Sanjay Kosara
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
| | - Ramesh Singh
- Department of Mechanical Engineering, Colorado State University Fort Collins CO USA
| | - Dhiraj Bhatia
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
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18
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Roozbahani GM, Colosi P, Oravecz A, Sorokina EM, Pfeifer W, Shokri S, Wei Y, Didier P, DeLuca M, Arya G, Tora L, Lakadamyali M, Poirier MG, Castro CE. Piggybacking functionalized DNA nanostructures into live cell nuclei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573746. [PMID: 38260628 PMCID: PMC10802371 DOI: 10.1101/2023.12.30.573746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
DNA origami (DO) are promising tools for in vitro or in vivo applications including drug delivery; biosensing, detecting biomolecules; and probing chromatin sub-structures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing visualizing and controlling important biological processes in live cells. Here we present an approach to deliver DO strucures into live cell nuclei. We show that labelled DOs do not undergo detectable structural degradation in cell culture media or human cell extracts for 24 hr. To deliver DO platforms into the nuclei of human U2OS cells, we conjugated 30 nm long DO nanorods with an antibody raised against the largest subunit of RNA Polymerase II (Pol II), a key enzyme involved in gene transcription. We find that DOs remain structurally intact in cells for 24hr, including within the nucleus. Using fluorescence microscopy we demonstrate that the electroporated anti-Pol II antibody conjugated DOs are efficiently piggybacked into nuclei and exihibit sub-diffusive motion inside the nucleus. Our results reveal that functionalizing DOs with an antibody raised against a nuclear factor is a highly effective method for the delivery of nanodevices into live cell nuclei.
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Affiliation(s)
- Golbarg M. Roozbahani
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Patricia Colosi
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Attila Oravecz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, 67404, France
- Université de Strasbourg, Illkirch, 67404, France
| | - Elena M. Sorokina
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wolfgang Pfeifer
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Siamak Shokri
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yin Wei
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Pascal Didier
- Université de Strasbourg, Illkirch, 67404, France
- Laboratoire de Biophotonique et Pharmacologie, Illkirch, 67401, France
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, United States
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, 67404, France
- Université de Strasbourg, Illkirch, 67404, France
| | - Melike Lakadamyali
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
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19
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Al-Atawi AA, Alyahyan S, Alatawi MN, Sadad T, Manzoor T, Farooq-i-Azam M, Khan ZH. Stress Monitoring Using Machine Learning, IoT and Wearable Sensors. SENSORS (BASEL, SWITZERLAND) 2023; 23:8875. [PMID: 37960574 PMCID: PMC10648446 DOI: 10.3390/s23218875] [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: 10/10/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023]
Abstract
The Internet of Things (IoT) has emerged as a fundamental framework for interconnected device communication, representing a relatively new paradigm and the evolution of the Internet into its next phase. Its significance is pronounced in diverse fields, especially healthcare, where it finds applications in scenarios such as medical service tracking. By analyzing patterns in observed parameters, the anticipation of disease types becomes feasible. Stress monitoring with wearable sensors and the Internet of Things (IoT) is a potential application that can enhance wellness and preventative health management. Healthcare professionals have harnessed robust systems incorporating battery-based wearable technology and wireless communication channels to enable cost-effective healthcare monitoring for various medical conditions. Network-connected sensors, whether within living spaces or worn on the body, accumulate data crucial for evaluating patients' health. The integration of machine learning and cutting-edge technology has sparked research interest in addressing stress levels. Psychological stress significantly impacts a person's physiological parameters. Stress can have negative impacts over time, prompting sometimes costly therapies. Acute stress levels can even constitute a life-threatening risk, especially in people who have previously been diagnosed with borderline personality disorder or schizophrenia. To offer a proactive solution within the realm of smart healthcare, this article introduces a novel machine learning-based system termed "Stress-Track". The device is intended to track a person's stress levels by examining their body temperature, sweat, and motion rate during physical activity. The proposed model achieves an impressive accuracy rate of 99.5%, showcasing its potential impact on stress management and healthcare enhancement.
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Affiliation(s)
- Abdullah A. Al-Atawi
- Department of Computer Science, Applied College, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Saleh Alyahyan
- Applied College in Dwadmi, Shaqra University, Dawadmi 17464, Saudi Arabia;
| | - Mohammed Naif Alatawi
- Information Technology Department, Faculty of Computers and Information Technology, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Tariq Sadad
- Department of Computer Science, University of Engineering & Technology, Mardan 23200, Pakistan
| | - Tareq Manzoor
- Energy Research Centre, COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan;
| | - Muhammad Farooq-i-Azam
- Department of Electrical and Computer Engineering, COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan;
| | - Zeashan Hameed Khan
- Interdisciplinary Research Center for Intelligent Manufacturing & Robotics (IRC-IMR), King Fahd University of Petroleum & Minerals (KFUPM), Dhahran 31261, Saudi Arabia
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Feng F, Zhang L, Zheng P, Xiao SJ. Construction of DNA Bilayer Tiles and Arrays Using Circular DNA Molecules as Scaffolds. Chembiochem 2023; 24:e202300420. [PMID: 37464981 DOI: 10.1002/cbic.202300420] [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: 06/04/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi-arm junction (mAJ) tiles and arrays is well-known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E-tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface-mediated assembly.
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Affiliation(s)
- Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ling Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
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Ji H, Zhu Q. Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery. J Control Release 2023; 361:803-818. [PMID: 37597810 DOI: 10.1016/j.jconrel.2023.08.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.
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Affiliation(s)
- Haofei Ji
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
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Talaat FM, El-Balka RM. Stress monitoring using wearable sensors: IoT techniques in medical field. Neural Comput Appl 2023; 35:1-14. [PMID: 37362562 PMCID: PMC10237081 DOI: 10.1007/s00521-023-08681-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/10/2023] [Indexed: 06/28/2023]
Abstract
The concept "Internet of Things" (IoT), which facilitates communication between linked devices, is relatively new. It refers to the next generation of the Internet. IoT supports healthcare and is essential to numerous applications for tracking medical services. By examining the pattern of observed parameters, the type of the disease can be anticipated. For people with a range of diseases, health professionals and technicians have developed an excellent system that employs commonly utilized techniques like wearable technology, wireless channels, and other remote equipment to give low-cost healthcare monitoring. Whether put in living areas or worn on the body, network-related sensors gather detailed data to evaluate the patient's physical and mental health. The main objective of this study is to examine the current e-health monitoring system using integrated systems. Automatically providing patients with a prescription based on their status is the main goal of the e-health monitoring system. The doctor can keep an eye on the patient's health without having to communicate with them. The purpose of the study is to examine how IoT technologies are applied in the medical industry and how they help to raise the bar of healthcare delivered by healthcare institutions. The study will also include the uses of IoT in the medical area, the degree to which it is used to enhance conventional practices in various health fields, and the degree to which IoT may raise the standard of healthcare services. The main contributions in this paper are as follows: (1) importing signals from wearable devices, extracting signals from non-signals, performing peak enhancement; (2) processing and analyzing the incoming signals; (3) proposing a new stress monitoring algorithm (SMA) using wearable sensors; (4) comparing between various ML algorithms; (5) the proposed stress monitoring algorithm (SMA) is composed of four main phases: (a) data acquisition phase, (b) data and signal processing phase, (c) prediction phase, and (d) model performance evaluation phase; and (6) grid search is used to find the optimal values for hyperparameters of SVM (C and gamma). From the findings, it is shown that random forest is best suited for this classification, with decision tree and XGBoost following closely behind.
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Affiliation(s)
- Fatma M. Talaat
- Faculty of Artificial Intelligence, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Rana Mohamed El-Balka
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
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