1
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Xiao Y, Liang Z, Shyngys M, Baekova A, Cheung S, Muljadi MB, Bai Q, Zeng L, Choi CHJ. In Vivo Interactions of Nucleic Acid Nanostructures With Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2314232. [PMID: 39263835 DOI: 10.1002/adma.202314232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 07/03/2024] [Indexed: 09/13/2024]
Abstract
Nucleic acid nanostructures, derived from the assembly of nucleic acid building blocks (e.g., plasmids and oligonucleotides), are important intracellular carriers of therapeutic cargoes widely utilized in preclinical nanomedicine applications, yet their clinical translation remains scarce. In the era of "translational nucleic acid nanotechnology", a deeper mechanistic understanding of the interactions of nucleic acid nanostructures with cells in vivo will guide the development of more efficacious nanomedicines. This review showcases the recent progress in dissecting the in vivo interactions of four key types of nucleic acid nanostructures (i.e., tile-based, origami, spherical nucleic acid, and nucleic acid nanogel) with cells in rodents over the past five years. Emphasis lies on the cellular-level distribution of nucleic acid nanostructures in various organs and tissues and the cellular responses induced by their cellular entry. Next, in the spirit of preclinical translation, this review features the latest interactions of nucleic acid nanostructures with cells in large animals and humans. Finally, the review offers directions for studying the interactions of nucleic acid nanostructures with cells from both materials and biology perspectives and concludes with some regulatory updates.
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Affiliation(s)
- Yu Xiao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Zhihui Liang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Moldir Shyngys
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Aiana Baekova
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Suen Cheung
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Mathias Billy Muljadi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Qianqian Bai
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Lula Zeng
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Chung Hang Jonathan Choi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Shatin, New Territories, Hong Kong
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2
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Zhu S, Peng H, Kong H, Yan Q, Xia K, Wang L, Zhu Y, Luo S. Visualization of the hepatic and renal cell uptake and trafficking of tetrahedral DNA origami in tumour. Cell Prolif 2024; 57:e13643. [PMID: 38572799 PMCID: PMC11294413 DOI: 10.1111/cpr.13643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
DNA nanostructures, known for their programmability, ease of modification, and favourable biocompatibility, have gained widespread application in the biomedical field. Among them, Tetrahedral DNA Origami (TDOs), as a novel DNA nanostructure, possesses well-defined structures, multiple modification sites, and large cavities, making it a promising drug carrier. However, current understanding of TDOs' interactions with biological systems, particularly with target cells and organs, remains unexplored, limiting its further applications in biomedicine. In this work, we prepared TDOs with an average particle size of 40 nm and labelled them with Cy5 fluorescent molecules. Following intravenous injection in mice, the uptake of TDOs by different types of liver and kidney cells was observed. Results indicated that TDOs accumulate in renal tubules and are metabolized by Kupffer cells, epithelial cells, and hepatocytes in the liver. Additionally, in a tumour-bearing mouse model, TDOs passively targeted tumour tissues and exhibited excellent tumour penetration and retention after rapid metabolism in hepatocytes. Our findings provide crucial insights for the development of TDO-based drug delivery systems.
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Affiliation(s)
- Shitai Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied Physics, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongzhen Peng
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghaiChina
- Institute of Materiobiology, College of Sciences, Shanghai UniversityShanghaiChina
| | - Huating Kong
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of SciencesShanghaiChina
| | - Qinglong Yan
- Institute of Materiobiology, College of Sciences, Shanghai UniversityShanghaiChina
- Xiangfu LaboratoryJiashanChina
| | - Kai Xia
- Xiangfu LaboratoryJiashanChina
- Shanghai Frontier Innovation Research InstituteShanghaiChina
| | - Lihua Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied Physics, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- Institute of Materiobiology, College of Sciences, Shanghai UniversityShanghaiChina
| | - Ying Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied Physics, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- Institute of Materiobiology, College of Sciences, Shanghai UniversityShanghaiChina
| | - Shihua Luo
- Department of TraumatologyRui Jin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghaiChina
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3
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Bardales AC, Smirnov V, Taylor K, Kolpashchikov DM. DNA Logic Gates Integrated on DNA Substrates in Molecular Computing. Chembiochem 2024; 25:e202400080. [PMID: 38385968 DOI: 10.1002/cbic.202400080] [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: 02/09/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
Due to nucleic acid's programmability, it is possible to realize DNA structures with computing functions, and thus a new generation of molecular computers is evolving to solve biological and medical problems. Pioneered by Milan Stojanovic, Boolean DNA logic gates created the foundation for the development of DNA computers. Similar to electronic computers, the field is evolving towards integrating DNA logic gates and circuits by positioning them on substrates to increase circuit density and minimize gate distance and undesired crosstalk. In this minireview, we summarize recent developments in the integration of DNA logic gates into circuits localized on DNA substrates. This approach of all-DNA integrated circuits (DNA ICs) offers the advantages of biocompatibility, increased circuit response, increased circuit density, reduced unit concentration, facilitated circuit isolation, and facilitated cell uptake. DNA ICs can face similar challenges as their equivalent circuits operating in bulk solution (bulk circuits), and new physical challenges inherent in spatial localization. We discuss possible avenues to overcome these obstacles.
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Affiliation(s)
- Andrea C Bardales
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Viktor Smirnov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, 9 Lomonosova Str., St. Petersburg, Russian Federation
| | - Katherine Taylor
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Physical Sciences Bld. Rm. 255, Orlando, FL 32816-2366, Florida
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4
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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5
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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6
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Wang W, Chen Y, Yin H, Lv J, Lin M, Wu ZS. Center backbone-rigidified DNA polygonal nanostructures and bottom face-templated polyhedral pyramids with structural stability in a complex biological medium. Acta Biomater 2023; 161:100-111. [PMID: 36905953 DOI: 10.1016/j.actbio.2023.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/15/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Due to the sequence programmability, good biocompatibility, versatile functionalities and vast sequence space, DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures in one, two and three dimensions that are capable of engineering of multiple functional nucleic acids into a useful tool to implement intended tasks in biological and medical field. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging mainly because of the molecular flexibility-based uncontrollability of size and shape. In this contribution, utilizing gel electrophoretic analysis and atomic force microscopy, we demonstrate the modeling assembly technique for the construction of wireframe DNA nanostructures that can be divided into two categories: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the construction of DNA polygons and polyhedral pyramids, respectively. The highest assembly efficiency (AE) is about 100%, while the lowest AE is not less than 50%. Moreover, when adding one edge for polygons or one side face for pyramids, we only need to add one oligonucleotide strand. Especially, the advanced polygons (e.g., pentagon and hexagon) of definite shape are for the first time constructed. Along this line, introduction of cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours even if the vulnerable nicks are not sealed. The proposed modeling assembly technique represents important progress toward the development of DNA nanotechnology and is expected to promote the application of DNA nanostructures in biological and biomedical fields. STATEMENT OF SIGNIFICANCE: DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging. In this contribution, we demonstrate the modeling technique for the construction of different wireframe DNA nanostructures: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the assembly of DNA polygons and polyhedral pyramids, respectively. Moreover, cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours, promoting the application of DNA nanostructures in biological and biomedical fields.
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Affiliation(s)
- Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Yaxin Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Hongwei Yin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Jingrui Lv
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Mengling Lin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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7
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Zhao M, Wang R, Yang K, Jiang Y, Peng Y, Li Y, Zhang Z, Ding J, Shi S. Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharm Sin B 2023; 13:916-941. [PMID: 36970219 PMCID: PMC10031267 DOI: 10.1016/j.apsb.2022.10.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.
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Affiliation(s)
- Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Rujing Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kunmeng Yang
- The First Norman Bethune College of Clinical Medicine, Jilin University, Changchun 130061, China
| | - Yuhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Yachen Peng
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yuke Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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8
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Peng Y, Pang H, Gao Z, Li D, Lai X, Chen D, Zhang R, Zhao X, Chen X, Pei H, Tu J, Qiao B, Wu Q. Kinetics-accelerated one-step detection of MicroRNA through spatially localized reactions based on DNA tile self-assembly. Biosens Bioelectron 2023; 222:114932. [PMID: 36462429 DOI: 10.1016/j.bios.2022.114932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022]
Abstract
The localization of isothermal amplification systems has elicited extensive attention due to the enhanced reaction kinetics when detecting ultra-trace small-molecule nucleic acids. Therefore, the seek for an appropriate localization cargo of spatially confined reactions is urgent. Herein, we have developed a novel approach to localize the catalytic hairpin assembly (CHA) system into the DNA tile self-assembly nanostructure. Thanks to the precise programming and robust probe loading capacity, this strategy achieved a 2.3 × 105-fold higher local reaction concentration than a classical CHA system with enhanced reaction kinetics in theory. From the experimental results, this strategy could reach the reaction plateau faster and get access to a magnified effect of 1.57-6.99 times higher in the linear range of microRNA (miRNA) than the simple CHA system. Meanwhile, this strategy satisfied the demand for the one-step detection of miRNA in cell lysates at room temperature with good sensitivity and specificity. These features indicated its excellent potential for ultra-trace molecule detection in clinical diagnosis and provided new insights into the field of bioassays based on DNA tile self-assembly nanotechnology.
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Affiliation(s)
- Yanan Peng
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Huajie Pang
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Zhijun Gao
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Dongxia Li
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Xiangde Lai
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Delun Chen
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Materials Science and Engineering, Hainan University, Haikou, 570228, China
| | - Rui Zhang
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Xuan Zhao
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China; Department of Clinical Laboratory, Hainan Cancer Hospital, Haikou, 570311, China
| | - Xinping Chen
- Department of Clinical Laboratory, Hainan Cancer Hospital, Haikou, 570311, China
| | - Hua Pei
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China
| | - Jinchun Tu
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Materials Science and Engineering, Hainan University, Haikou, 570228, China
| | - Bin Qiao
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China.
| | - Qiang Wu
- Department of Clinical Laboratory of the Second Affiliated Hospital, School of Tropical Medicine, Key Laboratory of Emergency and Trauma of Ministry of Education, Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, 571199, China.
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9
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Poppleton E, Urbanek N, Chakraborty T, Griffo A, Monari L, Göpfrich K. RNA origami: design, simulation and application. RNA Biol 2023; 20:510-524. [PMID: 37498217 PMCID: PMC10376919 DOI: 10.1080/15476286.2023.2237719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023] Open
Abstract
Design strategies for DNA and RNA nanostructures have developed along parallel lines for the past 30 years, from small structural motifs derived from biology to large 'origami' structures with thousands to tens of thousands of bases. With the recent publication of numerous RNA origami structures and improved design methods-even permitting co-transcriptional folding of kilobase-sized structures - the RNA nanotechnolgy field is at an inflection point. Here, we review the key achievements which inspired and enabled RNA origami design and draw comparisons with the development and applications of DNA origami structures. We further present the available computational tools for the design and the simulation, which will be key to the growth of the RNA origami community. Finally, we portray the transition from RNA origami structure to function. Several functional RNA origami structures exist already, their expression in cells has been demonstrated and first applications in cell biology have already been realized. Overall, we foresee that the fast-paced RNA origami field will provide new molecular hardware for biophysics, synthetic biology and biomedicine, complementing the DNA origami toolbox.
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Affiliation(s)
- Erik Poppleton
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Molecular Biomechanics, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Niklas Urbanek
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Taniya Chakraborty
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alessandra Griffo
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Luca Monari
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institut de Science Et D’ingénierie Supramoléculaires (ISIS), Université de Strasbourg, Strasbourg, France
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
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10
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Xie M, Hu Y, Yin J, Zhao Z, Chen J, Chao J. DNA Nanotechnology-Enabled Fabrication of Metal Nanomorphology. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9840131. [PMID: 35935136 PMCID: PMC9275100 DOI: 10.34133/2022/9840131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
In recent decades, DNA nanotechnology has grown into a highly innovative and widely established field. DNA nanostructures have extraordinary structural programmability and can accurately organize nanoscale materials, especially in guiding the synthesis of metal nanomaterials, which have unique advantages in controlling the growth morphology of metal nanomaterials. This review started with the evolution in DNA nanotechnology and the types of DNA nanostructures. Next, a DNA-based nanofabrication technology, DNA metallization, was introduced. In this section, we systematically summarized the DNA-oriented synthesis of metal nanostructures with different morphologies and structures. Furthermore, the applications of metal nanostructures constructed from DNA templates in various fields including electronics, catalysis, sensing, and bioimaging were figured out. Finally, the development prospects and challenges of metal nanostructures formed under the morphology control by DNA nanotechnology were discussed.
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Affiliation(s)
- Mo Xie
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Yang Hu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jue Yin
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Ziwei Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Jing Chen
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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11
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Wang ST, Minevich B, Liu J, Zhang H, Nykypanchuk D, Byrnes J, Liu W, Bershadsky L, Liu Q, Wang T, Ren G, Gang O. Designed and biologically active protein lattices. Nat Commun 2021; 12:3702. [PMID: 34140491 PMCID: PMC8211860 DOI: 10.1038/s41467-021-23966-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/13/2021] [Indexed: 01/13/2023] Open
Abstract
Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.
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Affiliation(s)
- Shih-Ting Wang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York City, NY, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Honghu Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Dmytro Nykypanchuk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - James Byrnes
- Energy Sciences Directorate/Photon Science Division, NSLS II, Brookhaven National Laboratory, Upton, NY, USA
| | - Wu Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lev Bershadsky
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Tong Wang
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York City, NY, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA.
- Department of Chemical Engineering, Columbia University, New York City, NY, USA.
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA.
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12
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Glaser M, Deb S, Seier F, Agrawal A, Liedl T, Douglas S, Gupta MK, Smith DM. The Art of Designing DNA Nanostructures with CAD Software. Molecules 2021; 26:molecules26082287. [PMID: 33920889 PMCID: PMC8071251 DOI: 10.3390/molecules26082287] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.
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Affiliation(s)
- Martin Glaser
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
| | - Sourav Deb
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
| | - Florian Seier
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
| | - Amay Agrawal
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany;
| | - Shawn Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA;
| | - Manish K. Gupta
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
- Correspondence: (M.K.G.); (D.M.S.)
| | - David M. Smith
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
- Correspondence: (M.K.G.); (D.M.S.)
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13
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He L, Mu J, Gang O, Chen X. Rationally Programming Nanomaterials with DNA for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003775. [PMID: 33898180 PMCID: PMC8061415 DOI: 10.1002/advs.202003775] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/23/2020] [Indexed: 05/05/2023]
Abstract
DNA is not only a carrier of genetic information, but also a versatile structural tool for the engineering and self-assembling of nanostructures. In this regard, the DNA template has dramatically enhanced the scalability, programmability, and functionality of the self-assembled DNA nanostructures. These capabilities provide opportunities for a wide range of biomedical applications in biosensing, bioimaging, drug delivery, and disease therapy. In this review, the importance and advantages of DNA for programming and fabricating of DNA nanostructures are first highlighted. The recent progress in design and construction of DNA nanostructures are then summarized, including DNA conjugated nanoparticle systems, DNA-based clusters and extended organizations, and DNA origami-templated assemblies. An overview on biomedical applications of the self-assembled DNA nanostructures is provided. Finally, the conclusion and perspectives on the self-assembled DNA nanostructures are presented.
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Affiliation(s)
- Liangcan He
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
| | - Jing Mu
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Oleg Gang
- Department of Chemical Engineering and Department of Applied Physics and Applied MathematicsColumbia UniversityNew YorkNY10027USA
- Center for Functional NanomaterialsBrookhaven National LaboratoryUptonNY11973USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
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14
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Hagan MF, Grason GM. Equilibrium mechanisms of self-limiting assembly. REVIEWS OF MODERN PHYSICS 2021; 93:025008. [PMID: 35221384 PMCID: PMC8880259 DOI: 10.1103/revmodphys.93.025008] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of self-limiting assembly, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories: self-closing assemblies and open-boundary assemblies. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.
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Affiliation(s)
- Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
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15
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Piao J, Yuan W, Dong Y. Recent Progress of DNA Nanostructures on Amphiphilic Membranes. Macromol Biosci 2021; 21:e2000440. [PMID: 33759366 DOI: 10.1002/mabi.202000440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/24/2021] [Indexed: 11/11/2022]
Abstract
Employing DNA nanostructures mimicking membrane proteins on artificial amphiphilic membranes have been widely developed to understand the structures and functions of the natural membrane systems. In this review, the recent developments in artificial systems constructed by amphiphilic membranes and DNA nanostructures are summarized. First, the preparations and properties of the amphipathic bilayer models are introduced. Second, the interactions are discussed between the membrane and the DNA nanostructures, as well as their coassembly behaviors. Next, the alternative systems related to membrane protein-mediated signal transmission, selective distribution, transmembrane channels, and membrane fusion are also introduced. Moreover, the constructions of membrane skeleton protein-mimicking DNA nanostructures are also highlighted.
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Affiliation(s)
- Jiafang Piao
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Wei Yuan
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
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16
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Lu J, Hu P, Cao L, Wei Z, Xiao F, Chen Z, Li Y, Tian L. Genetically Encoded and Biologically Produced All‐DNA Nanomedicine Based on One‐Pot Assembly of DNA Dendrimers for Targeted Gene Regulation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jingxiong Lu
- Department of Materials Science and Engineering Southern University of Science and Technology 1088 Xueyuan Blvd., Nanshan District Shenzhen Guangdong 518055 China
- Institute of Medi-X Academy for Advanced Interdisciplinary Studies Southern University of Science and Technology 1088 Xueyuan Blvd., Nanshan District Shenzhen Guangdong 518055 China
| | - Pengchao Hu
- Department of Biology Southern University of Science and Technology 1088 Xueyuan Blvd. Nanshan District Shenzhen, Guangdong 518055 China
| | - Lingyan Cao
- Department of Prosthodontics Ninth People's Hospital Shanghai Jiao Tong University School of Medicine 639 Zhizaoju Road Shanghai 200011 China
| | - Zixiang Wei
- Department of Materials Science and Engineering Southern University of Science and Technology 1088 Xueyuan Blvd., Nanshan District Shenzhen Guangdong 518055 China
| | - Fan Xiao
- Department of Materials Science and Engineering Southern University of Science and Technology 1088 Xueyuan Blvd., Nanshan District Shenzhen Guangdong 518055 China
| | - Zhe Chen
- Department of Materials Science and Engineering Southern University of Science and Technology 1088 Xueyuan Blvd., Nanshan District Shenzhen Guangdong 518055 China
| | - Yan Li
- Department of Biology Southern University of Science and Technology 1088 Xueyuan Blvd. Nanshan District Shenzhen, Guangdong 518055 China
| | - Leilei Tian
- Department of Materials Science and Engineering Southern University of Science and Technology 1088 Xueyuan Blvd., Nanshan District Shenzhen Guangdong 518055 China
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17
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Lu J, Hu P, Cao L, Wei Z, Xiao F, Chen Z, Li Y, Tian L. Genetically Encoded and Biologically Produced All-DNA Nanomedicine Based on One-Pot Assembly of DNA Dendrimers for Targeted Gene Regulation. Angew Chem Int Ed Engl 2021; 60:5377-5385. [PMID: 33226694 DOI: 10.1002/anie.202012916] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/15/2020] [Indexed: 12/11/2022]
Abstract
All-DNA nanomedicines have emerged as potential anti-tumor drugs. DNA nanotechnology provides all-DNA nanomedicines with unlimited possibilities in controlling the diversification of size, shape, and loads of the therapeutic motifs. As DNA is a biological polymer, it is possible to genetically encode and produce the all-DNA nanomedicines in living bacteria. Herein, DNA-dendrimer-based nanomedicines are designed to adapt to the biological production, which is constructed by the flexible 3-arm building blocks to enable a highly efficient one-pot DNA assembly. For the first time, a DNA nanomedicine, D4-3-As-DzSur, is successfully genetically encoded, biotechnologically produced, and directly self-assembled. The performance of the biologically produced D4-3-As-DzSur in targeted gene regulation has been confirmed by in vitro and in vivo studies. The biological production capability will fulfill the low-cost and large-scale production of all-DNA nanomedicines and promote clinical applications.
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Affiliation(s)
- Jingxiong Lu
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
- Institute of Medi-X, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
| | - Pengchao Hu
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
| | - Lingyan Cao
- Department of Prosthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Zixiang Wei
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
| | - Fan Xiao
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
| | - Zhe Chen
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
| | - Yan Li
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong, 518055, China
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18
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Higashi SL, Rozi N, Hanifah SA, Ikeda M. Supramolecular Architectures of Nucleic Acid/Peptide Hybrids. Int J Mol Sci 2020; 21:E9458. [PMID: 33322664 PMCID: PMC7763079 DOI: 10.3390/ijms21249458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
Supramolecular architectures that are built artificially from biomolecules, such as nucleic acids or peptides, with structural hierarchical orders ranging from the molecular to nano-scales have attracted increased attention in molecular science research fields. The engineering of nanostructures with such biomolecule-based supramolecular architectures could offer an opportunity for the development of biocompatible supramolecular (nano)materials. In this review, we highlighted a variety of supramolecular architectures that were assembled from both nucleic acids and peptides through the non-covalent interactions between them or the covalently conjugated molecular hybrids between them.
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Affiliation(s)
- Sayuri L. Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan;
| | - Normazida Rozi
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.R.); (S.A.H.)
| | - Sharina Abu Hanifah
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.R.); (S.A.H.)
| | - Masato Ikeda
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan;
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Institute for Glyco-Core Research (iGCORE), Gifu University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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19
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Bottom-Up Self-Assembly Based on DNA Nanotechnology. NANOMATERIALS 2020; 10:nano10102047. [PMID: 33081252 PMCID: PMC7603033 DOI: 10.3390/nano10102047] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 11/23/2022]
Abstract
Manipulating materials at the atomic scale is one of the goals of the development of chemistry and materials science, as it provides the possibility to customize material properties; however, it still remains a huge challenge. Using DNA self-assembly, materials can be controlled at the nano scale to achieve atomic- or nano-scaled fabrication. The programmability and addressability of DNA molecules can be applied to realize the self-assembly of materials from the bottom-up, which is called DNA nanotechnology. DNA nanotechnology does not focus on the biological functions of DNA molecules, but combines them into motifs, and then assembles these motifs to form ordered two-dimensional (2D) or three-dimensional (3D) lattices. These lattices can serve as general templates to regulate the assembly of guest materials. In this review, we introduce three typical DNA self-assembly strategies in this field and highlight the significant progress of each. We also review the application of DNA self-assembly and propose perspectives in this field.
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20
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Wang Y, Ge W, Lu B, Zhu JJ, Xiao SJ. Two-layer stacked multi-arm junction tiles and nanostructures assembled with small circular DNA molecules serving as scaffolds. NANOSCALE 2020; 12:19597-19603. [PMID: 32996986 DOI: 10.1039/d0nr05860b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One-layer multi-arm junction (mAJ) motifs have been investigated extensively for many kinds of planar 2D (two-dimension) lattices, surface-curved 3D (three-dimension) polyhedra, and complex 3D wireframe and tensegrity structures. Herein, we report the weaving strategy to achieve two-layer stacked multi-arm junction tiles (abbreviated as mAJ2) of 3AJ2 and 4AJ2, and several primary tessellation nanostructures of nanocages and 2D rhombus lattices carrying beautifully embossed 4-point stars. Challenges for perfect tessellation are also raised regarding the increase of motif complexity from 2D to 3D.
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Affiliation(s)
- Yu Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China.
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21
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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22
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McCluskey JB, Clark DS, Glover DJ. Functional Applications of Nucleic Acid-Protein Hybrid Nanostructures. Trends Biotechnol 2020; 38:976-989. [PMID: 32818445 DOI: 10.1016/j.tibtech.2020.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 01/09/2023]
Abstract
Combining the diverse chemical functionality of proteins with the predictable structural assembly of nucleic acids has enabled the creation of hybrid nanostructures for a range of biotechnology applications. Through the attachment of proteins onto or within nucleic acid nanostructures, materials with dynamic capabilities can be created that include switchable enzyme activity, targeted drug delivery, and multienzyme cascades for biocatalysis. Investigations of difficult-to-study biological mechanisms have also been aided by using DNA-protein assemblies that mimic natural processes in a controllable manner. Furthermore, advances that enable the recombinant production and intracellular assembly of hybrid nanostructures have the potential to overcome the significant manufacturing cost that has limited the use of DNA and RNA nanotechnology.
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Affiliation(s)
- Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Douglas S Clark
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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23
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Wang H, Peng P, Wang Q, Du Y, Tian Z, Li T. Environment-Recognizing DNA-Computation Circuits for the Intracellular Transport of Molecular Payloads for mRNA Imaging. Angew Chem Int Ed Engl 2020; 59:6099-6107. [PMID: 31981393 DOI: 10.1002/anie.201916432] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/21/2020] [Indexed: 01/04/2023]
Abstract
Programming intelligent DNA nanocarriers for the targeted transport of molecular payloads in living cells has attracted extensive attention. In vivo activation of these nanocarriers usually relies on external light irradiation. An interest is emerging in the automatic recognition of intracellular surroundings by nanocarriers and their in situ activation under the control of programmed DNA-computation circuits. Herein, we report the integration of DNA circuits with framework nucleic acid (FNA) nanocarriers that consist of a truncated square pyramid (TSP) cage and a built-in duplex cargo containing an antisense strand of the target mRNA. An i-motif and ATP aptamer embedded in the TSP are employed as logic-controlling units to respond to H+ and ATP inside cellular compartments, triggering the release of the sensing element for fluorescent mRNA imaging. Logic-controlled FNA devices could be used to target drug delivery, enabling precise disease treatment.
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Affiliation(s)
- Huihui Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Yi Du
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Zhijin Tian
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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24
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Wang H, Peng P, Wang Q, Du Y, Tian Z, Li T. Environment‐Recognizing DNA‐Computation Circuits for the Intracellular Transport of Molecular Payloads for mRNA Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916432] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Huihui Wang
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Pai Peng
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Qiwei Wang
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Yi Du
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Zhijin Tian
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
| | - Tao Li
- Department of ChemistryUniversity of Science and Technology of China 96 Jinzhai Road Hefei Anhui 230026 China
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25
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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26
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Chen W, Guo J, Cai Y, Fu Q, Chen B, Chou JJ. Unidirectional Presentation of Membrane Proteins in Nanoparticle-Supported Liposomes. Angew Chem Int Ed Engl 2019; 58:9866-9870. [PMID: 30990942 PMCID: PMC6660371 DOI: 10.1002/anie.201903093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 12/30/2022]
Abstract
Presentation of membrane proteins to host immune systems has been a challenging problem owing to complexity arising from the poor in vivo stability of the membrane-mimetic media often used for solubilizing the membrane proteins. The use of functionalized, biocompatible nanoparticles as substrates is shown to guide the formation of proteoliposomes, which can present many copies of membrane proteins in a unidirectional manner. The approach was demonstrated to present the membrane-proximal region of the HIV-1 envelope glycoprotein. These nanoparticle-supported liposomes are broadly applicable as membrane antigen vehicles for inducing host immune responses.
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Affiliation(s)
- Wen Chen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, United States
| | - Junling Guo
- Department of Biomass Science and Engineering, Sichuan University, 252 Shuncheng Street, Chengdu, Sichuan 610065, China
| | - Yongfei Cai
- Division of Molecular Medicine, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, United States
| | - Qingshan Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, United States
| | - Bing Chen
- Division of Molecular Medicine, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, 3 Blackfan Street, Boston, MA 02115, United States
| | - James J. Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, United States
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27
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Chen W, Cai Y, Fu Q, Chen B, Guo J, Chou JJ. Unidirectional Presentation of Membrane Proteins in Nanoparticle‐Supported Liposomes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Wen Chen
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School 250 Longwood Avenue Boston MA 02115 USA
| | - Yongfei Cai
- Division of Molecular MedicineBoston Children's HospitalDepartment of PediatricsHarvard Medical School 3 Blackfan Street Boston MA 02115 USA
| | - Qingshan Fu
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School 250 Longwood Avenue Boston MA 02115 USA
| | - Bing Chen
- Division of Molecular MedicineBoston Children's HospitalDepartment of PediatricsHarvard Medical School 3 Blackfan Street Boston MA 02115 USA
| | - Junling Guo
- Department of Biomass Science and EngineeringSichuan University 24 South Section Yihuan Road Chengdu Sichuan 610065 China
| | - James J. Chou
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School 250 Longwood Avenue Boston MA 02115 USA
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28
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Li S, Yu Y, Liu J, Xu S, Zhang S, Li M, Zhang SXA. Reactions Coupled Self- and Co-Assembly: A Highly Dynamic Process and the Resultant Spatially Inhomogeneous Structure. Chem Asian J 2019; 14:2155-2161. [PMID: 31025817 DOI: 10.1002/asia.201900409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/25/2019] [Indexed: 11/08/2022]
Abstract
Reactions coupled self-assembly represents a step forward towards biomimetic behavior in the field of supramolecular research. Here, two pH-dependent reactions of thiol-disulfide exchange and ligand exchange were used to couple with the self-assembly of an AuI -thiolate coordination polymer consisting of two ligands. Thanks to the comparable rates between the reactions and self-assembly, the compositions of the assemblies change continuously with time, resulting in a highly dynamic assembly process and spatially inhomogeneous structure that are very common in life systems but cannot be easily obtained with one-pot artificial methods.
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Affiliation(s)
- Song Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Yang Yu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Jun Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Shujue Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Shengrui Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Minjie Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Sean Xiao-An Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
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Fu J, Oh SW, Monckton K, Arbuckle-Keil G, Ke Y, Zhang T. Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900256. [PMID: 30884139 DOI: 10.1002/smll.201900256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/19/2019] [Indexed: 05/28/2023]
Abstract
The behaviors of living cells are governed by a series of regulated and confined biochemical reactions. The design and successful construction of synthetic cellular reactors can be useful in a broad range of applications that will bring significant scientific and economic impact. Over the past few decades, DNA self-assembly has enabled the design and fabrication of sophisticated 1D, 2D, and 3D nanostructures, and is applied to organizing a variety of biomolecular components into prescribed 2D and 3D patterns. In this Concept, the recent and exciting progress in DNA-scaffolded compartmentalizations and their applications in enzyme encapsulation, lipid membrane assembly, artificial transmembrane nanopores, and smart drug delivery are in focus. Taking advantage of these features promises to deliver breakthroughs toward the attainment of new synthetic and biomimetic reactors.
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Affiliation(s)
- Jinglin Fu
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Sung Won Oh
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Kristin Monckton
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Georgia Arbuckle-Keil
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ting Zhang
- Department of Chemistry and Center for Computational and Integrative Biology, Rutgers University-Camden, 315 Penn Street, Camden, NJ, 08102, USA
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30
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Zhang Y, Pan V, Li X, Yang X, Li H, Wang P, Ke Y. Dynamic DNA Structures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900228. [PMID: 30970183 PMCID: PMC7252325 DOI: 10.1002/smll.201900228] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Indexed: 05/19/2023]
Abstract
Dynamic DNA structures, a type of DNA construct built using programmable DNA self-assembly, have the capability to reconfigure their conformations in response to environmental stimulation. A general strategy to design dynamic DNA structures is to integrate reconfigurable elements into conventional static DNA structures that may be assembled from a variety of methods including DNA origami and DNA tiles. Commonly used reconfigurable elements range from strand displacement reactions, special structural motifs, target-binding DNA aptamers, and base stacking components, to DNA conformational change domains, etc. Morphological changes of dynamic DNA structures may be visualized by imaging techniques or may be translated to other detectable readout signals (e.g., fluorescence). Owing to their programmable capability of recognizing environmental cues with high specificity, dynamic DNA structures embody the epitome of robust and versatile systems that hold great promise in sensing and imaging biological analytes, in delivering molecular cargos, and in building programmable systems that are able to conduct sophisticated tasks.
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Affiliation(s)
- Yingwei Zhang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Xue Li
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xueqin Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Haofei Li
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
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31
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Li N, Shang Y, Han Z, Wang T, Wang ZG, Ding B. Fabrication of Metal Nanostructures on DNA Templates. ACS APPLIED MATERIALS & INTERFACES 2019; 11:13835-13852. [PMID: 30480424 DOI: 10.1021/acsami.8b16194] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Metal nanoarchitectures fabrication based on DNA assembly has attracted a good deal of attention. DNA nanotechnology enables precise organization of nanoscale objects with extraordinary structural programmability. The spatial addressability of DNA nanostructures and sequence-dependent recognition allow functional elements to be precisely positioned; thus, novel functional materials that are difficult to produce using conventional methods could be fabricated. This review focuses on the recent development of the fabrication strategies toward manipulating the shape and morphology of metal nanoparticles and nanoassemblies based on the rational design of DNA structures. DNA-mediated metallization, including DNA-templated conductive nanowire fabrication and sequence-selective metal deposition, etc., is briefly introduced. The modifications of metal nanoparticles (NPs) with DNA and subsequent construction of heterogeneous metal nanoarchitectures are highlighted. Importantly, DNA-assembled dynamic metal nanostructures that are responsive to different stimuli are also discussed as they allow the design of smart and dynamic materials. Meanwhile, the prospects and challenges of these shape-and morphology-controlled strategies are summarized.
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Affiliation(s)
- Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Zihong Han
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Ting Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
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32
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Wu N, Chen F, Zhao Y, Yu X, Wei J, Zhao Y. Functional and Biomimetic DNA Nanostructures on Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14721-14730. [PMID: 30044097 DOI: 10.1021/acs.langmuir.8b01818] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sophisticated and dynamic membrane-anchored DNA nanostructures were developed to mimic a variety of membrane proteins, which play crucial roles in cellular functions. DNA biomimetic constructions bound on membranes are capable of modulating the morphologies, physical properties, and functions of lipid membranes, via mobility on membranes and/or inherent architectural features. This inspired young field of DNA-lipid-based nanobiomimetic systems is on the foundation of DNA nanotechnology. In this review, we highlight key successes in the development of structural DNA nanotechnology and demonstrate some typical static and dynamic complex DNA nanostructures first. Then, we discuss the biophysical properties of lipid membranes. Primary approaches are shown to attach hydrophilic DNA to hydrophobic lipid membranes. With appropriate designs, membrane-floating DNA nanostructures assemble and disassemble on membranes, modulated by external stimuluses. The aggregation of DNA nanostructures could influence the physical properties of lipid membranes. We also summarize artificial nanochannels made of DNA, analogous to transmembrane proteins. Transformations of DNA nanopores might be achieved under certain conditions and realize the transport of small molecules across membranes. Next, we focus on membrane-shaping functions of membrane-anchored DNA nanostructures. Curvature of the membrane is closely related to the rich diversity of cellular functions. Mimicking membrane-sculpting proteins, such as BAR family domains and SNARE proteins etc., DNA biomimetic nanostructures induce the transformations of lipid membranes and modulate membrane adhesion and membrane fusion processes. Although recent studies in DNA nanostructure-lipid membrane biomimetic nanosystems have made great progress, this field is still facing many challenges. In the future, the designs of more elaborated DNA architectures will be explored. Sophisticated dynamic DNA nanostructures inspired by natural membrane machines will be driven by the synergistic effect of multiple interactions, including hydrophobic force, electrostatic force, and ligand-receptor interactions by chemical modifications on bases, to expand their applications in vivo from model membrane to cell membrane to karyotheca.
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Affiliation(s)
- Na Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Xu Yu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
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Guo X, Wang XM, Wei S, Xiao SJ. Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Two-Dimensional Lattices. Chembiochem 2018; 19:1379-1385. [PMID: 29644789 DOI: 10.1002/cbic.201800122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Indexed: 11/10/2022]
Abstract
Design rules for DNA nanotechnology have been mostly learnt from using linear single-stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half-turns) tile for assembling 2D lattices is constructed from only two linear ss-oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands are reported. A cDAO tile of cDAO-c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three-way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double-helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles.
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Affiliation(s)
- Xin Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
| | - Xue-Mei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
| | - Shuai Wei
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China.,State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, P.R. China
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Augspurger EE, Rana M, Yigit MV. Chemical and Biological Sensing Using Hybridization Chain Reaction. ACS Sens 2018; 3:878-902. [PMID: 29733201 DOI: 10.1021/acssensors.8b00208] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.
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35
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Gigadalton-scale shape-programmable DNA assemblies. Nature 2018; 552:78-83. [PMID: 29219966 DOI: 10.1038/nature24651] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.
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36
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Ke Y, Castro C, Choi JH. Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research. Annu Rev Biomed Eng 2018; 20:375-401. [PMID: 29618223 DOI: 10.1146/annurev-bioeng-062117-120904] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.
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Affiliation(s)
- Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, Georgia 30322, USA;
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43214, USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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37
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Wu X, Wang S, Li M, Wang A, Zhou Y, Li P, Wang Y. Nanocarriers for TRAIL delivery: driving TRAIL back on track for cancer therapy. NANOSCALE 2017; 9:13879-13904. [PMID: 28914952 DOI: 10.1039/c7nr04959e] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Since its initial identification, tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) has been shown to be capable of selectively inducing apoptosis in cancer cells. However, translation of the encouraging preclinical studies of this cytokine into the clinic has been restricted by its extremely short half-life, the presence of resistant cancer cell populations, and its inefficient in vivo delivery. Recently, there has been exceptional progress in developing novel formulations to increase the circulatory half-life of TRAIL and new combinations to treat cancers that are resistant to TRAIL. In particular, TRAIL-based nanotherapies offer the potential to improve the stability of TRAIL and prolong its half-life in plasma, to specifically deliver TRAIL to a particular target site, and to overcome resistance to TRAIL. The aim of this review is to provide an overview of the state-of-the art drug delivery systems that are currently being tested or developed to improve the biological attributes of TRAIL-based therapies.
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Affiliation(s)
- Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan Province, China
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38
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Wu D, Wang L, Li W, Xu X, Jiang W. DNA nanostructure-based drug delivery nanosystems in cancer therapy. Int J Pharm 2017; 533:169-178. [PMID: 28923770 DOI: 10.1016/j.ijpharm.2017.09.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 01/04/2023]
Abstract
DNA as a novel biomaterial can be used to fabricate different kinds of DNA nanostructures based on its principle of GC/AT complementary base pairing. Studies have shown that DNA nanostructure is a nice drug carrier to overcome big obstacles existing in cancer therapy such as systemic toxicity and unsatisfied drug efficacy. Thus, different types of DNA nanostructure-based drug delivery nanosystems have been designed in cancer therapy. To improve treating efficacy, they are also developed into more functional drug delivery nanosystems. In recent years, some important progresses have been made. The objective of this review is to make a retrospect and summary about these different kinds of DNA nanostructure-based drug delivery nanosystems and their latest progresses: (1) active targeting; (2) mutidrug co-delivery; (3) construction of stimuli-responsive/intelligent nanosystems.
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Affiliation(s)
- Dandan Wu
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Wei Li
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China
| | - Xiaowen Xu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China
| | - Wei Jiang
- Key Laboratory of Natural Products Chemical Biology, Ministry of Education, School of Pharmacy, Shandong University, Jinan, 250012, PR China; School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China.
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39
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Tian C, Cordeiro MAL, Lhermitte J, Xin HL, Shani L, Liu M, Ma C, Yeshurun Y, DiMarzio D, Gang O. Supra-Nanoparticle Functional Assemblies through Programmable Stacking. ACS NANO 2017; 11:7036-7048. [PMID: 28541660 DOI: 10.1021/acsnano.7b02671] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The quest for the by-design assembly of material and devices from nanoscale inorganic components is well recognized. Conventional self-assembly is often limited in its ability to control material morphology and structure simultaneously. Here, we report a general method of assembling nanoparticles in a linear "pillar" morphology with regulated internal configurations. Our approach is inspired by supramolecular systems, where intermolecular stacking guides the assembly process to form diverse linear morphologies. Programmable stacking interactions were realized through incorporation of DNA coded recognition between the designed planar nanoparticle clusters. This resulted in the formation of multilayered pillar architectures with a well-defined internal nanoparticle organization. By controlling the number, position, size, and composition of the nanoparticles in each layer, a broad range of nanoparticle pillars were assembled and characterized in detail. In addition, we demonstrated the utility of this stacking assembly strategy for investigating plasmonic and electrical transport properties.
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Affiliation(s)
- Cheng Tian
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Marco Aurelio L Cordeiro
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Julien Lhermitte
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Huolin L Xin
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Lior Shani
- Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University , 52900 Ramat-Gan, Israel
| | - Mingzhao Liu
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Chunli Ma
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Yosef Yeshurun
- Department of Physics and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University , 52900 Ramat-Gan, Israel
| | - Donald DiMarzio
- NexGen - Next Generation Engineering, Northrop Grumman Corporation , One Space Park, Redondo Beach, California 90278, United States
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory , Upton, New York 11973, United States
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40
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Li Y, Mao C, Deng Z. Supramolecular Wireframe DNA Polyhedra: Assembly and Applications. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yulin Li
- School of Chemistry and Chemical Engineering; Hefei University of Technology, 193 Tunxi Road; Hefei Anhui 230009 China
| | - Chengde Mao
- Department of Chemistry; Purdue University; West Lafayette Indiana 47907 USA
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science; University of Science and Technology of China; Hefei Anhui 230026 China
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41
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Wei J, Li YL, Gao PC, Lu Q, Wang ZF, Zhou JJ, Jiang Y. Assembling gold nanoparticles into flower-like structures by complementary base pairing of DNA molecules with mediation by apoferritins. Chem Commun (Camb) 2017; 53:4581-4584. [PMID: 28387779 DOI: 10.1039/c6cc09858d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Apoferritin caged gold nanoparticles (AuNPs) were assembled into flower-like structures by precise base pairing of the attached DNA molecules. The key step was to use the eight hydrophilic channels through the apoferritin to control the exact number and locations of the DNA molecules that grafted onto the caged AuNP.
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Affiliation(s)
- Jing Wei
- School of Chemistry and Chemical Engineering, Jiangsu province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing, Jiangsu 211189, P. R. China.
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Karimi M, Zangabad PS, Mehdizadeh F, Malekzad H, Ghasemi A, Bahrami S, Zare H, Moghoofei M, Hekmatmanesh A, Hamblin MR. Nanocaged platforms: modification, drug delivery and nanotoxicity. Opening synthetic cages to release the tiger. NANOSCALE 2017; 9:1356-1392. [PMID: 28067384 PMCID: PMC5300024 DOI: 10.1039/c6nr07315h] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nanocages (NCs) have emerged as a new class of drug-carriers, with a wide range of possibilities in multi-modality medical treatments and theranostics. Nanocages can overcome such limitations as high toxicity caused by anti-cancer chemotherapy or by the nanocarrier itself, due to their unique characteristics. These properties consist of: (1) a high loading-capacity (spacious interior); (2) a porous structure (analogous to openings between the bars of the cage); (3) enabling smart release (a key to unlock the cage); and (4) a low likelihood of unfavorable immune responses (the outside of the cage is safe). In this review, we cover different classes of NC structures such as virus-like particles (VLPs), protein NCs, DNA NCs, supramolecular nanosystems, hybrid metal-organic NCs, gold NCs, carbon-based NCs and silica NCs. Moreover, NC-assisted drug delivery including modification methods, drug immobilization, active targeting, and stimulus-responsive release mechanisms are discussed, highlighting the advantages, disadvantages and challenges. Finally, translation of NCs into clinical applications, and an up-to-date assessment of the nanotoxicology considerations of NCs are presented.
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Affiliation(s)
- Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Parham Sahandi Zangabad
- Research Center for Pharmaceutical Nanotechnology (RCPN), Tabriz University of Medical Science (TUOMS), Tabriz, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran, Iran
- Department of Materials Science and Engineering, Sharif University of Technology, 11365-9466, Tehran, Iran
- Nanomedicine Research Association (NRA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | | | - Hedieh Malekzad
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran, Iran
- Faculty of Chemistry, Kharazmi University of Tehran, Tehran, Iran
| | - Alireza Ghasemi
- Department of Materials Science and Engineering, Sharif University of Technology, 11365-9466, Tehran, Iran
| | - Sajad Bahrami
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Zare
- Biomaterials Group, Materials Science & Engineering Department, Iran University of Science & Technology, P.O. Box 1684613114 Tehran, Iran
| | - Mohsen Moghoofei
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amin Hekmatmanesh
- Laboratory of Intelligent Machines, Lappeenranta University of Technology, 53810, Finland
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Dermatology, Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA
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43
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Tian C, Kim H, Sun W, Kim Y, Yin P, Liu H. DNA Nanostructures-Mediated Molecular Imprinting Lithography. ACS NANO 2017; 11:227-238. [PMID: 28052196 DOI: 10.1021/acsnano.6b04777] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This paper describes the fabrication of polymer stamps using DNA nanostructure templates. This process creates stamps having diverse nanoscale features with dimensions ranging from several tens of nanometers to micrometers. DNA nanostructures including DNA nanotubes, stretched λ-DNA, two-dimensional (2D) DNA brick crystals with three-dimensional (3D) features, hexagonal DNA 2D arrays, and triangular DNA origami were used as master templates to transfer patterns to poly(methyl methacrylate) and poly(l-lactic acid) with high fidelity. The resulting polymer stamps were used as molds to transfer the pattern to acryloxy perfluoropolyether polymer. This work establishes an approach to using self-assembled DNA templates for applications in soft lithography.
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Affiliation(s)
- Cheng Tian
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Hyojeong Kim
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Wei Sun
- Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Yunah Kim
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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44
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Abstract
Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.
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Affiliation(s)
- Cheng Tian
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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45
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Wang P, Wu S, Tian C, Yu G, Jiang W, Wang G, Mao C. Retrosynthetic Analysis-Guided Breaking Tile Symmetry for the Assembly of Complex DNA Nanostructures. J Am Chem Soc 2016; 138:13579-13585. [PMID: 27726355 DOI: 10.1021/jacs.6b06074] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | | | | | | | | | - Guansong Wang
- Institute
of Respiratory Diseases, Xinqiao Hospital, Chongqing 400037, China
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46
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Pan W, Wen H, Niu L, Su C, Liu C, Zhao J, Mao C, Liang D. Effects of chain flexibility on the properties of DNA hydrogels. SOFT MATTER 2016; 12:5537-5541. [PMID: 27121600 DOI: 10.1039/c6sm00283h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The effect of chain rigidity on the mechanic properties of DNA hydrogels was studied. Counterintuitively, the hydrogel formed by mainly flexible chains exhibited better stability, stretchability, and much mechanical properties than the hydrogel containing only rigid chains. Calculations showed that the crosslinking ratio in the hydrogel formed by flexible chains was about twice that of the hydrogel formed by rigid chains under the same conditions. We attributed this to the ease of conformational adjustment of flexible chains. Incorporation of 25% rigid chains further improved the performance of DNA hydrogel by shrinking the pore size and tuning its distribution.
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Affiliation(s)
- Wei Pan
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Bejing 100871, China.
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47
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Wang Y, You Z, Du J, Li H, Chen H, Li J, Dong W, He B, Mao C, Wang G. Self-assembled triangular DNA nanoparticles are an efficient system for gene delivery. J Control Release 2016; 233:126-35. [DOI: 10.1016/j.jconrel.2016.05.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 02/10/2016] [Accepted: 05/13/2016] [Indexed: 12/19/2022]
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48
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Sun W, Ji W, Hu Q, Yu J, Wang C, Qian C, Hochu G, Gu Z. Transformable DNA nanocarriers for plasma membrane targeted delivery of cytokine. Biomaterials 2016; 96:1-10. [PMID: 27131597 DOI: 10.1016/j.biomaterials.2016.04.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/29/2016] [Accepted: 04/13/2016] [Indexed: 01/24/2023]
Abstract
Direct delivery of cytokines using nanocarriers holds great promise for cancer therapy. However, the nanometric scale of the vehicles made them susceptible to size-dependent endocytosis, reducing the plasma membrane-associated apoptosis signaling. Herein, we report a tumor microenvironment-responsive and transformable nanocarrier for cell membrane targeted delivery of cytokine. This formulation is comprised of a phospholipase A2 (PLA2) degradable liposome as a shell, and complementary DNA nanostructures (designated as nanoclews) decorated with cytokines as the cores. Utilizing the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) as a model cytokine, we demonstrate that the TRAIL loaded DNA nanoclews are capable of transforming into nanofibers after PLA2 activation. The nanofibers with micro-scaled lengths efficiently present the loaded TRAIL to death receptors on the cancer cell membrane and amplified the apoptotic signaling with reduced TRAIL internalization.
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Affiliation(s)
- Wujin Sun
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wenyan Ji
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Quanyin Hu
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jicheng Yu
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chao Wang
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chenggen Qian
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gabrielle Hochu
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA
| | - Zhen Gu
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Division of Molecular Pharmaceutics and Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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49
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Jia R, Wang T, Jiang Q, Wang Z, Song C, Ding B. Self-Assembled DNA Nanostructures for Drug Delivery. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201500838] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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50
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Zhang D, Paukstelis PJ. Enhancing DNA Crystal Durability through Chemical Crosslinking. Chembiochem 2016; 17:1163-70. [DOI: 10.1002/cbic.201500610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Diana Zhang
- Department of Chemistry & Biochemistry; University of Maryland; 8314 Paint Branch Drive College Park 20742 MD USA
| | - Paul J. Paukstelis
- Department of Chemistry & Biochemistry; University of Maryland; 8314 Paint Branch Drive College Park 20742 MD USA
- Maryland NanoCenter; University of Maryland; College Park 20742 MD USA
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