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Wu J, Zheng X, Lin W, Chen L, Wu ZS. Persistent Targeting DNA Nanocarrier Made of 3D Structural Unit Assembled from Only One Basic Multi-Palindromic Oligonucleotide for Precise Gene Cancer Therapy. Adv Healthc Mater 2024; 13:e2303865. [PMID: 38289018 DOI: 10.1002/adhm.202303865] [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: 11/06/2023] [Revised: 01/19/2024] [Indexed: 02/13/2024]
Abstract
Construction of a simple, reconfigurable, and stimuli-responsive DNA nanocarrier remains a technical challenge. In this contribution, by designing three palindromic fragments, a simplest four-sticky end-contained 3D structural unit (PS-unit) made of two same DNA components is proposed. Via regulating the rotation angle of central longitudinal axis of PS-unit, the oriented assembly of one-component spherical architecture is accomplished with high efficiency. Introduction of an aptamer and sticky tail warehouse into one component creates a size-change-reversible targeted siRNA delivery nanovehicle. Volume swelling of 20 nm allows one carrier to load 1987 siPLK1s. Once entering cancer cells and responding to glutathione (GSH) stimuli, siPLK1s are almost 100% released and original size of nanovehicle is restored, inhibiting the expression of PLK1 protein and substantially suppressing tumor growth (superior to commercial transfection agents) in tumor-bearing mice without systemic toxicity.
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Affiliation(s)
- Jingting 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
| | - Xiaoqi Zheng
- 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
| | - Wenqing 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
| | - Linhuan 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
| | - 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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2
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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3
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Lyu J, Yang M, Zhang C, Luo Y, Qin T, Su Z, Huang Z. DNA nanostructures directed by RNA clamps. NANOSCALE 2021; 13:19870-19874. [PMID: 34825903 DOI: 10.1039/d1nr03919a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA chains can be folded rationally by using DNA staples, and the programmed structures are of great potential in nanomaterial studies. However, due to the short DNA staples forming duplexes and displaying limitations in structural diversity and stability, the folded DNA nanostructures are usually generated with structural mis-formations, low yields and poor efficiencies, which can restrict their folding patterns and applications. To overcome these problems, we set out to use RNA as a clamp to form polygons, and herein demonstrated the ability to use a structural RNA-but not its corresponding DNA-to fold DNA chains into nanostructures with high efficiency (up to a 95.1% yield). Furthermore, we discovered that the 2'-methylated version of the RNA can, compared to the unmodified RNA, even more efficiently fold DNA chains (up to a 98.5% yield). Interestingly, the RNA clamp can fold DNA scaffolds with one, two or four folding units into the same square shape. Furthermore, the RNA can direct the DNA chains with three, four and five folding units into triangular, square and pentagonal nano-shapes, respectively. In addition, we confirmed their enlarged nano-shapes by performing electron microscopy (EM) imaging. These formed nanostructures revealed the potential cooperation between the DNA scaffold and RNA clamp. Moreover, our research demonstrated a novel strategy, involving using RNA clamps displaying structural diversity and duplex stability, for folding DNA into diverse nanostructures.
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Affiliation(s)
- Jiazhen Lyu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Mei Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Tong Qin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Zhen Huang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China.,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610000, Sichuan, P. R. China.
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Yan J, Zhan X, Zhang Z, Chen K, Wang M, Sun Y, He B, Liang Y. Tetrahedral DNA nanostructures for effective treatment of cancer: advances and prospects. J Nanobiotechnology 2021; 19:412. [PMID: 34876145 PMCID: PMC8650297 DOI: 10.1186/s12951-021-01164-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/24/2021] [Indexed: 11/10/2022] Open
Abstract
Recently, DNA nanostructures with vast application potential in the field of biomedicine, especially in drug delivery. Among these, tetrahedral DNA nanostructures (TDN) have attracted interest worldwide due to their high stability, excellent biocompatibility, and simplicity of modification. TDN could be synthesized easily and reproducibly to serve as carriers for, chemotherapeutic drugs, nucleic acid drugs and imaging probes. Therefore, their applications include, but are not restricted to, drug delivery, molecular diagnostics, and biological imaging. In this review, we summarize the methods of functional modification and application of TDN in cancer treatment. Also, we discuss the pressing questions that should be targeted to increase the applicability of TDN in the future.
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Affiliation(s)
- Jianqin Yan
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao, 266021, China
| | - Xiaohui Zhan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
- School of Biomedical Engineering, Sichuan University, Chengdu, 610064, China
| | - Zhuangzhuang Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
- School of Biomedical Engineering, Sichuan University, Chengdu, 610064, China
| | - Keqi Chen
- Department of Clinical Laboratory, Qingdao Special Servicemen Recuperation Centre of PLA Navy, Qingdao, 266021, China
| | - Maolong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao, 266000, China
| | - Yong Sun
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao, 266021, China.
| | - Bin He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, China
- School of Biomedical Engineering, Sichuan University, Chengdu, 610064, China
| | - Yan Liang
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao, 266021, China.
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Xue C, Hu S, Gao ZH, Wang L, Luo MX, Yu X, Li BF, Shen Z, Wu ZS. Programmably tiling rigidified DNA brick on gold nanoparticle as multi-functional shell for cancer-targeted delivery of siRNAs. Nat Commun 2021; 12:2928. [PMID: 34006888 PMCID: PMC8131747 DOI: 10.1038/s41467-021-23250-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023] Open
Abstract
Small interfering RNA (siRNA) is an effective therapeutic to regulate the expression of target genes in vitro and in vivo. Constructing a siRNA delivery system with high serum stability, especially responsive to endogenous stimuli, remains technically challenging. Herein we develop anti-degradation Y-shaped backbone-rigidified triangular DNA bricks with sticky ends (sticky-YTDBs) and tile them onto a siRNA-packaged gold nanoparticle in a programmed fashion, forming a multi-functional three-dimensional (3D) DNA shell. After aptamers are arranged on the exterior surface, a biocompatible siRNA-encapsulated core/shell nanoparticle, siRNA/Ap-CS, is achieved. SiRNAs are internally encapsulated in a 3D DNA shell and are thus protected from enzymatic degradation by the outermost layer of YTDB. The siRNAs can be released by endogenous miRNA and execute gene silencing within tumor cells, causing cell apoptosis higher than Lipo3000/siRNA formulation. In vivo treatment shows that tumor growth is completely (100%) inhibited, demonstrating unique opportunities for next-generation anticancer-drug carriers for targeted cancer therapies.
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Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zhi-Hua Gao
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Lei Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Meng-Xue Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Xin Yu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Bi-Fei Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
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Sato Y, Suzuki Y. DNA nanotechnology provides an avenue for the construction of programmable dynamic molecular systems. Biophys Physicobiol 2021; 18:116-126. [PMID: 34123692 PMCID: PMC8164909 DOI: 10.2142/biophysico.bppb-v18.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/23/2021] [Indexed: 12/01/2022] Open
Abstract
Self-assembled supramolecular structures in living cells and their dynamics underlie various cellular events, such as endocytosis, cell migration, intracellular transport, cell metabolism, and gene expression. Spatiotemporally regulated association/dissociation and generation/degradation of assembly components is one of the remarkable features of biological systems. The significant advancement in DNA nanotechnology over the last few decades has enabled the construction of various-shaped nanostructures via programmed self-assembly of sequence-designed oligonucleotides. These nanostructures can further be assembled into micrometer-sized structures, including ordered lattices, tubular structures, macromolecular droplets, and hydrogels. In addition to being a structural material, DNA is adopted to construct artificial molecular circuits capable of activating/inactivating or producing/decomposing target DNA molecules based on strand displacement or enzymatic reactions. In this review, we provide an overview of recent studies on artificially designed DNA-based self-assembled systems that exhibit dynamic features, such as association/dis-sociation of components, phase separation, stimulus responsivity, and DNA circuit-regulated structural formation. These biomacromolecule-based, bottom-up approaches for the construction of artificial molecular systems will not only throw light on bio-inspired nano/micro engineering, but also enable us to gain insights into how autonomy and adaptability of living systems can be realized.
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Affiliation(s)
- Yusuke Sato
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
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7
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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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8
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Yang J, Jiang Q, He L, Zhan P, Liu Q, Liu S, Fu M, Liu J, Li C, Ding B. Self-Assembled Double-Bundle DNA Tetrahedron for Efficient Antisense Delivery. ACS APPLIED MATERIALS & INTERFACES 2018; 10:23693-23699. [PMID: 29963858 DOI: 10.1021/acsami.8b07889] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA nanostructures are promising biomaterials capable of arranging multiple functional components with nanometer precision. Here, a double-bundle DNA tetrahedron is rationally designed to integrate with antisense oligonucleotides silencing proto-oncogene c-raf and nuclear targeting peptides. The functionalized DNA tetrahedron can be internalized by A549 cells and assists the delivery of antisense oligonucleotides toward the nucleus to increase the chance to downregulate target mRNA in nucleus and cytoplasm. Antisense strands released from the tetrahedron in response to the intracellular reducing environment can inhibit cell proliferation at a low concentration without transfection reagent. Finally, efficient knockdown of c-raf gene is observed, which verified our design. This designer DNA-based nanocarrier system will open a new avenue for efficient delivery of nucleic acid drugs.
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Affiliation(s)
- Juanjuan Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Pengfei Zhan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Shaoli Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Meifang Fu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Can Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for Nanoscience and Technology , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , China
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9
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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10
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Jorge AF, Aviñó A, Pais AACC, Eritja R, Fàbrega C. DNA-based nanoscaffolds as vehicles for 5-fluoro-2'-deoxyuridine oligomers in colorectal cancer therapy. NANOSCALE 2018; 10:7238-7249. [PMID: 29632908 DOI: 10.1039/c7nr08442k] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs, are considered one of the most successful agents in the treatment of colorectal cancer, yet poor specificity and tumor cell resistance remain the major limiting bottlenecks. Here, we exploited for the first time the ability of two DNA nanoscaffolds, a DNA tetrahedron (Td) and rectangle DNA origami, to incorporate 5-fluoro-2'-deoxyuridine (FdUn) oligomers. In addition, cholesterol moieties were synthetically attached to Td and DNA origami staples to enhance cellular uptake. DNA nanostructures functionalized with FdUn exhibited an enhanced cytotoxicity and higher ability to trigger apoptosis in colorectal cancer cells relative to conventional 5-FU and FdU, especially having cholesterol as an internalization helper. The cholesterol content mostly correlates with the increase of the FdUn nanostructure cytotoxicity. DNA nanoscaffolds bearing FdUn were able to circumvent the low sensitivity of colorectal cancer cells towards 5-FU. Both DNA nanostructures attained a comparable cytotoxic effect yet Td displays higher antiproliferative action. The ability to reduce the proliferation of cancer cells is mainly related to the concentration of DNA nanostructures. The present work suggests that self-assembled DNA nanoparticles are privileged vehicles for delivering fluoropyrimidines, opening new avenues to the development of promising therapeutics for cancer treatment.
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Affiliation(s)
- A F Jorge
- Coimbra Chemistry Centre (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
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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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12
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Liu X, Wang L, Yan H, Chang Y. Assembly and Assessment of DNA Scaffolded Vaccines. Methods Mol Biol 2016; 1404:301-311. [PMID: 27076307 DOI: 10.1007/978-1-4939-3389-1_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Vaccines play an important role in preventing many life-threatening infectious diseases. To meet the demand of vaccination for treating a wide range of diseases, rational vaccine design has been recognized as a desirable and necessary strategy for development of safe and effective vaccines. DNA nanostructures are advantageous in the design and construction of synthetic vaccines, owing to their robust self-assembly, programmability, and precision control in complex organization, as well as their intrinsic adjuvant activity. Here, we describe a modular assembly of DNA scaffolded vaccine complex, composing of a model antigen, streptavidin, and adjuvant, CpG oligonucleotide. The DNA-assembled vaccines were found to elicit strong antigen-specific antibody responses, but causing little or no adverse reactions. Conceivably, this vaccine platform can be further optimized for improved immunogenicity and extended to the construction of various subunit vaccines.
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Affiliation(s)
- Xiaowei Liu
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Lili Wang
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, Sichuan Province, 610041, China.,Department of Stomatology, Sichuan Provincial People's Hospital, Sichuan Academy of Medical Sciences, Chengdu, Sichuan, 610101, China
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287, USA
| | - Yung Chang
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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13
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Bhatia D, Arumugam S, Nasilowski M, Joshi H, Wunder C, Chambon V, Prakash V, Grazon C, Nadal B, Maiti PK, Johannes L, Dubertret B, Krishnan Y. Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways. NATURE NANOTECHNOLOGY 2016; 11:1112-1119. [PMID: 27548358 PMCID: PMC5122452 DOI: 10.1038/nnano.2016.150] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/15/2016] [Indexed: 05/07/2023]
Abstract
Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.
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Affiliation(s)
- Dhiraj Bhatia
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bellary Road, Bangalore 560065, India
| | - Senthil Arumugam
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Michel Nasilowski
- Laboratoire Physique et Etude des Matériaux UMR8213 École Supérieure de Physique et de Chimie Industrielles ParisTech-CNRS - Université Pierre et Marie Curie Sorbonne Universités 10 rue Vauquelin, 75005 Paris, France
| | - Himanshu Joshi
- Department of Physics, Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Christian Wunder
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Valérie Chambon
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Ved Prakash
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bellary Road, Bangalore 560065, India
- Department of Chemistry, The University of Chicago, 929 E, 57th Street, Chicago, Illinois 60637, USA
| | | | - Brice Nadal
- Nexdot, 10 rue Vauquelin, 75005 Paris, France
| | - Prabal K Maiti
- Department of Physics, Center for Condensed Matter Theory, Indian Institute of Science, Bangalore 560012, India
| | - Ludger Johannes
- Chemical Biology of Membranes and Therapeutic Delivery unit, Institut Curie, PSL Research University, Institut national de la santé et de la recherche médicale, U 1143, Centre national de la recherche scientifique, Unité mixte de recherche 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Benoit Dubertret
- Laboratoire Physique et Etude des Matériaux UMR8213 École Supérieure de Physique et de Chimie Industrielles ParisTech-CNRS - Université Pierre et Marie Curie Sorbonne Universités 10 rue Vauquelin, 75005 Paris, France
| | - Yamuna Krishnan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vigyan Kendra, Bellary Road, Bangalore 560065, India
- Department of Chemistry, The University of Chicago, 929 E, 57th Street, Chicago, Illinois 60637, USA
- Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, 5812 South Ellis Avenue, Chicago, Illinois 60637, USA
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14
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Lee DS, Qian H, Tay CY, Leong DT. Cellular processing and destinies of artificial DNA nanostructures. Chem Soc Rev 2016; 45:4199-225. [DOI: 10.1039/c5cs00700c] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review gives a panoramic view of the many DNA nanotechnology applications in cells, mechanistic understanding of how and where their interactions occur and their subsequent outcomes.
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Affiliation(s)
- Di Sheng Lee
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
- Department of Materials Science and Engineering
| | - Hang Qian
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
| | - Chor Yong Tay
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
- School of Materials Science and Engineering
| | - David Tai Leong
- Department of Chemical and Biomolecular Engineering
- National University of Singapore
- Singapore 117585
- Singapore
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15
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DNA nanotechnology-based development of delivery systems for bioactive compounds. Eur J Pharm Sci 2014; 58:26-33. [DOI: 10.1016/j.ejps.2014.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/04/2014] [Accepted: 03/12/2014] [Indexed: 12/25/2022]
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16
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Tintoré M, Eritja R, Fábrega C. DNA Nanoarchitectures: Steps towards Biological Applications. Chembiochem 2014; 15:1374-90. [DOI: 10.1002/cbic.201402014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/26/2022]
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17
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Abstract
CONSPECTUS: Not only can triangulated wireframe network and tensegrity design be found in architecture, but it is also essential for the stability and organization of biological matter. Whether the scaffolding material is metal as in Buckminster Fuller's geodesic domes and Kenneth Snelson's floating compression sculptures or proteins like actin or spectrin making up the cytoskeleton of biological cells, wireframe and tensegrity construction can provide great stability while minimizing the material required. Given the mechanical properties of single- and double-stranded DNA, it is not surprising to find many variants of wireframe and tensegrity constructions in the emerging field of DNA nanotechnology, in which structures of almost arbitrary shape can be built with nanometer precision. The success of DNA self-assembly relies on the well-controlled hybridization of complementary DNA strands. Consequently, understanding the fundamental physical properties of these molecules is essential. Many experiments have shown that double-stranded DNA (in its most commonly occurring helical form, the B-form) behaves in a first approximation like a relatively stiff cylindrical beam with a persistence length of many times the length of its building blocks, the base pairs. However, it is harder to assign a persistence length to single-stranded DNA. Here, normally the Kuhn length is given, a measure that describes the length of individual rigid segments in a freely jointed chain. This length is on the order of a few nucleotides. Two immediate and important consequences arise from this high flexibility: single-stranded DNA is almost always present in a coiled conformation, and it behaves, just like all flexible polymers in solution, as an entropic spring. In this Account, we review the relation between the mechanical properties of DNA and design considerations for wireframe and tensegrity structures built from DNA. We illustrate various aspects of the successful evolution of DNA nanotechnology starting with the construction of four-way junctions and then allude to simple geometric objects such as the wireframe cube presented by Nadrian Seeman along with a variety of triangulated wireframe constructions. We examine DNA tensegrity triangles that self-assemble into crystals with sizes of several hundred micrometers as well as prestressed DNA origami tensegrity architecture, which uses single-stranded DNA with its entropic spring behavior as tension bearing components to organize stiff multihelix bundles in three dimensions. Finally, we discuss emerging applications of the aforementioned design principles in diverse fields such as diagnostics, drug delivery, or crystallography. Despite great advances in related research fields like protein and RNA engineering, DNA self-assembly is currently the most accessible technique to organize matter on the nanoscale, and we expect many more exciting applications to emerge.
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Affiliation(s)
- Stephanie S. Simmel
- Faculty
of Physics and Center
for Nanoscience, Ludwig-Maximilians-Universität München, München 80539, Germany
| | - Philipp C. Nickels
- Faculty
of Physics and Center
for Nanoscience, Ludwig-Maximilians-Universität München, München 80539, Germany
| | - Tim Liedl
- Faculty
of Physics and Center
for Nanoscience, Ludwig-Maximilians-Universität München, München 80539, Germany
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18
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Qian H, Tian C, Yu J, Guo F, Zheng MS, Jiang W, Dong QF, Mao C. Self-assembly of DNA nanotubes with defined diameters and lengths. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:855-858. [PMID: 24745047 DOI: 10.1002/smll.201301891] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanotubes with different sizes can be readily assembled from simple DNA nanomotifs, which consist of just a few unique DNA sequences. Such structurally well-defi ned DNA-nanotubes will have great potential in many technological applications ranging from drug delivery, to determination of biomacromolecular 3D structures, to nanoplasmonic devices.
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19
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20
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Chen Q, Liu H, Lee W, Sun Y, Zhu D, Pei H, Fan C, Fan X. Self-assembled DNA tetrahedral optofluidic lasers with precise and tunable gain control. LAB ON A CHIP 2013; 13:3351-4. [PMID: 23846506 DOI: 10.1039/c3lc50629k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We have applied self-assembled DNA tetrahedral nanostructures for the precise and tunable control of the gain in an optofluidic fluorescence resonance energy transfer (FRET) laser. By adjusting the ratio of the donor and the acceptor attached to the tetrahedral vertices, 3.8 times reduction in the lasing threshold and 28-fold enhancement in the lasing efficiency were demonstrated. This work takes advantage of the self-recognition and self-assembly capabilities of biomolecules with well-defined structures and addressability, enabling nano-engineering of the laser down to the molecular level.
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Affiliation(s)
- Qiushu Chen
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Ave., Ann Arbor, MI 48109, United States
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21
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22
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Liu Z, Li Y, Tian C, Mao C. A Smart DNA Tetrahedron That Isothermally Assembles or Dissociates in Response to the Solution pH Value Changes. Biomacromolecules 2013; 14:1711-4. [PMID: 23647463 DOI: 10.1021/bm400426f] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Zhiyu Liu
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
| | - Yingmei Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
| | - Cheng Tian
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana
47907, United
States
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23
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Krishnan Y, Bathe M. Designer nucleic acids to probe and program the cell. Trends Cell Biol 2012; 22:624-33. [DOI: 10.1016/j.tcb.2012.10.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
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24
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Liu X, Xu Y, Yu T, Clifford C, Liu Y, Yan H, Chang Y. A DNA nanostructure platform for directed assembly of synthetic vaccines. NANO LETTERS 2012; 12:4254-9. [PMID: 22746330 PMCID: PMC3808986 DOI: 10.1021/nl301877k] [Citation(s) in RCA: 223] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Safe and effective vaccines offer the best intervention for disease control. One strategy to maximize vaccine immunogenicity without compromising safety is to rationally design molecular complexes that mimic the natural structure of immunogenic microbes but without the disease-causing components. Here we use highly programmable DNA nanostructures as platforms to assemble a model antigen and CpG adjuvants together into nanoscale complexes with precise control of the valency and spatial arrangement of each element. Our results from immunized mice show that compared to a mixture of antigen and CpG molecules, the assembled antigen-adjuvant-DNA complexes induce strong and long-lasting antibody responses against the antigen without stimulating a reaction to the DNA nanostructure itself. This result demonstrates the potential of DNA nanostructures to serve as general platforms for the rational design and construction of a variety of vaccines.
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Affiliation(s)
- Xiaowei Liu
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Yang Xu
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Tao Yu
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Oral Maxillofacial Surgery, West China College of Stomatology, Sichuan University, Chengdu, Sichuan Province, 610041, China
| | - Craig Clifford
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Yan Liu
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Yan
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
- Corresponding Author: , School of Life Sciences and the Biodesign Institute, Or , Department of Chemistry and Biochemistry and the Biodesign Institute, 1001 S. McAllister Ave, Tempe, AZ 85287
| | - Yung Chang
- Center for Infectious Diseases and Vaccinology, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Corresponding Author: , School of Life Sciences and the Biodesign Institute, Or , Department of Chemistry and Biochemistry and the Biodesign Institute, 1001 S. McAllister Ave, Tempe, AZ 85287
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25
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Zhang C, Tian C, Li X, Qian H, Hao C, Jiang W, Mao C. Reversibly Switching the Surface Porosity of a DNA Tetrahedron. J Am Chem Soc 2012; 134:11998-2001. [DOI: 10.1021/ja305969c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Hang Qian
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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26
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Abstract
This paper reports a strategy for DNA self-assembly. Cross-over-based DNA nanomotifs are held together by T-junctions instead of commonly used sticky-end cohesion. We have demonstrated this strategy by assembling a DNA tetrahedron, an octahedron, and an icosahedron. The resulting DNA polyhedra contain out-pointing, short DNA hairpin spikes. These hairpins are well-structured relative to the polyhedra core and provide potential locations for introduction of functional chemicals such as proteins and gold nanoparticles. The T-linked DNA polyhedra have been characterized by polyacrylamide gel electrophoresis, atomic force microscopy, and dynamic light scattering.
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Affiliation(s)
- Xiang Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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27
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Bhatia D, Chakraborty S, Krishnan Y. Gene delivery: Designer DNA give RNAi more spine. NATURE NANOTECHNOLOGY 2012; 7:344-346. [PMID: 22659610 DOI: 10.1038/nnano.2012.87] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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28
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Greene DG, Keum JW, Bermudez H. The role of defects on the assembly and stability of DNA nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:1320-1325. [PMID: 22354792 DOI: 10.1002/smll.201102221] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 12/13/2011] [Indexed: 05/31/2023]
Abstract
Defects are known to underlie the mechanical properties of materials, especially so at the nanoscale. Using four compositionally identical DNA triangles, defect density is found to be inversely correlated with assembly efficiency and melting temperature. These findings are supported by a series of experiments with more complex DNA pyramids. Because they are naturally responsive to stresses, defects present an attractive opportunity as design elements for responsive DNA materials.
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Affiliation(s)
- Daniel G Greene
- Department of Chemical Engineering, University of Massachusetts, Amherst, MA, USA
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29
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Zhang X, Yadavalli VK. Functional self-assembled DNA nanostructures for molecular recognition. NANOSCALE 2012; 4:2439-2446. [PMID: 22399156 DOI: 10.1039/c2nr11711h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nucleic acids present a wonderful toolkit of structural motifs for nanoconstruction. Functional DNA nanostructures can enable protein recognition by the use of aptamers attached to a basic core shape formed by DNA self-assembly. Here, we present a facile, programmable strategy for the assembly of discrete aptamer-tagged DNA shapes and nanostructures that can function for molecular recognition and binding in an aqueous environment. These nanostructures, presented here to bind two different protein targets, are easily synthesized in large numbers, and are portable and stable over long periods of time. This construction modality can facilitate on-demand production of libraries of diverse shapes to recognize and bind proteins or catalyze reactions via functional nucleic acid tags.
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Affiliation(s)
- Xiaojuan Zhang
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
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30
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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31
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Bhatia D, Sharma S, Krishnan Y. Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol 2011; 22:475-84. [PMID: 21652202 DOI: 10.1016/j.copbio.2011.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/10/2011] [Accepted: 05/15/2011] [Indexed: 02/05/2023]
Abstract
Structural DNA nanotechnology seeks to create architectures of highly precise dimensions using the physical property that short lengths of DNA behave as rigid rods and the chemical property of Watson-Crick base-pairing that acts as a specific molecular glue with which such rigid rods may be joined. Thus DNA has been used as a molecular scale construction material to make molecular devices that can be broadly classified under two categories (i) rigid scaffolds and (ii) switchable architectures. This review details the growing impact of such synthetic nucleic acid based molecular devices in biology and biotechnology. Notably, a significant trend is emerging that integrates morphology-rich nucleic acid motifs and alternative molecular glues into DNA and RNA architectures to achieve biological functionality.
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Affiliation(s)
- Dhiraj Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India
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32
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Wong NY, Zhang C, Tan LH, Lu Y. Site-specific attachment of proteins onto a 3D DNA tetrahedron through backbone-modified phosphorothioate DNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1427-1430. [PMID: 21520410 DOI: 10.1002/smll.201100140] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Ngo Yin Wong
- Material Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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