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Lhermitte JR, Tian C, Stein A, Rahman A, Zhang Y, Wiegart L, Fluerasu A, Gang O, Yager KG. Robust X-ray angular correlations for the study of meso-structures. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717003946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
As self-assembling nanomaterials become more sophisticated, it is becoming increasingly important to measure the structural order of finite-sized assemblies of nano-objects. These mesoscale clusters represent an acute challenge to conventional structural probes, owing to the range of implicated size scales (10 nm to several micrometres), the weak scattering signal and the dynamic nature of meso-clusters in native solution environments. The high X-ray flux and coherence of modern synchrotrons present an opportunity to extract structural information from these challenging systems, but conventional ensemble X-ray scattering averages out crucial information about local particle configurations. Conversely, a single meso-cluster scatters too weakly to recover the full diffraction pattern. Using X-ray angular cross-correlation analysis, it is possible to combine multiple noisy measurements to obtain robust structural information. This paper explores the key theoretical limits and experimental challenges that constrain the application of these methods to probing structural order in real nanomaterials. A metric is presented to quantify the signal-to-noise ratio of angular correlations, and it is used to identify several experimental artifacts that arise. In particular, it is found that background scattering, data masking and inter-cluster interference profoundly affect the quality of correlation analyses. A robust workflow is demonstrated for mitigating these effects and extracting reliable angular correlations from realistic experimental data.
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52
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Li Y, Mao C, Deng Z. Supramolecular Wireframe DNA Polyhedra: Assembly and Applications. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yulin Li
- School of Chemistry and Chemical Engineering; Hefei University of Technology, 193 Tunxi Road; Hefei Anhui 230009 China
| | - Chengde Mao
- Department of Chemistry; Purdue University; West Lafayette Indiana 47907 USA
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science; University of Science and Technology of China; Hefei Anhui 230026 China
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53
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Shen C, Lan X, Zhu C, Zhang W, Wang L, Wang Q. Spiral Patterning of Au Nanoparticles on Au Nanorod Surface to Form Chiral AuNR@AuNP Helical Superstructures Templated by DNA Origami. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29. [PMID: 28218431 DOI: 10.1002/adma.201606533] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/20/2017] [Indexed: 05/17/2023]
Abstract
Plasmonic motifs with precise surface recognition sites are crucial for assembling defined nanostructures with novel functionalities and properties. In this work, a unique and effective strategy is successfully developed to pattern DNA recognition sites in a helical arrangement around a gold nanorod (AuNR), and a new set of heterogeneous AuNR@AuNP plasmonic helices is fabricated by attaching complementary-DNA-modified gold nanoparticles (AuNPs) to the predesigned sites on the AuNR surface. AuNR is first assembled to one side of a bifacial rectangular DNA origami, where eight groups of capture strands are selectively patterned on the other side. The subsequently added link strands make the rectangular DNA origami roll up around the AuNR into a tubular shape, therefore giving birth to a chiral patterning of DNA recognition sites on the surface of AuNR. Following the hybridization with the AuNPs capped with the complementary strands to the capture strands on the DNA origami, left-handed and right-handed AuNR@AuNP helical superstructures are precisely formed by tuning the pattern of the recognition sites on the AuNR surface. Our strategy of nanoparticle surface patterning innovatively realizes hierarchical self-assembly of plasmonic superstructures with tunable chiroptical responses, and will certainly broaden the horizon of bottom-up construction of other functional nanoarchitectures with growing complexity.
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Affiliation(s)
- Chenqi Shen
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Xiang Lan
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Chenggan Zhu
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Wei Zhang
- Institute of Applied Physics and Computational Mathematics, Beijing, 100088, China
| | - Leyu Wang
- College of Science, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interfaces, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Shanghai, 200031, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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54
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Joshi H, Bhatia D, Krishnan Y, Maiti PK. Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations. NANOSCALE 2017; 9:4467-4477. [PMID: 28304019 DOI: 10.1039/c6nr08036g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics (MD) simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (Rg), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNPs) encapsulated within DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra compared to empty icosahedra. This is consistent with the experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully position DNA polyhedra as targetable nanocapsules for payload delivery. These insights can be exploited for precise molecular display for diverse biological applications.
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Affiliation(s)
- Himanshu Joshi
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Dhiraj Bhatia
- Institut Curie, PSL Research University, Chemical Biology of Membranes and Therapeutic Delivery unit, INSERM, U 1143, CNRS, UMR 3666, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Yamuna Krishnan
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA and Grossman Institute of Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, Illinois 60637, USA
| | - Prabal K Maiti
- Centre for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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55
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Khisamutdinov EF, Jasinski DL, Li H, Zhang K, Chiu W, Guo P. Fabrication of RNA 3D Nanoprisms for Loading and Protection of Small RNAs and Model Drugs. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:10079-10087. [PMID: 27758001 PMCID: PMC5224701 DOI: 10.1002/adma.201603180] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/30/2016] [Indexed: 05/22/2023]
Abstract
Constructing containers with defined shape and size to load and protect therapeutics and subsequently control their release in the human body has long been a dream. The fabrication of 3D RNA prisms, characterized by atomic force microscopy, cryo-electron microscopy, dynamic light scattering, and polyacrylamide gel electrophoresis, is reported for the loading and protection of small molecules, proteins, small RNA molecules, and their controlled release.
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Affiliation(s)
- Emil F. Khisamutdinov
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Daniel L. Jasinski
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Hui Li
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - 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
| | - Peixuan Guo
- Nanobiotechnology Center, Markey Cancer Center, and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA
- College of Pharmacy, Department of Physiology & Cell Biology, College of Medicine, and Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
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56
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Wu XR, Wu CW, Zhang C. Discrete DNA three-dimensional nanostructures: the synthesis and applications. CHINESE JOURNAL OF POLYMER SCIENCE 2016. [DOI: 10.1007/s10118-017-1871-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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57
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Pan T, Song W, Gao H, Li T, Cao X, Zhong S, Wang Y. miR-29b-Loaded Gold Nanoparticles Targeting to the Endoplasmic Reticulum for Synergistic Promotion of Osteogenic Differentiation. ACS APPLIED MATERIALS & INTERFACES 2016; 8:19217-19227. [PMID: 27399270 DOI: 10.1021/acsami.6b02969] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Precise control of stem cells, such as human bone marrow-derived mesenchymal stem cells (hMSCs), is critical for the development of effective cellular therapies for tissue engineering and regeneration medicine. Emerging evidence suggests that several miRNAs act as key regulators of diverse biological processes, including differentiation of various stem cells. In this study, we have described a delivery system for miR-29b using PEI-capped gold nanoparticles (AuNPs) to synergistically promote osteoblastic differentiation. The cell proliferation assay revealed that AuNPs and AuNPs/miR-29b exert negligible cytotoxicity to hMSCs and MC3T3-E1 cells. With the assistance of AuNPs as a delivery vector, miR-29b could efficiently enter the cytoplasm and regulate osteogenesis. AuNPs/miR-29b more effectively promoted osteoblast differentiation and mineralization through induced the expression of osteogenesis genes (RUNX2, OPN, OCN, ALP) for the long-term, compared to the widely used commercial transfection reagent, Lipofectamine. With no obvious cytotoxicity, PEI-capped AuNPs showed great potential as an adequate miRNA vector for osteogenesis differentiation. Interestingly, we observed loading of AuNPs as well as AuNPs/miR-29b into the lumen of the endoplasmic reticulum (ER). Our findings collectively suggest that AuNPs, together with miR-29b, exert a synergistic promotory effect on osteogenic differentiation of hMSCs and MC3T3-E1 cells.
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Affiliation(s)
- Ting Pan
- Department of Biomedical Engineering, School of Materials Science and Engineering, South China University of Technology , Guangzhou, 510641, China
- National Engineering Research Center for Tissue Restoration and Reconstruction , Guangzhou, 510006, China
| | - Wenjing Song
- National Engineering Research Center for Tissue Restoration and Reconstruction , Guangzhou, 510006, China
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou, 510006, China
| | - Huichang Gao
- Department of Biomedical Engineering, School of Materials Science and Engineering, South China University of Technology , Guangzhou, 510641, China
- National Engineering Research Center for Tissue Restoration and Reconstruction , Guangzhou, 510006, China
| | - Tianjie Li
- Department of Biomedical Engineering, School of Materials Science and Engineering, South China University of Technology , Guangzhou, 510641, China
- National Engineering Research Center for Tissue Restoration and Reconstruction , Guangzhou, 510006, China
| | - Xiaodong Cao
- Department of Biomedical Engineering, School of Materials Science and Engineering, South China University of Technology , Guangzhou, 510641, China
- National Engineering Research Center for Tissue Restoration and Reconstruction , Guangzhou, 510006, China
| | - Shizhen Zhong
- School of Basic Medical Sciences, Southern Medical University , Guangzhou 510515, People's Republic of China
| | - Yingjun Wang
- Department of Biomedical Engineering, School of Materials Science and Engineering, South China University of Technology , Guangzhou, 510641, China
- National Engineering Research Center for Tissue Restoration and Reconstruction , Guangzhou, 510006, China
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58
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Stewart PL. Cryo-electron microscopy and cryo-electron tomography of nanoparticles. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [DOI: 10.1002/wnan.1417] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/11/2016] [Accepted: 06/02/2016] [Indexed: 01/04/2023]
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59
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Liu M, Fu J, Qi X, Wootten S, Woodbury NW, Liu Y, Yan H. A Three-Enzyme Pathway with an Optimised Geometric Arrangement to Facilitate Substrate Transfer. Chembiochem 2016; 17:1097-101. [DOI: 10.1002/cbic.201600103] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Minghui Liu
- Biodesign Center for Molecular Design and Biomimetics; The Biodesign Institute; Arizona State University; 1001 S. McAllister Avenue Tempe AZ 85281 USA
| | - Jinglin Fu
- Department of Chemistry; Center for Computational and Integrative Biology; Rutgers University-Camden; 315 Penn Street Camden NJ 08102 USA
| | - Xiaodong Qi
- Biodesign Center for Molecular Design and Biomimetics; The Biodesign Institute; Arizona State University; 1001 S. McAllister Avenue Tempe AZ 85281 USA
| | - Shaun Wootten
- Biodesign Center for Molecular Design and Biomimetics; The Biodesign Institute; Arizona State University; 1001 S. McAllister Avenue Tempe AZ 85281 USA
| | - Neal W. Woodbury
- Biodesign Center for Innovations in Medicine; The Biodesign Institute; Arizona State University; 1001 S McAllister Avenue Tempe AZ 85281 USA
- School of Molecular Sciences; Arizona State University; Physical Sciences Building Room D-102 P. O. Box 871604 Tempe AZ 85287-1604 USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics; The Biodesign Institute; Arizona State University; 1001 S. McAllister Avenue Tempe AZ 85281 USA
- School of Molecular Sciences; Arizona State University; Physical Sciences Building Room D-102 P. O. Box 871604 Tempe AZ 85287-1604 USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics; The Biodesign Institute; Arizona State University; 1001 S. McAllister Avenue Tempe AZ 85281 USA
- School of Molecular Sciences; Arizona State University; Physical Sciences Building Room D-102 P. O. Box 871604 Tempe AZ 85287-1604 USA
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60
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Liu W, Tagawa M, Xin HL, Wang T, Emamy H, Li H, Yager KG, Starr FW, Tkachenko AV, Gang O. Diamond family of nanoparticle superlattices. Science 2016; 351:582-6. [PMID: 26912698 DOI: 10.1126/science.aad2080] [Citation(s) in RCA: 255] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Diamond lattices formed by atomic or colloidal elements exhibit remarkable functional properties. However, building such structures via self-assembly has proven to be challenging because of the low packing fraction, sensitivity to bond orientation, and local heterogeneity. We report a strategy for creating a diamond superlattice of nano-objects via self-assembly and demonstrate its experimental realization by assembling two variant diamond lattices, one with and one without atomic analogs. Our approach relies on the association between anisotropic particles with well-defined tetravalent binding topology and isotropic particles. The constrained packing of triangular binding footprints of truncated tetrahedra on a sphere defines a unique three-dimensional lattice. Hence, the diamond self-assembly problem is solved via its mapping onto two-dimensional triangular packing on the surface of isotropic spherical particles.
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Affiliation(s)
- Wenyan Liu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Miho Tagawa
- Department of Materials Science and Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Huolin L Xin
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Tong Wang
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hamed Emamy
- Department of Physics, Wesleyan University, Middletown, CT 06459, USA
| | - Huilin Li
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA. Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kevin G Yager
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Francis W Starr
- Department of Physics, Wesleyan University, Middletown, CT 06459, USA
| | - Alexei V Tkachenko
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA.
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61
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Matthies M, Agarwal NP, Schmidt TL. Design and Synthesis of Triangulated DNA Origami Trusses. NANO LETTERS 2016; 16:2108-2113. [PMID: 26883285 DOI: 10.1021/acs.nanolett.6b00381] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA nanotechnology offers unique control over matter on the nanoscale. Here, we extend the DNA origami method to cover a range of wireframe truss structures composed of equilateral triangles, which use less material per volume than standard multiple-helix bundles. From a flat truss design, we folded tetrahedral, octahedral, or irregular dodecahedral trusses by exchanging few connector strands. Other than standard origami designs, the trusses can be folded in low-salt buffers that make them compatible with cell culture buffers. The structures also have defined cavities that may in the future be used to precisely position functional elements such as metallic nanoparticles or enzymes. Our graph routing program and a simple design pipeline will enable other laboratories to make use of this valuable and potent new construction principle for DNA-based nanoengineering.
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Affiliation(s)
- Michael Matthies
- Cluster of Excellence Center for Advancing Electronics Dresden (cfaed), TU Dresden , 01062 Dresden, Germany
| | - Nayan P Agarwal
- Cluster of Excellence Center for Advancing Electronics Dresden (cfaed), TU Dresden , 01062 Dresden, Germany
| | - Thorsten L Schmidt
- Cluster of Excellence Center for Advancing Electronics Dresden (cfaed), TU Dresden , 01062 Dresden, Germany
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62
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Zhang L, Zhang P, Zhao Q, Zhang Y, Cao L, Luan Y. Doxorubicin-loaded polypeptide nanorods based on electrostatic interactions for cancer therapy. J Colloid Interface Sci 2015; 464:126-36. [PMID: 26609932 DOI: 10.1016/j.jcis.2015.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 02/06/2023]
Abstract
An amphiphilic anionic polypeptide, methoxypolyethylene glycol-poly (glutamic acid) (mPEG-PGA), was synthesized, characterized and evaluated as a nanocarrier for the cationic anticancer drug doxorubicin hydrochloride (DOX·HCl). The complex self-assembled into nanorods in aqueous solutions via electrostatic interactions and exhibited a superior drug loading content (50.8%) and drug loading efficiency (90.2%). The average major axis of the drug-loaded nanorods was approximately 300nm, as determined by transmission electron microscopy. An in vitro release assay showed that drug-loaded nanorods exhibited pH-sensitivity and sustained release. Haemolysis assays demonstrated that the polypeptide was haemocompatible, and the polypeptide drug carrier significantly reduced the haemolysis ratio of DOX·HCl. The pharmacokinetics study showed that DOX-loaded nanorods significantly prolonged the resident time in blood. An in vitro cytotoxicity study and cellular uptake assays demonstrated that the DOX-loaded nanorods resulted in higher cell proliferation inhibition and a higher level of tumour cell uptake in A549 cells than with free DOX·HCl. The prolonged circulation and enhanced antitumor efficacy of DOX-loaded nanorods shows promise for efficient cancer chemotherapy.
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Affiliation(s)
- Longlong Zhang
- School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems, Shandong University, 44 West Wenhua Road, Jinan, Shandong Province 250012, PR China.
| | - Pei Zhang
- School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems, Shandong University, 44 West Wenhua Road, Jinan, Shandong Province 250012, PR China.
| | - Qingyun Zhao
- Hospital of Traditional Chinese Medicine of Jimo, Shandong Province, PR China.
| | - Yongchun Zhang
- School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems, Shandong University, 44 West Wenhua Road, Jinan, Shandong Province 250012, PR China.
| | - Longqiao Cao
- Jining First People's Hospital, Shandong Province, PR China.
| | - Yuxia Luan
- School of Pharmaceutical Science and Center for Pharmaceutical Research & Drug Delivery Systems, Shandong University, 44 West Wenhua Road, Jinan, Shandong Province 250012, PR China.
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63
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Yu G, Yan R, Zhang C, Mao C, Jiang W. Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5157-5163. [PMID: 26179326 DOI: 10.1002/smll.201500531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/13/2015] [Indexed: 06/04/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Chuan Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, 240 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
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64
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Tian Y, Wang T, Liu W, Xin HL, Li H, Ke Y, Shih WM, Gang O. Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames. NATURE NANOTECHNOLOGY 2015; 10:637-44. [PMID: 26005999 PMCID: PMC5282466 DOI: 10.1038/nnano.2015.105] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 04/20/2015] [Indexed: 05/17/2023]
Abstract
Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we report a strategy for assembling three-dimensional nanoparticle clusters that uses a molecular frame designed with encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA frame and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be assembled with designed particle arrangements.
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Affiliation(s)
- Ye Tian
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Tong Wang
- Biosciences Department, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Wenyan Liu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Huolin L Xin
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Huilin Li
- 1] Biosciences Department, Brookhaven National Laboratory, Upton, New York 11973, USA [2] Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5213, USA
| | - Yonggang Ke
- 1] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [3] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - William M Shih
- 1] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [3] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
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65
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Williford JM, Santos JL, Shyam R, Mao HQ. Shape Control in Engineering of Polymeric Nanoparticles for Therapeutic Delivery. Biomater Sci 2015; 3:894-907. [PMID: 26146550 PMCID: PMC4486355 DOI: 10.1039/c5bm00006h] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nanoparticle-mediated delivery of therapeutics holds great potential for the diagnosis and treatment of a wide range of diseases. Significant advances have been made in the design of new polymeric nanoparticle carriers through modulation of their physical and chemical structures and biophysical properties. Nanoparticle shape has been increasingly proposed as an important attribute dictating their transport properties in biological milieu. In this review, we highlight three major methods for preparing polymeric nanoparticles that allow for exquisite control of particle shape. Special attention is given to various approaches to controlling nanoparticle shape by tuning copolymer structural parameters and assembly conditions. This review also provides comparisons of these methods in terms of their unique capabilities, materials choices, and specific delivery cargos, and summarizes the biological effects of nanoparticle shape on transport properties at the tissue and cellular levels.
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Affiliation(s)
- John-Michael Williford
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
| | - Jose Luis Santos
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Rishab Shyam
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
| | - Hai-Quan Mao
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21287
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD 21218
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66
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Lu F, Yager KG, Zhang Y, Xin H, Gang O. Superlattices assembled through shape-induced directional binding. Nat Commun 2015; 6:6912. [PMID: 25903309 PMCID: PMC4423233 DOI: 10.1038/ncomms7912] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/12/2015] [Indexed: 01/18/2023] Open
Abstract
Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks--cubes and octahedrons--when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.
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Affiliation(s)
- Fang Lu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Kevin G. Yager
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Yugang Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Huolin Xin
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA
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67
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Li Y, Liu Z, Yu G, Jiang W, Mao C. Self-assembly of molecule-like nanoparticle clusters directed by DNA nanocages. J Am Chem Soc 2015; 137:4320-3. [PMID: 25823595 DOI: 10.1021/jacs.5b01196] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Analogous to the atom-molecule relationship, nanoparticle (NP) clusters (or NP-molecules) with defined compositions and directional bonds could potentially integrate the properties of the component individual NPs, leading to emergent properties. Despite extensive efforts in this direction, no general approach is available for assembly of such NP-molecules. Here we report a general method for building this type of structures by encapsulating NPs into self-assembled DNA polyhedral wireframe nanocages, which serve as guiding agents for further assembly. As a demonstration, a series of NP-molecules have been assembled and validated. Such NP-molecules will, we believe, pave a way to explore new nanomaterials with emergent functions/properties that are related to, but do not belong to the individual component nanoparticles.
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Affiliation(s)
- Yulin Li
- †Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhiyu Liu
- †Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Guimei Yu
- ‡Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Wen Jiang
- ‡Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chengde Mao
- †Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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68
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Li Y, Tian C, Liu Z, Jiang W, Mao C. Structural Transformation: Assembly of an Otherwise Inaccessible DNA Nanocage. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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69
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Li Y, Tian C, Liu Z, Jiang W, Mao C. Structural Transformation: Assembly of an Otherwise Inaccessible DNA Nanocage. Angew Chem Int Ed Engl 2015; 54:5990-3. [DOI: 10.1002/anie.201500755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Indexed: 11/10/2022]
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70
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Shaikh AJ, Rabbani F, Sherazi TA, Iqbal Z, Mir S, Shahzad SA. Binding strength of porphyrin-gold nanoparticle hybrids based on number and type of linker moieties and a simple method to calculate inner filter effects of gold nanoparticles using fluorescence spectroscopy. J Phys Chem A 2015; 119:1108-16. [PMID: 25611751 DOI: 10.1021/jp510924n] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Gold nanoparticle-porphyrin assemblies were formed by binding functionalized porphyrins to gold nanoparticles (Au-NPs). Spectroscopic properties of hybrids and binding strength of porphyrins to Au-NPs were observed based on number and type of linker moieties using fluorescence spectroscopy. Binding appears to be dependent on number rather than type of linker moieties present on the porphyrin molecules, as tetraaminophenyl porphyrin shows the highest binding among the molecules we studied and causes agglomeration of nanoparticles due to presence of four linker groups. The inner filter effects of Au-NPs are considerably high due to their high extinction coefficient and cause large errors in the evaluation of quenching efficiencies. We have described a very simple method to calculate the inner filter effects of Au-NPs by first loading them with porphyrins and then replacing them with nonfluorescent ligands. The difference in the fluorescence of unbound porphyrins in the presence and absence of Au-NPs describes their inner filter effects.
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Affiliation(s)
- Ahson J Shaikh
- Department of Chemistry, COMSATS Institute of Information Technology , Abbottabad-22060, Pakistan
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71
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Zhang ZM, Gao PC, Wang ZF, Sun BW, Jiang Y. DNA-caged gold nanoparticles for controlled release of doxorubicin triggered by a DNA enzyme and pH. Chem Commun (Camb) 2015; 51:12996-9. [DOI: 10.1039/c5cc05164a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA polyhedron-caged AuNPs were self-assembled using four-point-star DNAs, with three strands hybridizing to each other and the fourth strand attaching to the AuNPs. The caged AuNPs can act as doxorubicin nanocarriers; a DNA enzyme and pH can trigger controlled release.
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Affiliation(s)
- Zi-Mou Zhang
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- P. R. China
| | - Peng-Cheng Gao
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- P. R. China
| | - Zhi-Fei Wang
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- P. R. China
| | - Bai-Wang Sun
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- P. R. China
| | - Yong Jiang
- School of Chemistry and Chemical Engineering
- Southeast University
- Nanjing
- P. R. China
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72
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Takenaka T, Endo M, Suzuki Y, Yang Y, Emura T, Hidaka K, Kato T, Miyata T, Namba K, Sugiyama H. Photoresponsive DNA nanocapsule having an open/close system for capture and release of nanomaterials. Chemistry 2014; 20:14951-4. [PMID: 25223393 DOI: 10.1002/chem.201404757] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Indexed: 11/10/2022]
Abstract
A photofunctionalized square bipyramidal DNA nanocapsule (NC) was designed and prepared for the creation of a nanomaterial carrier. Photocontrollable open/close system and toehold system were introduced into the NC for the inclusion and release of a gold nanoparticle (AuNP) by photoirradiation and strand displacement. The reversible open and closed states were examined by gel electrophoresis and atomic force microscopy (AFM), and the open behavior was directly observed by high-speed AFM. The encapsulation of the DNA-modified AuNP within the NC was carried out by hybridization of a specific DNA strand (capture strand), and the release of the AuNP was examined by addition of toehold-containing complementary DNA strand (release strand). The release of the AuNP from the NC was achieved by the opening of the NC and subsequent strand displacement.
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Affiliation(s)
- Tomohiro Takenaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan)
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73
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Tetrahedron DNA dendrimers and their encapsulation of gold nanoparticles. Bioorg Med Chem 2014; 22:4391-4. [DOI: 10.1016/j.bmc.2014.05.062] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/20/2014] [Accepted: 05/28/2014] [Indexed: 11/20/2022]
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