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Bai Y, Xu P, Li S, Wang D, Zhang K, Zheng D, Yue D, Zhang G, He S, Li Y, Zou H, Deng Y. Signal amplification strategy of DNA self-assembled biosensor and typical applications in pathogenic microorganism detection. Talanta 2024; 272:125759. [PMID: 38350248 DOI: 10.1016/j.talanta.2024.125759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Biosensors have emerged as ideal analytical devices for various bio-applications owing to their low cost, convenience, and portability, which offer great potential for improving global healthcare. DNA self-assembly techniques have been enriched with the development of innovative amplification strategies, such as dispersion-to-localization of catalytic hairpin assembly, and dumbbell hybridization chain reaction, which hold great significance for building biosensors capable of realizing sensitive, rapid and multiplexed detection of pathogenic microorganisms. Here, focusing primarily on the signal amplification strategies based on DNA self-assembly, we concisely summarized the strengths and weaknesses of diverse isothermal nucleic acid amplification techniques. Subsequently, both single-layer and cascade amplification strategies based on traditional catalytic hairpin assembly and hybridization chain reaction were critically explored. Furthermore, a comprehensive overview of the recent advances in DNA self-assembled biosensors for the detection of pathogenic microorganisms is presented to summarize methods for biorecognition and signal amplification. Finally, a brief discussion is provided about the current challenges and future directions of DNA self-assembled biosensors.
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Affiliation(s)
- Yuxin Bai
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Pingyao Xu
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongming Zheng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Daifan Yue
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Guiji Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shuya He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Yan Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China.
| | - Haimin Zou
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
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Ma Y, Wang Q, Du S, Luo J, Sun X, Jia B, Ge J, Dong J, Jiang S, Li Z. Multipathway Regulation for Targeted Atherosclerosis Therapy Using Anti-miR-33-Loaded DNA Origami. ACS Nano 2024. [PMID: 38321605 DOI: 10.1021/acsnano.3c10213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Given the multifactorial pathogenesis of atherosclerosis (AS), a chronic inflammatory disease, combination therapy arises as a compelling approach to effectively address the complex interplay of pathogenic mechanisms for a more desired treatment outcome. Here, we present cRGD/ASOtDON, a nanoformulation based on a self-assembled DNA origami nanostructure for the targeted combination therapy of AS. cRGD/ASOtDON targets αvβ3 integrin receptors overexpressed on pro-inflammatory macrophages and activated endothelial cells in atherosclerotic lesions, alleviates the oxidative stress induced by extracellular and endogenous reactive oxygen species, facilitates the polarization of pro-inflammatory macrophages toward the anti-inflammatory M2 phenotype, and inhibits foam cell formation by promoting cholesterol efflux from macrophages by downregulating miR-33. The antiatherosclerotic efficacy and safety profile of cRGD/ASOtDON, as well as its mechanism of action, were validated in an AS mouse model. cRGD/ASOtDON treatment reversed AS progression and restored normal morphology and tissue homeostasis of the diseased artery. Compared to probucol, a clinical antiatherosclerotic drug with a similar mechanism of action, cRGD/ASOtDON enabled the desired therapeutic outcome at a notably lower dosage. This study demonstrates the benefits of targeted combination therapy in AS management and the potential of self-assembled DNA nanoformulations in addressing multifactorial inflammatory conditions.
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Affiliation(s)
- Yuxuan Ma
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Shiyu Du
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Jingwei Luo
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Xiaolei Sun
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Jia
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Jingru Ge
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Jun Dong
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, P. R. China
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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Kou B, Wang Z, Mousavi S, Wang P, Ke Y. Dynamic Gold Nanostructures Based on DNA Self Assembly. Small 2023:e2308862. [PMID: 38143287 DOI: 10.1002/smll.202308862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/10/2023] [Indexed: 12/26/2023]
Abstract
The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.
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Affiliation(s)
- Bo Kou
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Shikufa Mousavi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
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Shrivastava A, Du Y, Adepu HK, Li R, Madhvacharyula AS, Swett AA, Choi JH. Motility of Synthetic Cells from Engineered Lipids. ACS Synth Biol 2023; 12:2789-2801. [PMID: 37729546 DOI: 10.1021/acssynbio.3c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Synthetic cells are artificial systems that resemble natural cells. Significant efforts have been made over the years to construct synthetic protocells that can mimic biological mechanisms and perform various complex processes. These include compartmentalization, metabolism, energy supply, communication, and gene reproduction. Cell motility is also of great importance, as nature uses elegant mechanisms for intracellular trafficking, immune response, and embryogenesis. In this review, we discuss the motility of synthetic cells made from lipid vesicles and relevant molecular mechanisms. Synthetic cell motion may be classified into surface-based or solution-based depending on whether it involves interactions with surfaces or movement in fluids. Collective migration behaviors have also been demonstrated. The swarm motion requires additional mechanisms for intercellular signaling and directional motility that enable communication and coordination among the synthetic vesicles. In addition, intracellular trafficking for molecular transport has been reconstituted in minimal cells with the help of DNA nanotechnology. These efforts demonstrate synthetic cells that can move, detect, respond, and interact. We envision that new developments in protocell motility will enhance our understanding of biological processes and be instrumental in bioengineering and therapeutic applications.
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Affiliation(s)
- Aishwary Shrivastava
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Ruixin Li
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Alexander A Swett
- School of Mechanical Engineering, Purdue University, Neil Armstrong Hall of Engineering, 701 W. Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
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5
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Ji H, Zhu Q. Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery. J Control Release 2023; 361:803-818. [PMID: 37597810 DOI: 10.1016/j.jconrel.2023.08.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.
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Affiliation(s)
- Haofei Ji
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha 410013, Hunan, China.
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Fang L, Shi C, Wang Y, Xiong Z, Wang Y. Exploring the diverse biomedical applications of programmable and multifunctional DNA nanomaterials. J Nanobiotechnology 2023; 21:290. [PMID: 37612757 PMCID: PMC10464147 DOI: 10.1186/s12951-023-02071-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
DNA nanoparticles hold great promise for a range of biological applications, including the development of cutting-edge treatments and diagnostic tests. Their subnanometer-level addressability enables precise, specific modifications with a variety of chemical and biological entities, making them ideal as diagnostic instruments and carriers for targeted delivery. This paper focuses on the potential of DNA nanomaterials, which offer scalability, programmability, and functionality. For example, they can be engineered to provide highly specific biosensing and bioimaging capabilities and show promise as a platform for disease diagnosis and treatment. Successful operation of various biomedical nanomaterials has been demonstrated both in vitro and in vivo. However, there are still significant challenges to overcome, including the need to improve the scalability and reliability of the technology, and to ensure safety in clinical applications. We discuss these challenges and opportunities in detail and highlight the progress and prospects of DNA nanotechnology for biomedical applications.
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Affiliation(s)
- Liuru Fang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Chen Shi
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, Wuhan, 430022, China
| | - Yuhua Wang
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China.
| | - Zuzhao Xiong
- Hubei Province Key Laboratory of Systems Science in Metallurgical Process, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Yumei Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Zhao P, Zhong Y, Pan P, Zhang S, Tian Y, Zhang J, Yi G, Zhao Z, Wu T. DNA self-assembly nanoflower reverse P-glycoprotein mediated drug resistance in chronic myelogenous leukemia therapy. Front Bioeng Biotechnol 2023; 11:1265199. [PMID: 37671185 PMCID: PMC10475561 DOI: 10.3389/fbioe.2023.1265199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction: Chronic myelogenous leukemia (CML) is a clonal myeloproliferative disorder caused by the BCR-ABL chimeric tyrosine kinase. Vincristine (VCR) is widely used in leukemia therapy but is hindered by multidrug resistance (MDR). Methods: We prepared DNA nanoflower via self-assembly for the delivery of VCR and P-glycoprotein small interfering RNA (P-gp siRNA). Results and Discussion: The as-prepared nanoflower had a floriform shape with high loading efficiency of VCR (80%). Furthermore, the nanoflower could deliver VCR and P-gp siRNA into MDR CML cells and induce potent cytotoxicity both in vitro and in vivo, thus overcoming MDR of CML. Overall, this nanoflower is a promising tool for resistant CML therapy.
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Affiliation(s)
- Pengxuan Zhao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, School of Pharmacy, Hainan Medical University, Haikou, China
| | - Yeteng Zhong
- Department of Clinical Laboratory, The Second Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Pengcheng Pan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, School of Pharmacy, Hainan Medical University, Haikou, China
| | - Shasha Zhang
- Wuhan Wuchang Hospital, Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
- Public Research Center Hainan, Hainan Medical University, Haikou, China
| | - Yu Tian
- Analytical and Testing Center of Hainan University, Hainan University, Haikou, China
- Jiangsu Hengrui Pharmaceuticals Co., Ltd., Lianyungang, China
| | - Jun Zhang
- Department of Medical Ultrasound, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guohui Yi
- Public Research Center Hainan, Hainan Medical University, Haikou, China
| | - Zhendong Zhao
- Analytical and Testing Center of Hainan University, Hainan University, Haikou, China
| | - Tiantian Wu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Provincial Key Laboratory for Research and Development of Tropical Herbs, Haikou Key Laboratory of Li Nationality Medicine, School of Pharmacy, Hainan Medical University, Haikou, China
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8
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Liang L, Zheng P, Jia S, Ray K, Chen Y, Barman I. Plasmonic Nanodiamonds. Nano Lett 2023; 23:5746-5754. [PMID: 37289011 DOI: 10.1021/acs.nanolett.3c01514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
While nitrogen-vacancy (NV) centers in diamonds have emerged as promising solid-state quantum emitters for sensing applications, the tantalizing possibility of coupling them with photonic or broadband plasmonic nanostructures to create ultrasensitive biolabels has not been fully realized. Indeed, it remains technologically challenging to create free-standing hybrid diamond-based imaging nanoprobes with enhanced brightness and high temporal resolution. Herein, we leverage the bottom-up DNA self-assembly to develop hybrid free-standing plasmonic nanodiamonds, which feature a closed plasmonic nanocavity completely encapsulating a single nanodiamond. Correlated single nanoparticle spectroscopical characterizations suggest that the plasmonic nanodiamond displays dramatically and simultaneously enhanced brightness and emission rate. We believe that they hold huge potential to serve as a stable solid-state single-photon source and could serve as a versatile platform to study nontrivial quantum effects in biological systems with enhanced spatial and temporal resolution.
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Affiliation(s)
- Le Liang
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
- Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sisi Jia
- Zhangjiang Lab, Shanghai 201210, China
| | - Krishanu Ray
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
| | - Yun Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
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Liu Y, Wang J, Sun L, Wang B, Zhang Q, Zhang X, Cao B. Active Self-Assembly of Ladder-Shaped DNA Carrier for Drug Delivery. Molecules 2023; 28:molecules28020797. [PMID: 36677855 PMCID: PMC9862081 DOI: 10.3390/molecules28020797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
With the advent of nanotechnology, DNA molecules have been transformed from solely genetic information carriers to multifunctional materials, showing a tremendous potential for drug delivery and disease diagnosis. In drug delivery systems, DNA is used as a building material to construct drug carriers through a variety of DNA self-assembly methods, which can integrate multiple functions to complete in vivo and in situ tasks. In this study, ladder-shaped drug carriers are developed for drug delivery on the basis of a DNA nanoladder. We first demonstrate the overall structure of the nanoladder, in which a nick is added into each rung of the nanoladder to endow the nanoladder with the ability to incorporate a drug loading site. The structure is designed to counteract the decrement of stability caused by the nick and investigated in different conditions to gain insight into the properties of the nicked DNA nanoladders. As a proof of concept, we fix the biotin in every other nick as a loading site and assemble the protein (streptavidin) on the loading site to demonstrate the feasibility of the drug-carrying function. The protein can be fixed stably and can be extended to different biological and chemical drugs by altering the drug loading site. We believe this design approach will be a novel addition to the toolbox of DNA nanotechnology, and it will be useful for versatile applications such as in bioimaging, biosensing, and targeted therapy.
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Affiliation(s)
- Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jiaxin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
| | - Lijun Sun
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Ministry of Education, Dalian 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
- Correspondence:
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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Rahmani P, Goodlad M, Zhang Y, Li Y, Ye T. One-Step Ligand-Exchange Method to Produce Quantum Dot-DNA Conjugates for DNA-Directed Self-Assembly. ACS Appl Mater Interfaces 2022; 14:47359-47368. [PMID: 36219825 DOI: 10.1021/acsami.2c10580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To address the current challenges in making bright, stable, and small DNA-functionalized quantum dots (QDs), we have developed a one-step ligand-exchange method to produce QD-DNA conjugates from commonly available hydrophobic QDs. We show that by systematically adjusting the reaction conditions such as ligand-to-nanoparticle molar ratio, pH, and solvent composition, stable and highly photoluminescent water-soluble QD-DNA conjugates with relatively high ligand loadings can be produced. Moreover, by site specifically binding these QD-DNA conjugates to a DNA origami template, we demonstrate that these bioconjugates have sufficient colloidal stability for DNA-directed self-assembly. Fluorescence quenching by an adjacent gold nanoparticle (AuNP) was demonstrated. Such QD-AuNP dimers may serve as biosensors with improved sensitivity and reproducibility. Moreover, our simple method can facilitate the assembly of QDs into more complex superlattices and discrete clusters that may enable novel photophysical properties.
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Affiliation(s)
- Paniz Rahmani
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Melissa Goodlad
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Yehan Zhang
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Yichen Li
- Department of Materials and Biomaterials Science & Engineering, University of California, 5200 North Lake Road, Merced, California 95343, United States
| | - Tao Ye
- Department of Chemistry & Biochemistry, University of California, 5200 North Lake Road, Merced, California 95343, United States
- Department of Materials and Biomaterials Science & Engineering, University of California, 5200 North Lake Road, Merced, California 95343, United States
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11
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Yang X, Yang L, Yang D, Li M, Wang P. In Situ DNA Self-Assembly on the Cell Surface Drives Unidirectional Clustering of Membrane Proteins for the Modulation of Cell Behaviors. Nano Lett 2022; 22:3410-3416. [PMID: 35389660 DOI: 10.1021/acs.nanolett.2c00680] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cell membrane proteins play a pivotal role in regulating intracellular signal transductions and cell behaviors. Many membrane proteins form clusters in order to initiate downstream signaling pathways for the modulation of cell behaviors. Developing rational methods to program the in situ clustering of designated membrane proteins on the cell surface to form large assemblies remains challenging. Here we use the membrane-anchored DNA hybridization chain reaction (HCR) to induce DNA self-assembly on the live cell surface and drive the unidirectional clustering of membrane proteins for the modulation of cell behaviors. Reactive DNA strands are specifically anchored onto the membrane proteins of interest by using DNA aptamers. Upon activation, the chain reaction between the protein-anchored DNA strands drives the assembly of membrane proteins forming one-dimensional clusters. We demonstrate both homogeneous and heterogeneous clustering of membrane proteins on multiple cell types that exhibit a potent capability for modulating cell behaviors including migration, proliferation, and survival.
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Affiliation(s)
- Xueqin Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lijiao Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Li
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogene and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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12
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Park S, Tandon A, Raza MT, Lee S, Nguyen TBN, Vu THN, Ha TH, Park SH. Construction and Configuration Analysis of Zelkova Serrata Lenticel-Like Patterns Generated through DNA Algorithmic Self-Assembly. ACS Appl Bio Mater 2022; 5:97-104. [PMID: 35014830 DOI: 10.1021/acsabm.1c00455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Multiple models and simulations have been proposed and performed to understand the mechanism of the various pattern formations existing in nature. However, the logical implementation of those patterns through efficient building blocks such as nanomaterials and biological molecules is rarely discussed. This study adopts a cellular automata model to generate simulation patterns (SPs) and experimental patterns (EPs) obtained from DNA lattices similar to the discrete horizontal brown-color line-like patterns on the bark of the Zelkova serrata tree, known as lenticels [observation patterns (OPs)]. SPs and EPs are generated through the implementation of six representative rules (i.e., R004, R105, R108, R110, R126, and R218) in three-input/one-output algorithmic logic gates. The EPs obtained through DNA algorithmic self-assembly are visualized by atomic force microscopy. Three different modules (A, B, and C) are introduced to analyze the similarities between the SPs, EPs, and OPs of Zelkova serrata lenticels. Each module has unique configurations with specific orientations allowing the calculation of the deviation of the SPs and the EPs with respect to the OPs within each module. The findings show that both the SP and the EP generated under R105 and R126 and analyzed with module B provide a higher similarity of Zelkova serrata lenticel-like patterns than the other four rules. This study provides a perspective regarding the use of DNA algorithmic self-assembly for the construction of various complex natural patterns.
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Affiliation(s)
- Suyoun Park
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Anshula Tandon
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Muhammad Tayyab Raza
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sungjin Lee
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Thi Bich Ngoc Nguyen
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Thi Hong Nhung Vu
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Tai Hwan Ha
- Core Facility Management Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Sung Ha Park
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
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13
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Zhang Y, Feng Y, Liang Y, Yang J, Zhang C. Development of Synthetic DNA Circuit and Networks for Molecular Information Processing. Nanomaterials (Basel) 2021; 11:2955. [PMID: 34835719 DOI: 10.3390/nano11112955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/23/2022]
Abstract
Deoxyribonucleic acid (DNA), a genetic material, encodes all living information and living characteristics, e.g., in cell, DNA signaling circuits control the transcription activities of specific genes. In recent years, various DNA circuits have been developed to implement a wide range of signaling and for regulating gene network functions. In particular, a synthetic DNA circuit, with a programmable design and easy construction, has become a crucial method through which to simulate and regulate DNA signaling networks. Importantly, the construction of a hierarchical DNA circuit provides a useful tool for regulating gene networks and for processing molecular information. Moreover, via their robust and modular properties, DNA circuits can amplify weak signals and establish programmable cascade systems, which are particularly suitable for the applications of biosensing and detecting. Furthermore, a biological enzyme can also be used to provide diverse circuit regulation elements. Currently, studies regarding the mechanisms and applications of synthetic DNA circuit are important for the establishment of more advanced artificial gene regulation systems and intelligent molecular sensing tools. We therefore summarize recent relevant research progress, contributing to the development of nanotechnology-based synthetic DNA circuits. By summarizing the current highlights and the development of synthetic DNA circuits, this paper provides additional insights for future DNA circuit development and provides a foundation for the construction of more advanced DNA circuits.
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14
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Wang H, Liu Y, Zhu X, Chen C, Fu Z, Wang M, Lin D, Chen Z, Lu C, Yang H. Multistage Cooperative Nanodrug Combined with PD-L1 for Enhancing Antitumor Chemoimmunotherapy. Adv Healthc Mater 2021; 10:e2101199. [PMID: 34382363 DOI: 10.1002/adhm.202101199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/02/2021] [Indexed: 12/13/2022]
Abstract
Combinatorial CpG oligonucleotide (CPG) and chemotherapy drug represent a promising approach to reactivate immune system. However, these two agents possess different physicochemical properties, hindering the application of direct self-assembly of these two cargos into a single nanostructure. Here, a multistage cooperative nanodrug is developed by the direct self-assembly of cis-platinum (CDDP, Pt), l-arginine (l-Arg, R), and CPG (defined as PtR/CPG) for antitumor chemoimmunotherapy. First, the CDDP can induce cell apoptosis. Meanwhile, CDDP also promotes the production of H2 O2 , catalyzing the conversion of l-Arg into nitric oxide (NO). The generated NO decreases the multidrug resistance of cells toward CDDP. Thus, the synergistic effects of CDDP and NO can trigger immunogenic cell death to produce tumor-associated antigens (TAAs). The TAAs and CPG will induce the maturation of dendritic cells (DCs) and enhance antigen presentation ability of DCs. In this way, the PtR/CPG can reverse the immunosuppressive microenvironment, sensitizing tumors to immune checkpoint inhibitors mediated by the programmed death-ligand 1 (PD-L1) antibody. Furthermore, the PtR/CPG combined with the PD-L1 antibody decreases the exhaustion and dysfunction of cytotoxic T lymphocytes to elicit durable systemic immune response. As a result, the prepared PtR/CPG nanodrug in combination with PD-L1 may be highly significant for cancer immunotherapy.
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Affiliation(s)
- Haihui Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Yongfei Liu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Xiaohui Zhu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Chengyun Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Zhangcheng Fu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Min Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Danying Lin
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Zhaowei Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
- State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P. R. China
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Liu Y, Ma L, Jiang S, Han C, Tang P, Yang H, Duan X, Liu N, Yan H, Lan X. DNA Programmable Self-Assembly of Planar, Thin-Layered Chiral Nanoparticle Superstructures with Complex Two-Dimensional Patterns. ACS Nano 2021; 15:16664-16672. [PMID: 34636539 DOI: 10.1021/acsnano.1c06639] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Planar, thin-layered chiral plasmonic superstructures with complex two-dimensional (2D) patterns, namely, double-layered binary stars (bi-stars) and pinwheels, were realized through DNA programmable 2D supramolecular self-assembly of gold nanorods (AuNRs). The chirality of the chiral superstructures was defined by a finite number of AuNR pairs as enantiomeric motifs, and their sizes (∼240 nm) were precisely defined by the underlying DNA template. These planar, thin-layered chiral nanoparticle superstructures exhibited prescribed shapes and sizes at the dried state on the substrate surface and are characteristic of giant anisotropy of chiroptical responses, with enhanced g-factors from the axial incident excitation as compared to the in-plane excitation. This work will inspire possibilities for the construction of 2D chiral materials, for example, chiral metasurfaces, for the on-chip manipulation of chiral light-matter interactions via programmable self-assembly of nanoparticles.
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Affiliation(s)
- Yan Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, People's Republic of China
- Center for Advanced Low-dimension Materials, Donghua University, Shanghai 201620, People's Republic of China
| | - Li Ma
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, People's Republic of China
- Center for Advanced Low-dimension Materials, Donghua University, Shanghai 201620, People's Republic of China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, People's Republic of China
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Cong Han
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, People's Republic of China
- Center for Advanced Low-dimension Materials, Donghua University, Shanghai 201620, People's Republic of China
| | - Pan Tang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, People's Republic of China
- Center for Advanced Low-dimension Materials, Donghua University, Shanghai 201620, People's Republic of China
| | - Hao Yang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, People's Republic of China
- Center for Advanced Low-dimension Materials, Donghua University, Shanghai 201620, People's Republic of China
| | - Xiaoyang Duan
- 2nd Physics Institute, University of Stuttgart, Pfaffenwaldring 57, Stuttgart 70569, Germany
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart 70569, Germany
| | - Na Liu
- 2nd Physics Institute, University of Stuttgart, Pfaffenwaldring 57, Stuttgart 70569, Germany
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, Stuttgart 70569, Germany
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiang Lan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Donghua University, Shanghai 201620, People's Republic of China
- Center for Advanced Low-dimension Materials, Donghua University, Shanghai 201620, People's Republic of China
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16
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Abstract
Many molecular systems in nature undergo autonomous addition and extraction of components in order to execute diverse functions, which rely on molecular components that can sense, process, and transmit information from the environment. Building artificial molecular systems using a similar strategy may lead to the construction of life-like synthetic materials. Herein, we report the design of a dynamic multicomponent molecular system from DNA self-assembly, which is capable of autonomously adding and extracting molecular components initiated by molecular triggers. Orthogonality was integrated into molecular components by harnessing the design capacity of DNA sequences. As a proof of concept, we built a three-component DNA tubular system, which can selectively add or extract one, two, or three components in an orthogonal and programmable manner. We further demonstrated that molecular extraction may be designed in response to environmental cues such as protons. Moreover, the tubes can be disassembled on demand to facilitate their uptake by cells. This work may prime the design of artificial multicomponent molecular systems with increasing complexity, diversity, and functionality that may guide the development of new synthetic materials beyond DNA self-assembly.
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Affiliation(s)
- Donglei Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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17
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Zheng M, Li Q, Li Q, Paluzzi VE, Choi JH, Mao C. Engineering the Nanoscaled Morphologies of Linear DNA Homopolymers. Macromol Rapid Commun 2021; 42:e2100217. [PMID: 34173292 DOI: 10.1002/marc.202100217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/24/2021] [Indexed: 12/26/2022]
Abstract
Supramolecular polymers have unique characteristics such as self-healing and easy processing. However, the scope of their structures is limited to mostly either flexible, random coils or rigid, straight chains. By broadening this scope, novel properties, functions, and applications can be explored. Here, DNA is used as a model system to engineer innovative, nanoscaled morphologies of supramolecular polymers. Each polymer chain consists of multiple copies of the same short (38-46 nucleotides long) DNA strand. The component DNA strands first dimerize into homo-dimers, which then further assemble into long polymer chains. By subtly tuning the design, a range of polymer morphologies are obtained; including straight chains, spirals, and closed rings with finite sizes. Such structures are confirmed by AFM imaging and predicted by molecular coarse simulation.
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Affiliation(s)
- Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.,College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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Parikka JM, Sokołowska K, Markešević N, Toppari JJ. Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:1502. [PMID: 33801952 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
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19
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Baral B, Dutta J, Subudhi U. Biophysical interaction between self-assembled branched DNA nanostructures with bovine serum albumin and bovine liver catalase. Int J Biol Macromol 2021; 177:119-128. [PMID: 33609575 DOI: 10.1016/j.ijbiomac.2021.02.095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/30/2021] [Accepted: 02/13/2021] [Indexed: 12/15/2022]
Abstract
Branched DNA (bDNA) nanostructures have emerged as self-assembled biomaterials and are being considered for biomedical applications. Herein, we report the biophysical interaction between self-assembled bDNA nanostructure with circulating protein bovine serum albumin (BSA) and cellular enzyme bovine liver catalase (BLC). The binding between bDNA and BSA or BLC was confirmed through the decrease in fluorescence spectra. The Stern-Volmer data supports for non-covalent bonding with ~1 binding site in case of BSA and BLC thus advocating a static binding. Furthermore, FTIR and ITC study confirmed the binding of bDNAs with proteins through hydrogen bonding and van der Waals interaction. The negative free energy observed in ITC represent spontaneous reaction for BLC-bDNA interaction. The biophysical interaction between bDNA nanostructures and proteins was also supported by DLS and zeta potential measurement. With an increase in bDNA concentrations up to 100 nM, no significant change in absorbance and CD spectra was observed for both BLC and BSA which suggests structural stability and unaffected secondary conformation of proteins in presence of bDNA. Furthermore, the catalytic activity of BLC was unaltered in presence of bDNAscr even with increasing the incubation period from 1 h to 24 h. Interestingly, the time-dependent decrease in activity of BLC was protected by bDNAmix. The thermal melting study suggests a higher Tm value for proteins in presence of bDNAmix which demonstrates that interaction with bDNAmix increases the thermal stability of proteins. Collectively these data suggest that self-assembled DNA nanostructure may bind to BSA for facilitating circulation in plasma or binding to intracellular proteins like BLC for stabilization, however the secondary conformation of protein or catalytic activity of enzyme is unaltered in presence of bDNA nanostructure. Thus, the newly established genomic sequence-driven self-assembled DNA nanostructure can be explored for in vitro or in vivo experimental work in recent future.
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Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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20
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Caprara D, Ripanti F, Capocefalo A, Ceccarini M, Petrillo C, Postorino P. Exploiting SERS sensitivity to monitor DNA aggregation properties. Int J Biol Macromol 2020; 170:88-93. [PMID: 33358955 DOI: 10.1016/j.ijbiomac.2020.12.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 01/11/2023]
Abstract
In the last decades, DNA has been considered far more than the system carrying the essential genetic instructions. Indeed, because of the remarkable properties of the base-pairing specificity and thermoreversibility of the interactions, DNA plays a central role in the design of innovative architectures at the nanoscale. Here, combining complementary DNA strands with a custom-made solution of silver nanoparticles, we realize plasmonic aggregates to exploit the sensitivity of Surface Enhanced Raman Spectroscopy (SERS) for the identification/detection of the distinctive features of DNA hybridization, both in solution and on dried samples. Moreover, SERS allows monitoring the DNA aggregation process by following the temperature variation of a specific spectroscopic marker associated with the Watson-Crick hydrogen bond formation. This temperature-dependent behavior enables us to precisely reconstruct the melting profile of the selected DNA sequences by spectroscopic measurements only.
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Affiliation(s)
- Debora Caprara
- Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | | | - Angela Capocefalo
- Istituto dei Sistemi Complessi-CNR c/o Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Marina Ceccarini
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Caterina Petrillo
- Physics and Geology Department, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Paolo Postorino
- Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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21
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Jaekel A, Lill P, Whitelam S, Saccà B. Insights into the Structure and Energy of DNA Nanoassemblies. Molecules 2020; 25:E5466. [PMID: 33255286 DOI: 10.3390/molecules25235466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.
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22
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Wang Y, Wang D, Jia F, Miller A, Tan X, Chen P, Zhang L, Lu H, Fang Y, Kang X, Cai J, Ren M, Zhang K. Self-Assembled DNA-PEG Bottlebrushes Enhance Antisense Activity and Pharmacokinetics of Oligonucleotides. ACS Appl Mater Interfaces 2020; 12:45830-45837. [PMID: 32936615 PMCID: PMC8110734 DOI: 10.1021/acsami.0c13995] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Herein, we report a novel strategy to enhance the antisense activity and the pharmacokinetics of therapeutic oligonucleotides. Through the DNA hybridization chain reaction, DNA hairpins modified with poly(ethylene glycol) (PEG) form a bottlebrush architecture consisting of a double-stranded DNA backbone, PEG side chains, and antisense overhangs. The assembled structure exhibits high PEG density on the surface, which suppresses unwanted interactions between the DNA and proteins (e.g., enzymatic degradation) while allowing the antisense overhangs to hybridize with the mRNA target and thereby deplete target protein expression. We show that these PEGylated bottlebrushes targeting oncogenic KRAS can achieve much higher antisense efficacy compared with unassembled hairpins with or without PEGylation and can inhibit the proliferation of lung cancer cells bearing the G12C mutant KRAS gene. Meanwhile, these structures exhibit elevated blood retention times in vivo due to the biological stealth properties of PEG and the high molecular weight of the overall assembly. Collectively, this self-assembly approach bears the characteristics of a simple, safe, yet highly translatable strategy to improve the biopharmaceutical properties of therapeutic oligonucleotides.
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Affiliation(s)
- Yuyan Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dali Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Fei Jia
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Andrew Miller
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Xuyu Tan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Peiru Chen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Lei Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hao Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yang Fang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Xi Kang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Jiansong Cai
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Mengqi Ren
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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23
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Abstract
DNA is an excellent biological material that has received growing attention in the field of nanotechnology due to its unique capability for precisely engineering materials via sequence specific interactions. Self-assembled DNA nanostructures of prescribed physicochemical properties have demonstrated potent drug delivery efficiency in vitro and in vivo. By using various conjugation techniques, DNA nanostructures may be precisely integrated with a large diversity of functional moieties, such as targeting ligands, proteins, and inorganic nanoparticles, to enrich their functionalities and to enhance their performance. In this review, we start with introducing strategies on constructing DNA nanostructures. We then summarize the biological barriers ahead of drug delivery using DNA nanostructures, followed by introducing existing rational solutions to overcome these biological barriers. Lastly, we discuss challenges and opportunities for DNA nanostructures toward real applications in clinical settings.
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Affiliation(s)
- Fan Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Xia
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Oncology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
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24
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Saleh OA, Jeon BJ, Liedl T. Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary. Proc Natl Acad Sci U S A 2020; 117:16160-6. [PMID: 32601183 DOI: 10.1073/pnas.2001654117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biomolecules can undergo liquid-liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA "nanostar" particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this "active dissolution" process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution ("boiling") temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation ("bubbling") events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.
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25
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Tandon A, Song Y, Mitta SB, Yoo S, Park S, Lee S, Raza MT, Ha TH, Park SH. Demonstration of Arithmetic Calculations by DNA Tile-Based Algorithmic Self-Assembly. ACS Nano 2020; 14:5260-5267. [PMID: 32159938 DOI: 10.1021/acsnano.0c01387] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Owing to its high information density, energy efficiency, and massive parallelism, DNA computing has undergone several advances and made significant contributions to nanotechnology. Notably, arithmetic calculations implemented by multiple logic gates such as adders and subtractors have received much attention because of their well-established logic algorithms and feasibility of experimental implementation. Although small molecules have been used to implement these computations, a DNA tile-based calculator has been rarely addressed owing to complexity of rule design and experimental challenges for direct verification. Here, we construct a DNA-based calculator with three types of building blocks (propagator, connector, and solution tiles) to perform addition and subtraction operations through algorithmic self-assembly. An atomic force microscope is used to verify the solutions. Our method provides a potential platform for the construction of various types of DNA algorithmic crystals (such as flip-flops, encoders, and multiplexers) by embedding multiple logic gate operations in the DNA base sequences.
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Affiliation(s)
- Anshula Tandon
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Yongwoo Song
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sekhar Babu Mitta
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sanghyun Yoo
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Suyoun Park
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sungjin Lee
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Muhammad Tayyab Raza
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Tai Hwan Ha
- Future Biotechnology Research Division, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Sung Ha Park
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
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26
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Abstract
The rise of material science and nanotechnology created a demand for a next generation of materials and procedures that can transcend the shaping of simple geometrical nano-objects. As a legacy of the technological progress made in the Human Genome Project, DNA was identified as a possible candidate. The low production costs of custom-made DNA molecules and the possibilities concerning the structural manipulation triggered significant advances in the field of DNA nanotechnology in the last decade. To facilitate the development of new DNA nanostructures and provide users an insight in less intuitive complexities and physical properties of the DNA folding, several in silico modelling tools were published. Here, we summarize the main characteristics of these specialised tools, describe the most common design principles and discuss tools and strategies used to predict the properties of DNA nanostructures.
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27
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Abstract
Self-assembled DNA structures hold great application potentials in many fields. The DNA structure of a specific feature, however, generally requires a distinct set of DNA strands with unique sequences, which is costly and error-prone. Herein, we expanded the modularity of DNA bricks to assemble a number of DNA structures including objects and lattices from the same set of DNA strands. We designed DNA superbricks composed of ∼200 conventional DNA bricks of 52 nucleotides. By modularly programming the sticky interactions between DNA superbricks, we have successfully assembled seven DNA structures of designer features including DNA objects and one-dimensional and two-dimensional DNA brick lattices.
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Affiliation(s)
- Xue Li
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Donglei Yang
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Bo Kou
- School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing 211167, China
| | - Luyao Shen
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Haofei Li
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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28
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Zhang J, Guo Y, Pan G, Wang P, Li Y, Zhu X, Zhang C. Injectable Drug-Conjugated DNA Hydrogel for Local Chemotherapy to Prevent Tumor Recurrence. ACS Appl Mater Interfaces 2020; 12:21441-21449. [PMID: 32314901 DOI: 10.1021/acsami.0c03360] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Considering the high rate of postsurgical tumor recurrence due to the possible residual cancer cells and the non-negligible toxicity of postsurgical systemic chemotherapy, we designed an injectable DNA hydrogel assembled by chemodrug-grafted DNA strands for localized chemotherapy. First, a multitude of camptothecin was successfully grafted on backbones of the phosphorothioate DNAs, which could be assembled into two types of Y-shaped building blocks and then hierarchically associated together to form drug-containing hydrogels. The injectable feature of drug-containing DNA hydrogels enables a minimally invasive approach for local drug administration. Owing to the enzymatic degradation, the hydrogel can gradually disassemble into nanosized particles, allowing its good permeation into the residual tumor tissue and efficient uptake by cells. Together with its sustained and responsive drug release behaviors, the drug-containing DNA hydrogel can significantly inhibit the regrowth of tumor cells and prevent cancer recurrence. Compared to the control groups, mice treated with our drug-containing DNA hydrogel show the lowest tumor relapse rate (1/3) and substantial slow tumor progression. Despite the long-term local embedding, negligible systemic toxicity and organ damages are observed after the treatment with our drug-grafted DNA hydrogel. With excellent antitumor efficacy and low side effects in vivo, our DNA-drug conjugate (DDC)-based hydrogel represents a promising candidate for local adjuvant therapy in cancer treatment.
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Affiliation(s)
- Jiao Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuanyuan Guo
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Gaifang Pan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Wang
- Weigao Research Center, 304, Building 2, Lane 720, Cailun Road, Shanghai 201203, China
| | - Yuehua Li
- Department of Radiology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University School of Medicine, 600 Yi Shan Road, Shanghai 200233, China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
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29
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Wang X, Yu J, Lan W, Yang S, Wang S, Mi Y, Ye Q, Li Y, Liu Y. Novel Stable DNA Nanoscale Material and Its Application on Specific Enrichment of DNA. ACS Appl Mater Interfaces 2020; 12:19834-19839. [PMID: 32250112 DOI: 10.1021/acsami.0c02242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA nanostructures are a new type of technology for constructing nanomaterials that has been developed in recent years. By relying on the complementary pairing of DNA molecules to form a double-stranded property, DNA molecules can construct a variety of nanoscale structures of 2D and 3D shapes. However, most of the previously reported DNA nanostructures rely solely on hydrogen bonds to maintain structural stability, resulting in DNA structures that can be maintained only at low temperature and in the presence of Mg2+, which greatly limits the application of DNA nanostructures. This study designed a DNA nanonetwork structure (nanonet) and changed its topological structure to DNA nanomesh by using DNA topoisomerase to make it thermally stable, while escaping the dependence on Mg2+, and the stability of the structure can be maintained in a nonsolution state. Moreover, the nanomesh also has a large amount of ssDNA (about 50%), providing active sites capable of exerting biological functions. Using the above characteristics, we prepared the nanomesh into a device capable of adsorbing specific DNA molecules, and used the device to enrich DNA. We also tried to mount antibodies using DNA probes. Preliminary results show that the DNA nanomesh also has the ability to enrich specific proteins.
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Affiliation(s)
- Xueting Wang
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Jia Yu
- College of Life Sciences, Qingdao University, Qingdao 266071, P. R. China
| | - Wenjie Lan
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shuo Yang
- Department of Medicine, Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Shiqing Wang
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Yue Mi
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Qing Ye
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics and TEDA Applied Physics, Nankai University, Tianjin 300071, P. R. China
| | - Yuan Li
- State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Yin Liu
- School of Medicine, Nankai University, Tianjin 300071, P. R. China
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30
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Yu W, Sun J, Liu F, Yu S, Xu Z, Wang F, Liu X. Enhanced Immunostimulatory Activity of a Cytosine-Phosphate-Guanosine Immunomodulator by the Assembly of Polymer DNA Wires and Spheres. ACS Appl Mater Interfaces 2020; 12:17167-17176. [PMID: 32131585 DOI: 10.1021/acsami.9b21075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Unmethylated cytosine-phosphate-guanosine (CpG) oligodeoxynucleotides are immunostimulatory nucleic acids wildly utilized as adjuvants or for vaccines to treat diseases. However, there is a lack of simple and efficient vectors for CpG oligodeoxynucleotide delivery with long-lasting immune stimulation. Herein, self-assembled polymer wires consisting of CpG motifs by hybridization chain reaction were constructed with excellent biocompatibility and immunostimulatory activity. The designed polymer DNA wires acted as programmable multivalent immunoadjuvants and triggered immune response, stimulated pro-inflammatory cytokine secretion, and induced the apoptosis of cancer cells. More strikingly, polymer nanospheres assembled from the polymer DNA wires and cationic poly-l-lysine further improved cellular uptake and continuously stimulate the lysosomal Toll-like receptor 9 of immune cells, thereby remarkably enhancing the activation of immune cells. These results demonstrated that self-assembled polymer DNA nanoassemblies with multivalent CpG could trigger strong immune response and further induce cancer cell death.
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Affiliation(s)
- Wenqian Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Junlin Sun
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Feng Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Shuyi Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Zhen Xu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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31
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Qu A, Wu X, Li S, Sun M, Xu L, Kuang H, Xu C. An NIR-Responsive DNA-Mediated Nanotetrahedron Enhances the Clearance of Senescent Cells. Adv Mater 2020; 32:e2000184. [PMID: 32100405 DOI: 10.1002/adma.202000184] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Senescence is a state of stable cell cycle arrest that can escape apoptosis and lead to aging and numerous age-related diseases. In this study, an upconversion-nanoparticle (UCNP)-centered Au20 -Au30 nanoparticles tetrahedron (UAuTe) is prepared by DNA hybridization, which can selectively accelerate the clearance of senescent cells. When the beta-2-microglobulin antibody (anti-B2MG) on the Au NPs recognizes senescent cells, the application of near-infrared (NIR) light induces the disassembly of the UAuTe by breaking the boronic ester linkage. Subsequently, the Granzyme B exposed on the UCNPs induces apoptosis in senescent cells, which can then be tracked by changes in fluorescence. It is found that, as compared to single Granzyme B, the UAuTe can not only control the Granzyme B delivery by NIR-responsivity, but also synergistically target and activate the Granzyme B in the senescent cell without the need of perforin. Moreover, this tool is applied successfully in vivo; the results demonstrate that the NIR-responsive tetrahedron can restore renal function, tissue homeostasis, fur density, and athletic ability in a mouse model of senescence after 30 d of treatment. The NIR-induced tetrahedron provides a practical strategy for clinical diagnosis and therapy, particularly for aging and age-related diseases.
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Affiliation(s)
- Aihua Qu
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Xiaoling Wu
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Si Li
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Maozhong Sun
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Liguang Xu
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Hua Kuang
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Chuanlai Xu
- Key Lab of Synthetic and Biological Colloids, Ministry of Education, International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
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32
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Wang D, Chai Y, Yuan Y, Yuan R. Lattice-Like DNA Tetrahedron Nanostructure as Scaffold to Locate GOx and HRP Enzymes for Highly Efficient Enzyme Cascade Reaction. ACS Appl Mater Interfaces 2020; 12:2871-2877. [PMID: 31849211 DOI: 10.1021/acsami.9b18702] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this work, the array arrangement of cascade enzymes was implemented by alternately and equidistantly anchoring two model enzymes glucose oxidase (GOx) and horseradish peroxidase (HRP) to the vertexes of rigid DNA tetrahedron units in lattice-like nucleic acid scaffold, in which the distance between any adjacent cascade enzymes had been regulated to the optimum for obtaining high enzyme cascade catalytic efficiency. Compared to the enzyme cascade system with no-array arrangement of cascade enzymes, the proposed enzyme cascade system allowed the intermediate H2O2 produced by GOx catalyzing substrate glucose to concurrently and equidistantly diffuse toward the four adjacent HRP enzyme surfaces. In this case, the invalid diffusion effect of intermediate H2O2 between cascade enzymes could be effectively avoided, thereby promoting the enzyme cascade reaction with high catalytic efficiency. The specific catalytic efficiency (kcat/Km) of the cascade enzyme system with array arrangement had been evaluated, which exhibited catalytic efficiency about 3.6 times higher than that of the randomly arranged cascade enzyme system. As a result, this strategy provided a new avenue for constructing a highly efficient enzyme cascade system with ultimate applications in biosynthesis, bioanalysis, and biodiagnostics.
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Affiliation(s)
- Ding Wang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Yali Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering , Southwest University , Chongqing 400715 , PR China
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33
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Shen Z, He L, Wang W, Tan L, Gan N. Highly sensitive and simultaneous detection of microRNAs in serum using stir-bar assisted magnetic DNA nanospheres-encoded probes. Biosens Bioelectron 2019; 148:111831. [PMID: 31706172 DOI: 10.1016/j.bios.2019.111831] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/17/2022]
Abstract
There are critical interests in the detection of microRNA (miRNA) because it can be a blood-borne biomarker, but analytical strategies are still limited by its small size, high sequence homology among family members and low abundance. In this work, three-dimensional magnetic DNA nanospheres were synthesized and immobilized on a gold stir-bar as encoded probes for miRNA capture and signal amplification. Electrochemical tags-labeled DNAs were immobilized on gold coated magnetic nanospheres via a hyperbranched hybridization chain reaction (HHCR). Subsequently, the magnetic DNA nanospheres were immobilized on the gold stir-bar as encoded probes. Target miRNAs were captured on the surface of the stir-bar by replacing the magnetic DNA nanospheres-encoded probes, and the probes were magnetically enriched for highly sensitive and selective electrochemical detection. The gold stir-bar assisted magnetic DNA nanospheres-encoded probes possess dual functions: They are as a nanocarrier to increase the loading amounts of HHCR products, and they are also a platform for efficient electrochemical signal amplification via magnetic enrichment. The method was successfully applied for the detection of miRNA21 and miRNA155 in a wide linear range of 5 fM to 2 nM, and with detection limits of 1.5 fM and 1.8 fM, respectively. The preliminary application of the method suggests that it has great potential in the detection of miRNAs in serum samples.
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Affiliation(s)
- Zhipeng Shen
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Liyong He
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Wenhai Wang
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China
| | - Lei Tan
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China.
| | - Ning Gan
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, China.
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34
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Abstract
DNA nanotechnology allows for the realization of complex nanoarchitectures in which the spatial arrangements of different constituents and most functions can be enabled by DNA. When optically active components are integrated in such systems, the resulting nanoarchitectures not only provide great insights into the self-assembly of nanoscale elements in a systematic way but also impart tailored optical functionality to DNA origami. In this Letter, we demonstrate DNA-assembled multilayer nanosystems, which can carry out coordinated and reversible sliding motion powered by DNA fuels. Gold nanoparticles cross-link DNA origami filaments to define the configurations of the multilayer nanoarchitectures as well as to mediate relative sliding between the neighboring origami filaments. Meanwhile, the gold nanoparticles serve as optical probes to dynamically interact with the fluorophores tethered on the filaments, rendering in situ detection of the stepwise sliding processes possible. This work seeds the basis to implement DNA-assembled complex optical nanoarchitectures with programmability and addressability, advancing the field with new momentum.
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Affiliation(s)
- Pengfei Zhan
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
| | - Steffen Both
- 4th
Physics Institute and Stuttgart Research Center of Photonic Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Thomas Weiss
- 4th
Physics Institute and Stuttgart Research Center of Photonic Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Na Liu
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff
Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
- E-mail: . Phone: 0049 711 6891838
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35
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Ohyama T. New Aspects of Magnesium Function: A Key Regulator in Nucleosome Self-Assembly, Chromatin Folding and Phase Separation. Int J Mol Sci 2019; 20:ijms20174232. [PMID: 31470631 PMCID: PMC6747271 DOI: 10.3390/ijms20174232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 02/07/2023] Open
Abstract
Metal cations are associated with many biological processes. The effects of these cations on nucleic acids and chromatin were extensively studied in the early stages of nucleic acid and chromatin research. The results revealed that some monovalent and divalent metal cations, including Mg2+, profoundly affect the conformations and stabilities of nucleic acids, the folding of chromatin fibers, and the extent of chromosome condensation. Apart from these effects, there have only been a few reports on the functions of these cations. In 2007 and 2013, however, Mg2+-implicated novel phenomena were found: Mg2+ facilitates or enables both self-assembly of identical double-stranded (ds) DNA molecules and self-assembly of identical nucleosomes in vitro. These phenomena may be deeply implicated in the heterochromatin domain formation and chromatin-based phase separation. Furthermore, a recent study showed that elevation of the intranuclear Mg2+ concentration causes unusual differentiation of mouse ES (embryonic stem) cells. All of these phenomena seem to be closely related to one another. Mg2+ seems to be a key regulator of chromatin dynamics and chromatin-based biological processes.
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Affiliation(s)
- Takashi Ohyama
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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36
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Nicoli F, Zhang T, Hübner K, Jin B, Selbach F, Acuna G, Argyropoulos C, Liedl T, Pilo-Pais M. DNA-Mediated Self-Assembly of Plasmonic Antennas with a Single Quantum Dot in the Hot Spot. Small 2019; 15:e1804418. [PMID: 30734483 DOI: 10.1002/smll.201804418] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/23/2018] [Indexed: 06/09/2023]
Abstract
DNA self-assembly is a powerful tool to arrange optically active components with high accuracy in a large parallel manner. A facile approach to assemble plasmonic antennas consisting of two metallic nanoparticles (40 nm) with a single colloidal quantum dot positioned at the hot spot is presented here. The design approach is based on DNA complementarity, stoichiometry, and steric hindrance principles. Since no intermediate molecules other than short DNA strands are required, the structures possess a very small gap (≈ 5 nm) which is desired to achieve high Purcell factors and plasmonic enhancement. As a proof-of-concept, the fluorescence emission from antennas assembled with both conventional and ultrasmooth spherical gold particles is measured. An increase in fluorescence is obtained, up to ≈30-fold, compared to quantum dots without antenna.
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Affiliation(s)
- Francesca Nicoli
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, München (LMU), 80539, Munich, Germany
| | - Tao Zhang
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, München (LMU), 80539, Munich, Germany
| | - Kristina Hübner
- Department of Chemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München (LMU), 81377, Munich, Germany
| | - Boyuan Jin
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Florian Selbach
- Department of Chemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München (LMU), 81377, Munich, Germany
| | - Guillermo Acuna
- Department of Physics, University of Fribourg, 1700, Fribourg, Switzerland
| | - Christos Argyropoulos
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, München (LMU), 80539, Munich, Germany
| | - Mauricio Pilo-Pais
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, München (LMU), 80539, Munich, Germany
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37
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Mitta SB, Han S, Vellampatti S, Tandon A, Shin J, Ha TH, Park SH. Streptavidin-Decorated Algorithmic DNA Lattices Constructed by Substrate-Assisted Growth Method. ACS Biomater Sci Eng 2018; 4:3617-3623. [PMID: 33450799 DOI: 10.1021/acsbiomaterials.8b00950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ultimate goal of DNA computing is to store information at higher density and solve complex problems with less computational time and minimal error. Most algorithmic DNA lattices have been constructed using the free-solution growth (FSG) annealing method, and hairpin-embedded DNA rule tiles have been introduced in most algorithmic implementations to differentiate 0- and 1-bit information. Here, we developed streptavidin (SA)-decorated algorithmic COPY (produced line-like patterns with biotinylated 1-bit rule tiles) and XOR (triangle-like patterns) lattices constructed by a substrate-assisted growth (SAG) method and FSG. SA decoration in algorithmic lattices provides an efficient platform for visualizing bit information, and the SAG method in algorithmic assembly offers full coverage of algorithmic lattices on a substrate with a relatively lower DNA concentration than previous methods. The algorithmic COPY and XOR lattices assembled with various ratios of 0- and 1-bit rule tiles were verified by atomic force microscopy. We found that even asymmetric DNA patterns produced by certain algorithmic logic gates could be easily constructed by SAG. Finally, we evaluated sorting factors and error rates of algorithmic COPY and XOR lattices to determine the bit population and quality of the algorithmic assembly. Because of the catalytic effect of the substrate, the sorting factor of algorithmic DX-DNA lattices did not greatly influence the specific rules (i.e., COPY and XOR logic gates) annealed by SAG. Additionally, we found that the overall error rates of algorithmic DX-DNA lattices prepared by the FSG and SAG methods were low, within the range of 1-3%. Hence, the self-assembled algorithmic patterns generated with DNA molecules may serve as a scaffold for molecular demultiplexing circuits and computing.
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Affiliation(s)
- Sekhar Babu Mitta
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Sungguk Han
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Srivithya Vellampatti
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Anshula Tandon
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Jihoon Shin
- Hazards Monitoring BNT Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Tai Hwan Ha
- Hazards Monitoring BNT Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.,Department of Nanobiotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Sung Ha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
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38
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Xu G, Zhao H, Reboud J, Cooper JM. Cycling of Rational Hybridization Chain Reaction To Enable Enzyme-Free DNA-Based Clinical Diagnosis. ACS Nano 2018; 12:7213-7219. [PMID: 29965722 PMCID: PMC6070952 DOI: 10.1021/acsnano.8b03183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
In order to combat the growing threat of global infectious diseases, there is a need for rapid diagnostic technologies that are sensitive and that can provide species specific information (as might be needed to direct therapy as resistant strains of microbes emerge). Here, we present a convenient, enzyme-free amplification mechanism for a rational hybridization chain reaction, which is implemented in a simple format for isothermal amplification and sensing, applied to the DNA-based diagnosis of hepatitis B virus (HBV) in 54 patients. During the cycled amplification process, DNA monomers self-assemble in an organized and controllable way only when a specific target HBV sequence is present. This mechanism is confirmed using super-resolution stochastic optical reconstruction microscopy. The enabled format is designed in a manner analogous to an enzyme-linked immunosorbent assay, generating colored products with distinct tonality and with a limit of detection of ca. five copies/reaction. This routine assay also showed excellent sensitivity (>97%) in clinical samples demonstrating the potential of this convenient, low cost, enzyme-free method for use in low resource settings.
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Affiliation(s)
- Gaolian Xu
- Nano
Biomedical Research Centre, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K.
| | - Hang Zhao
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K.
| | - Julien Reboud
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K.
| | - Jonathan M. Cooper
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K.
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39
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Lei Y, Qiao Z, Tang J, He X, Shi H, Ye X, Yan L, He D, Wang K. DNA nanotriangle-scaffolded activatable aptamer probe with ultralow background and robust stability for cancer theranostics. Theranostics 2018; 8:4062-4071. [PMID: 30128036 PMCID: PMC6096399 DOI: 10.7150/thno.24683] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/16/2018] [Indexed: 12/23/2022] Open
Abstract
Activatable aptamers have emerged as promising molecular tools for cancer theranostics, but reported monovalent activatable aptamer probes remain problematic due to their unsatisfactory affinity and poor stability. To address this problem, we designed a novel theranostic strategy of DNA nanotriangle-scaffolded multivalent split activatable aptamer probe (NTri-SAAP), which combines advantages of programmable self-assembly, multivalent effect and target-activatable architecture. Methods: NTri-SAAP was assembled by conjugating multiple split activatable aptamer probes (SAAPs) on a planar DNA nanotriangle scaffold (NTri). Leukemia CCRF-CEM cell line was used as the model to investigate its detection, imaging and therapeutic effect both in vitro and in vivo. Binding affinity and stability were evaluated using flow cytometry and nuclease resistance assays. Results: In the free state, NTri-SAAP was stable with quenched signals and loaded doxorubicin, while upon binding to target cells, it underwent a conformation change with fluorescence activation and drug release after internalization. Compared to monovalent SAAP, NTri-SAAP displayed greatly-improved target binding affinity, ultralow nonspecific background and robust stability in harsh conditions, thus affording contrast-enhanced tumor imaging within an extended time window of 8 h. Additionally, NTri-SAAP increased doxorubicin loading capacity by ~5 times, which further realized a high anti-tumor efficacy in vivo with 81.95% inhibition but no obvious body weight loss. Conclusion: These results strongly suggest that the biocompatible NTri-SAAP strategy would provide a promising platform for precise and high-quality theranostics.
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40
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Baker MAB, Tuckwell AJ, Berengut JF, Bath J, Benn F, Duff AP, Whitten AE, Dunn KE, Hynson RM, Turberfield AJ, Lee LK. Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering. ACS Nano 2018; 12:5791-5799. [PMID: 29812934 DOI: 10.1021/acsnano.8b01669] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The rational design of complementary DNA sequences can be used to create nanostructures that self-assemble with nanometer precision. DNA nanostructures have been imaged by atomic force microscopy and electron microscopy. Small-angle X-ray scattering (SAXS) provides complementary structural information on the ensemble-averaged state of DNA nanostructures in solution. Here we demonstrate that SAXS can distinguish between different single-layer DNA origami tiles that look identical when immobilized on a mica surface and imaged with atomic force microscopy. We use SAXS to quantify the magnitude of global twist of DNA origami tiles with different crossover periodicities: these measurements highlight the extreme structural sensitivity of single-layer origami to the location of strand crossovers. We also use SAXS to quantify the distance between pairs of gold nanoparticles tethered to specific locations on a DNA origami tile and use this method to measure the overall dimensions and geometry of the DNA nanostructure in solution. Finally, we use indirect Fourier methods, which have long been used for the interpretation of SAXS data from biomolecules, to measure the distance between DNA helix pairs in a DNA origami nanotube. Together, these results provide important methodological advances in the use of SAXS to analyze DNA nanostructures in solution and insights into the structures of single-layer DNA origami.
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Affiliation(s)
- Matthew A B Baker
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
| | - Andrew J Tuckwell
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
| | - Jonathan Bath
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Florence Benn
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Anthony P Duff
- Australian Nuclear Science and Technology Organisation , Lucas Heights 2234 , Australia
| | - Andrew E Whitten
- Australian Nuclear Science and Technology Organisation , Lucas Heights 2234 , Australia
| | - Katherine E Dunn
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Robert M Hynson
- Structural and Computational Biology Division , The Victor Chang Cardiac Research Institute , Darlinghurst 2010 , Australia
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics , University of Oxford , Parks Road , Oxford OX1 3PU , United Kingdom
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences , The University of New South Wales , Sydney 2052 , Australia
- Structural and Computational Biology Division , The Victor Chang Cardiac Research Institute , Darlinghurst 2010 , Australia
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41
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Guo B, Wen B, Cheng W, Zhou X, Duan X, Zhao M, Xia Q, Ding S. An enzyme-free and label-free surface plasmon resonance biosensor for ultrasensitive detection of fusion gene based on DNA self-assembly hydrogel with streptavidin encapsulation. Biosens Bioelectron 2018; 112:120-126. [PMID: 29702383 DOI: 10.1016/j.bios.2018.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 04/13/2018] [Indexed: 01/22/2023]
Abstract
In this research, an enzyme-free and label-free surface plasmon resonance (SPR) biosensing strategy has been developed for ultrasensitive detection of fusion gene based on the heterogeneous target-triggered DNA self-assembly aptamer-based hydrogel with streptavidin (SA) encapsulation. In the presence of target, the capture probes (Cp) immobilized on the chip surface can capture the PML/RARα, forming a Cp-PML/RARα duplex. After that, the aptamer-based network hydrogel nanostructure is formed on the gold surface via target-triggered self-assembly of X shaped polymers. Subsequently, the SA can be encapsulated into hydrogel by the specific binding of SA aptamer, forming the complex with super molecular weight. Thus, the developed strategy achieves dramatic enhancement of the SPR signal. Using PML/RARα "S" subtype as model analyte, the developed biosensing method can detect target down to 45.22 fM with a wide linear range from 100 fM to 10 nM. Moreover, the high efficiency biosensing method shows excellent practical ability to identify the clinical PCR products of PML/RARα. Thus, this proposed strategy presents a powerful platform for ultrasensitive detection of fusion gene and early diagnosis and monitoring of disease.
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Affiliation(s)
- Bin Guo
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; Department of Clinical Laboratory, The Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, China
| | - Bo Wen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaoyan Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xiaolei Duan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Min Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Qianfeng Xia
- Laboratory of Tropical Biomedicine and Biotechnology, Faculty of Tropical Biomedicine and Laboratory Medicine, Hainan medical University, Haikou, Hainan 571101, China.
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
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42
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Abstract
The field of DNA nanoscience has demonstrated many exquisite DNA nanostructures and intricate DNA nanodevices. However, the operation of each step of prior demonstrated DNA nanodevices requires the diffusion of DNA strands, and the speed of these devices is limited by diffusion kinetics. Here we demonstrate chains of localized DNA hybridization reactions on the surface of a self-assembled DNA origami rectangle. The localization design for our DNA nanodevices does not rely on the diffusion of DNA strands for each step, thus providing faster reaction kinetics. The locality also provides considerable increased scalability, since localized components of the devices can be reused in other locations. A variety of techniques, including atomic force microscopy, total internal reflection fluorescence, and ensemble fluorescence spectroscopy, are used to confirm the occurrence of localized DNA hybridization reactions on the surface of DNA origami. There are many potential biological applications for our localized DNA nanodevices, and the localization design is extensible to applications involving DNA nanodevices operating on other molecular surfaces, such as those of the cell.
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Affiliation(s)
- Hieu Bui
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
- National Research Council , 500 Fifth Street NW, Keck 576, Washington, DC 20001, United States
| | - Shalin Shah
- Department of Electrical and Computer Engineering, Duke University Durham, North Carolina 27708, United States
| | - Reem Mokhtar
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Tianqi Song
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Sudhanshu Garg
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - John Reif
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
- Department of Electrical and Computer Engineering, Duke University Durham, North Carolina 27708, United States
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43
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Abstract
Surface display of biomolecules on live cells offers new opportunities to treat human diseases and perform basic studies. Existing methods are primarily focused on monovalent functionalization, that is, the display of single biomolecules across the cell surface. Here we show that the surface of live cells can be functionalized to display polyvalent biomolecular structures through two-step reactions under physiological conditions. This polyvalent functionalization enables the cell surface to recognize the microenvironment one order of magnitude more effectively than with monovalent functionalization. Thus, polyvalent display of biomolecules on live cells holds great potential for various biological and biomedical applications.
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Affiliation(s)
- Peng Shi
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nan Zhao
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jinping Lai
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - James Coyne
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Erin R Gaddes
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
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44
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Song T, Garg S, Mokhtar R, Bui H, Reif J. Design and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation Using Autocatalytic Amplifiers. ACS Synth Biol 2018; 7:46-53. [PMID: 29202579 DOI: 10.1021/acssynbio.6b00390] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A main goal in DNA computing is to build DNA circuits to compute designated functions using a minimal number of DNA strands. Here, we propose a novel architecture to build compact DNA strand displacement circuits to compute a broad scope of functions in an analog fashion. A circuit by this architecture is composed of three autocatalytic amplifiers, and the amplifiers interact to perform computation. We show DNA circuits to compute functions sqrt(x), ln(x) and exp(x) for x in tunable ranges with simulation results. A key innovation in our architecture, inspired by Napier's use of logarithm transforms to compute square roots on a slide rule, is to make use of autocatalytic amplifiers to do logarithmic and exponential transforms in concentration and time. In particular, we convert from the input that is encoded by the initial concentration of the input DNA strand, to time, and then back again to the output encoded by the concentration of the output DNA strand at equilibrium. This combined use of strand-concentration and time encoding of computational values may have impact on other forms of molecular computation.
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Affiliation(s)
- Tianqi Song
- Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Sudhanshu Garg
- Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Reem Mokhtar
- Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Hieu Bui
- Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - John Reif
- Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
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45
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Lan X, Su Z, Zhou Y, Meyer T, Ke Y, Wang Q, Chiu W, Liu N, Zou S, Yan H, Liu Y. Programmable Supra-Assembly of a DNA Surface Adapter for Tunable Chiral Directional Self-Assembly of Gold Nanorods. Angew Chem Int Ed Engl 2017; 56:14632-14636. [PMID: 28971555 PMCID: PMC5851444 DOI: 10.1002/anie.201709775] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Indexed: 11/08/2022]
Abstract
An important challenge in molecular assembly and hierarchical molecular engineering is to control and program the directional self-assembly into chiral structures. Here, we present a versatile DNA surface adapter that can programmably self-assemble into various chiral supramolecular architectures, thereby regulating the chiral directional "bonding" of gold nanorods decorated by the surface adapter. Distinct optical chirality relevant to the ensemble conformation is demonstrated from the assembled novel stair-like and coil-like gold nanorod chiral metastructures, which is strongly affected by the spatial arrangement of neighboring nanorod pair. Our strategy provides new avenues for fabrication of tunable optical metamaterials by manipulating the directional self-assembly of nanoparticles using programmable surface adapters.
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Affiliation(s)
- Xiang Lan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Zhaoming Su
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yadong Zhou
- Chemistry Department, University of Central Florida, 4111 Libra Drive Orlando, FL, 32816-2366, USA
| | - Travis Meyer
- Wallace H. Coulter Department of Biomedical Engineering at, Georgia Institute of Technology and Emory University, 1760 Haygood Drive Health Sciences Research Bldg E186, Atlanta, GA, 30322, USA
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering at, Georgia Institute of Technology and Emory University, 1760 Haygood Drive Health Sciences Research Bldg E186, Atlanta, GA, 30322, USA
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Na Liu
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569, Stuttgart, Germany
- Kirchhoff Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120, Heidelberg, Germany
| | - Shengli Zou
- Chemistry Department, University of Central Florida, 4111 Libra Drive Orlando, FL, 32816-2366, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yan Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
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46
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Zhao M, Wang X, Ren S, Xing Y, Wang J, Teng N, Zhao D, Liu W, Zhu D, Su S, Shi J, Song S, Wang L, Chao J, Wang L. Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement. ACS Appl Mater Interfaces 2017; 9:21942-21948. [PMID: 28618781 DOI: 10.1021/acsami.7b05959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.
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Affiliation(s)
- Mengzhen Zhao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Xu Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Shaokang Ren
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Yikang Xing
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Jun Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Nan Teng
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Dongxia Zhao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Wei Liu
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Dan Zhu
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Shao Su
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Jiye Shi
- UCB Pharma , 208 Bath Road, Slough SL1 3WE, U.K
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China
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47
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Abstract
We demonstrate an optically controlled molecular-scale pass gate that uses the photoinduced dark states of fluorescent molecules to modulate the flow of excitons. The device consists of four fluorophores spatially arranged on a self-assembled DNA nanostructure. Together, they form a resonance energy transfer (RET) network resembling a standard transistor with a source, channel, drain, and gate. When the gate fluorophore is directly excited, the device is toggled on. Excitons flow freely from the source to the drain, producing strong output fluorescence. Without this excitation, exciton flow through the device is hindered by absorbing paths along the way, resulting in weak output fluorescence. In this Letter, we describe the design and fabrication of the pass gate. We perform a steady-state analysis revealing that the on/off fluorescence ratio for this particular implementation is ∼8.7. To demonstrate dynamic modulation of the pass gate, we toggle the gate excitation on and off and measure the corresponding change in output fluorescence. We characterize the rise and fall times of these transitions, showing that they are faster and/or more easily achieved than other methods of RET network modulation. The pass gate is the first dynamic RET-based logic gate exclusively modulated by dark states and serves as a proof-of-concept device for building more complex RET systems in the future.
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Affiliation(s)
- Craig D LaBoda
- Department of Electrical and Computer Engineering and ‡Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Alvin R Lebeck
- Department of Electrical and Computer Engineering and ‡Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Chris L Dwyer
- Department of Electrical and Computer Engineering and ‡Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
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48
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He L, Brasino M, Mao C, Cho S, Park W, Goodwin AP, Cha JN. DNA-Assembled Core-Satellite Upconverting-Metal-Organic Framework Nanoparticle Superstructures for Efficient Photodynamic Therapy. Small 2017; 13:10.1002/smll.201700504. [PMID: 28481463 PMCID: PMC6697551 DOI: 10.1002/smll.201700504] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/18/2017] [Indexed: 05/18/2023]
Abstract
DNA-mediated assembly of core-satellite structures composed of Zr(IV)-based porphyrinic metal-organic framework (MOF) and NaYF4 ,Yb,Er upconverting nanoparticles (UCNPs) for photodynamic therapy (PDT) is reported. MOF NPs generate singlet oxygen (1 O2 ) upon photoirradiation with visible light without the need for additional small molecule, diffusional photosensitizers such as porphyrins. Using DNA as a templating agent, well-defined MOF-UCNP clusters are produced where UCNPs are spatially organized around a centrally located MOF NP. Under NIR irradiation, visible light emitted from the UCNPs is absorbed by the core MOF NP to produce 1 O2 at significantly greater amounts than what can be produced from simply mixing UCNPs and MOF NPs. The MOF-UCNP core-satellite superstructures also induce strong cell cytotoxicity against cancer cells, which are further enhanced by attaching epidermal growth factor receptor targeting affibodies to the PDT clusters, highlighting their promise as theranostic photodynamic agents.
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Affiliation(s)
- Liangcan He
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Michael Brasino
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Chenchen Mao
- Department of Electrical, Computer and Energy Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Suehyun Cho
- Department of Electrical, Computer and Energy Engineering, University of Colorado, Boulder, CO, 80303, USA
| | - Wounjhang Park
- Department of Electrical, Computer and Energy Engineering, University of Colorado, Boulder, CO, 80303, USA
- Materials Science and Engineering Program, University of Colorado, Boulder, CO, 80303, USA
| | - Andrew P Goodwin
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
- Materials Science and Engineering Program, University of Colorado, Boulder, CO, 80303, USA
| | - Jennifer N Cha
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80303, USA
- Materials Science and Engineering Program, University of Colorado, Boulder, CO, 80303, USA
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49
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Bui H, Miao V, Garg S, Mokhtar R, Song T, Reif J. Design and Analysis of Localized DNA Hybridization Chain Reactions. Small 2017; 13:1602983. [PMID: 28092433 DOI: 10.1002/smll.201602983] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/15/2016] [Indexed: 06/06/2023]
Abstract
Theoretical models of localized DNA hybridization reactions on nanoscale substrates indicate potential benefits over conventional DNA hybridization reactions. Recently, a few approaches have been proposed to speed-up DNA hybridization reactions; however, experimental confirmation and quantification of the acceleration factor have been lacking. Here, a system to investigate localized DNA hybridization reactions on a nanoscale substrate is presented. The system consists of six metastable DNA hairpins that are tethered to a long DNA track. The localized DNA hybridization reaction of the proposed system is triggered by a DNA strand which initiates the subsequent self-assembly. Fluorescence kinetics indicates that the half-time completion of a localized DNA hybridization chain reaction is six times faster than the same reaction in the absence of the substrate. The proposed system provides one of the first known quantification of the speed-up of DNA hybridization reactions due to the locality effect.
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Affiliation(s)
- Hieu Bui
- Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA
| | - Vincent Miao
- Department of Biomedical Engineering, Duke University, 101 Science Drive, Campus Box, 90281, 27708, USA
| | - Sudhanshu Garg
- Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA
| | - Reem Mokhtar
- Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA
| | - Tianqi Song
- Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA
| | - John Reif
- Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA
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50
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Abstract
Multihelical DNA bundles could enhance the functionality of nanomaterials and serve as model architectures to mimic protein filaments on the molecular and cellular level. We report the self-assembly of micrometer-sized helical DNA nanotubes with widely controllable helical diameters ranging from tens of nanometers to a few micrometers. Nanoscale helical shapes of DNA tile tubes (4-, 6-, 8-, 10-, and 12-helix tile tubes) are achieved by introducing discrete amounts of bending and twist through base pair insertions and/or deletions. Microscale helical diameters, which require smaller amounts of twist and bending, are achieved by controlling the intrinsic "supertwist" present in tile tubes with uneven number of helices (11-, 13-, and 15-helix tile tubes). Supertwist fine-tuning also allows us to produce helical nanotubes of defined chirality.
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Affiliation(s)
- Alexander Mario Maier
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Wooli Bae
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Daniel Schiffels
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Johannes Friedrich Emmerig
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Maximilian Schiff
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität (LMU) , Geschwister-Scholl-Platz 1, 80539 München, Germany
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