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Hincapie R, Bhattacharya S, Keshavarz-Joud P, Chapman AP, Crooke SN, Finn MG. Preparation and Biological Properties of Oligonucleotide-Functionalized Virus-like Particles. Biomacromolecules 2023. [PMID: 37257068 DOI: 10.1021/acs.biomac.3c00178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Oligonucleotides are powerful molecules for programming function and assembly. When arrayed on nanoparticle scaffolds in high density, the resulting molecules, spherical nucleic acids (SNAs), become imbued with unique properties. We used the copper-catalyzed azide-alkyne cycloaddition to graft oligonucleotides on Qβ virus-like particles to see if such structures also gain SNA-like behavior. Copper-binding ligands were shown to promote the click reaction without degrading oligonucleotide substrates. Reactions were first optimized with a small-molecule fluorogenic reporter and were then applied to the more challenging synthesis of polyvalent protein nanoparticle-oligonucleotide conjugates. The resulting particles exhibited the enhanced cellular uptake and protection from nuclease-mediated oligonucleotide cleavage characteristic of SNAs, had similar residence time in the liver relative to unmodified particles, and were somewhat shielded from immune recognition, resulting in nearly 10-fold lower antibody titers relative to unmodified particles. Oligonucleotide-functionalized virus-like particles thus provide an interesting option for protein nanoparticle-mediated delivery of functional molecules.
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2
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Zhang X, Zeng R, Zhang T, Lv C, Zang J, Zhao G. Spatiotemporal control over 3D protein nanocage superlattices for the hierarchical encapsulation and release of different cargo molecules. J Mater Chem B 2022; 10:9968-9973. [PMID: 36472186 DOI: 10.1039/d2tb01961b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Taking inspiration from Nature, we have constructed a two-compartment system based on 3D ferritin nanocage superlattices, the self-assembly behavior of which can be spatiotemporally controlled using two designed switches. One pH switch regulates the assembly of the ferritin subunit into its shell-like structure, whereas the other metal switch is responsible for assembly of the 3D superlattices from ferritin nanocages as building blocks. Consequently, this system holds great promise for the hierarchical encapsulation and release of two different cargo molecules.
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Affiliation(s)
- Xiaorong Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Ruiqi Zeng
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.
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3
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Sato M. Two-Dimensional Structures Formed by Triblock Patchy Particles with Two Different Patches. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15404-15412. [PMID: 36446728 DOI: 10.1021/acs.langmuir.2c02699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Two-dimensional structures formed by spherical triblock patchy particles are examined by performing Monte Carlo simulations. In the model, the triblock patchy particles have two different types of patches at the polar positions. The patch sizes are different from each other, and the attractive interaction acts only between the same types of patches. The particles translate on a flat plane and rotate three-dimensionally. When varying the two patch sizes, the pressure, and interaction energy, various structures are observed. When the difference between two patch sizes is small, kagome lattices, hexagonal structures, and two-dimensional dodecagonal quasi-crystal structures are observed. When the difference between two patch sizes is large, chain-like structures are created. With lower temperature, sparse structures such as ring-like structures form.
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Affiliation(s)
- Masahide Sato
- Emerging Media Initiative, Kanazawa University, Kanazawa 920-1192, Japan
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4
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McNeale D, Dashti N, Cheah LC, Sainsbury F. Protein cargo encapsulation by
virus‐like
particles: Strategies and applications. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 15:e1869. [PMID: 36345849 DOI: 10.1002/wnan.1869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022]
Abstract
Viruses and the recombinant protein cages assembled from their structural proteins, known as virus-like particles (VLPs), have gained wide interest as tools in biotechnology and nanotechnology. Detailed structural information and their amenability to genetic and chemical modification make them attractive systems for further engineering. This review describes the range of non-enveloped viruses that have been co-opted for heterologous protein cargo encapsulation and the strategies that have been developed to drive encapsulation. Spherical capsids of a range of sizes have been used as platforms for protein cargo encapsulation. Various approaches, based on native and non-native interactions between the cargo proteins and inner surface of VLP capsids, have been devised to drive encapsulation. Here, we outline the evolution of these approaches, discussing their benefits and limitations. Like the viruses from which they are derived, VLPs are of interest in both biomedical and materials applications. The encapsulation of protein cargo inside VLPs leads to numerous uses in both fundamental and applied biocatalysis and biomedicine, some of which are discussed herein. The applied science of protein-encapsulating VLPs is emerging as a research field with great potential. Developments in loading control, higher order assembly, and capsid optimization are poised to realize this potential in the near future. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Donna McNeale
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery Griffith University Nathan Queensland Australia
| | - Noor Dashti
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland St Lucia Queensland Australia
| | - Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland St Lucia Queensland Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery Griffith University Nathan Queensland Australia
- Australian Institute for Bioengineering and Nanotechnology The University of Queensland St Lucia Queensland Australia
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5
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Uchida M, Brunk NE, Hewagama ND, Lee B, Prevelige PE, Jadhao V, Douglas T. Multilayered Ordered Protein Arrays Self-Assembled from a Mixed Population of Virus-like Particles. ACS NANO 2022; 16:7662-7673. [PMID: 35549153 DOI: 10.1021/acsnano.1c11272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biology shows many examples of spatially controlled assembly of cells and biomacromolecules into hierarchically organized structures, to which many of the complex biological functions are attributed. While such biological structures have inspired the design of synthetic materials, it is still a great challenge to control the spatial arrangement of individual building blocks when assembling multiple types of components into bulk materials. Here, we report self-assembly of multilayered, ordered protein arrays from mixed populations of virus-like particles (VLPs). We systematically tuned the magnitude of the surface charge of the VLPs via mutagenesis to prepare four different types of VLPs for mixing. A mixture of up to four types of VLPs selectively assembled into higher-order structures in the presence of oppositely charged dendrimers during a gradual lowering of the ionic strength of the solution. The assembly resulted in the formation of three-dimensional ordered VLP arrays with up to four distinct layers including a central core, with each layer comprising a single type of VLP. A coarse-grained computational model was developed and simulated using molecular dynamics to probe the formation of the multilayered, core-shell structure. Our findings establish a simple and versatile bottom-up strategy to synthesize multilayered, ordered materials by controlling the spatial arrangement of multiple types of nanoscale building blocks in a one-pot fabrication.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry and Biochemistry, California State University, Fresno, 2555 E. San Ramon Avenue, Fresno, California 93740, United States
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Nicholas E Brunk
- Intelligent Systems Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, Indiana 47408, United States
- Wolfram Research, 100 Trade Center Drive, Champaign, Illinois 61820, United States
- VeriSIM Life Inc., 1 Sansome Street, Suite 3500, San Francisco, California 94104, United States
| | - Nathasha D Hewagama
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Vikram Jadhao
- Intelligent Systems Engineering, Indiana University, 700 N. Woodlawn Avenue, Bloomington, Indiana 47408, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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6
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Uvarov DY, Gorbatov SA, Kolokolova MK, Kozlov MA, Kolotirkina NG, Zavarzin IV, Goze C, Denat F, Volkova YA. A Straightforward Strategy for the Preparation of Diverse BODIPY Functionalized with Polyamines and Polyoxyethylenes**. ChemistrySelect 2022. [DOI: 10.1002/slct.202104210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Denis Y. Uvarov
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky prosp. Moscow 119991, Russia
| | - Sergey A. Gorbatov
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky prosp. Moscow 119991, Russia
| | - Marya K. Kolokolova
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky prosp. Moscow 119991, Russia
| | - Mikhail A. Kozlov
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky prosp. Moscow 119991, Russia
| | - Natalya G. Kolotirkina
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky prosp. Moscow 119991, Russia
| | - Igor V. Zavarzin
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky prosp. Moscow 119991, Russia
| | - Christine Goze
- Institut de Chimie Moléculaire de l'Université de Bourgogne ICMUB UMR CNRS 6302 Université Bourgogne Franche-Comté, 9 avenue Alain Savary 21078 Dijon France
| | - Franck Denat
- Institut de Chimie Moléculaire de l'Université de Bourgogne ICMUB UMR CNRS 6302 Université Bourgogne Franche-Comté, 9 avenue Alain Savary 21078 Dijon France
| | - Yulia A. Volkova
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, 47 Leninsky prosp. Moscow 119991, Russia
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7
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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8
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Dehne H, Reitenbach A, Bausch AR. Reversible and spatiotemporal control of colloidal structure formation. Nat Commun 2021; 12:6811. [PMID: 34815410 PMCID: PMC8611085 DOI: 10.1038/s41467-021-27016-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022] Open
Abstract
Tuning colloidal structure formation is a powerful approach to building functional materials, as a wide range of optical and viscoelastic properties can be accessed by the choice of individual building blocks and their interactions. Precise control is achieved by DNA specificity, depletion forces, or geometric constraints and results in a variety of complex structures. Due to the lack of control and reversibility of the interactions, an autonomous oscillating system on a mesoscale without external driving was not feasible until now. Here, we show that tunable DNA reaction circuits controlling linker strand concentrations can drive the dynamic and fully reversible assembly of DNA-functionalized micron-sized particles. The versatility of this approach is demonstrated by programming colloidal interactions in sequential and spatial order to obtain an oscillatory structure formation process on a mesoscopic scale. The experimental results represent an approach for the development of active materials by using DNA reaction networks to scale up the dynamic control of colloidal self-organization.
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Affiliation(s)
- H Dehne
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27), Physics Departement, Technische Universität München, D-85748, Garching, Germany
| | - A Reitenbach
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27), Physics Departement, Technische Universität München, D-85748, Garching, Germany
| | - A R Bausch
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27), Physics Departement, Technische Universität München, D-85748, Garching, Germany.
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9
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Selivanovitch E, Uchida M, Lee B, Douglas T. Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover. ACS NANO 2021; 15:15687-15699. [PMID: 34473481 PMCID: PMC9136710 DOI: 10.1021/acsnano.1c05004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). The highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.
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Affiliation(s)
- Ekaterina Selivanovitch
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry and Biochemistry, California State University Fresno, Fresno, California 93740, Unites States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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10
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Chen G, Huang S, Shen Y, Kou X, Ma X, Huang S, Tong Q, Ma K, Chen W, Wang P, Shen J, Zhu F, Ouyang G. Protein-directed, hydrogen-bonded biohybrid framework. Chem 2021. [DOI: 10.1016/j.chempr.2021.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Sato M. Effect of the Interaction Length on Clusters Formed by Spherical One-Patch Particles on Flat Planes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:4213-4221. [PMID: 33780624 DOI: 10.1021/acs.langmuir.1c00102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Considering that one-patch particles rotate three-dimensionally and translate on a two-dimensional flat plane, I performed isothermal-isochoric Monte Carlo simulations to study how two-dimensional self-assemblies formed by spherical patchy particles depending on the interaction length and patch area. As the interaction potential between one-patch particles, the Kern-Frenkel (KF) potential is used in the simulations. With increasing patch area, the shape of the most numerous clusters changes from dimers to island-like clusters with a square lattice via triangular trimers, square tetramers, and chain-like clusters when the interaction length is as long as the particle radius. With a longer interaction length, other shapes of polygonal clusters such as another type of square tetramers, two types of pentagonal pentamers, hexagonal hexamers, and hexagonal heptamers also form.
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Affiliation(s)
- Masahide Sato
- Information Media Center, Kanazawa University, Kanazawa 920-1192, Japan
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12
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He L, Mu J, Gang O, Chen X. Rationally Programming Nanomaterials with DNA for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003775. [PMID: 33898180 PMCID: PMC8061415 DOI: 10.1002/advs.202003775] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/23/2020] [Indexed: 05/05/2023]
Abstract
DNA is not only a carrier of genetic information, but also a versatile structural tool for the engineering and self-assembling of nanostructures. In this regard, the DNA template has dramatically enhanced the scalability, programmability, and functionality of the self-assembled DNA nanostructures. These capabilities provide opportunities for a wide range of biomedical applications in biosensing, bioimaging, drug delivery, and disease therapy. In this review, the importance and advantages of DNA for programming and fabricating of DNA nanostructures are first highlighted. The recent progress in design and construction of DNA nanostructures are then summarized, including DNA conjugated nanoparticle systems, DNA-based clusters and extended organizations, and DNA origami-templated assemblies. An overview on biomedical applications of the self-assembled DNA nanostructures is provided. Finally, the conclusion and perspectives on the self-assembled DNA nanostructures are presented.
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Affiliation(s)
- Liangcan He
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
| | - Jing Mu
- Institute of Precision MedicinePeking University Shenzhen HospitalShenzhen518036China
| | - Oleg Gang
- Department of Chemical Engineering and Department of Applied Physics and Applied MathematicsColumbia UniversityNew YorkNY10027USA
- Center for Functional NanomaterialsBrookhaven National LaboratoryUptonNY11973USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of EngineeringNational University of SingaporeSingapore117597Singapore
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13
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Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:molecules26061502. [PMID: 33801952 PMCID: PMC8000633 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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14
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Sato M. Effect of Patch Area and Interaction Length on Clusters and Structures Formed by One-Patch Particles in Thin Systems. ACS OMEGA 2020; 5:28812-28822. [PMID: 33195934 PMCID: PMC7659161 DOI: 10.1021/acsomega.0c04159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Assuming that the interaction between particles is given by the Kern-Frenkel potential, Monte Carlo simulations are performed to study the clusters and structures formed by one-patch particles in a thin space between two parallel walls. In isothermal-isochoric systems with a short interaction length, tetrahedral tetramers, octahedral hexamers, and pentagonal dipyramidal heptamers are created with increasing patch area. In isothermal-isobaric systems, the double layers of a triangular lattice, which is the (111) face of the face-centered cubic (fcc) lattice, form when the pressure is high. For a long interaction length, a different type of cluster, trigonal prismatic hexamers, is created. The structures in the double layers also changed as follows: a simple hexagonal lattice or square lattice, which is the (100) face of the fcc structure, is created in isothermal-isobaric systems.
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15
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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16
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Zhao D, Kong Y, Zhao S, Xing H. Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications. Top Curr Chem (Cham) 2020; 378:41. [DOI: 10.1007/s41061-020-00305-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/31/2022]
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17
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18
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Marro N, Della Sala F, Kay ER. Programmable dynamic covalent nanoparticle building blocks with complementary reactivity. Chem Sci 2019; 11:372-383. [PMID: 32190260 PMCID: PMC7067244 DOI: 10.1039/c9sc04195h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/14/2019] [Indexed: 12/28/2022] Open
Abstract
A toolkit of two complementary dynamic covalent nanoparticles enables programmable and reversible nanoparticle functionalization and construction of adaptive binary assemblies.
Nanoparticle-based devices, materials and technologies will demand a new era of synthetic chemistry where predictive principles familiar in the molecular regime are extended to nanoscale building blocks. Typical covalent strategies for modifying nanoparticle-bound species rely on kinetically controlled reactions optimised for efficiency but with limited capacity for selective and divergent access to a range of product constitutions. In this work, monolayer-stabilized nanoparticles displaying complementary dynamic covalent hydrazone exchange reactivity undergo distinct chemospecific transformations by selecting appropriate combinations of ‘nucleophilic’ or ‘electrophilic’ nanoparticle-bound monolayers with nucleophilic or electrophilic molecular modifiers. Thermodynamically governed reactions allow modulation of product compositions, spanning mixed-ligand monolayers to exhaustive exchange. High-density nanoparticle-stabilizing monolayers facilitate in situ reaction monitoring by quantitative 19F NMR spectroscopy. Kinetic analysis reveals that hydrazone exchange rates are moderately diminished by surface confinement, and that the magnitude of this effect is dependent on mechanistic details: surface-bound electrophiles react intrinsically faster, but are more significantly affected by surface immobilization than nucleophiles. Complementary nanoparticles react with each other to form robust covalently connected binary aggregates. Endowed with the adaptive characteristics of the dynamic covalent linking process, the nanoscale assemblies can be tuned from extended aggregates to colloidally stable clusters of equilibrium sizes that depend on the concentration of a monofunctional capping agent. Just two ‘dynamic covalent nanoparticles’ with complementary thermodynamically governed reactivities therefore institute a programmable toolkit offering flexible control over nanoparticle surface functionalization, and construction of adaptive assemblies that selectively combine several nanoscale building blocks.
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Affiliation(s)
- Nicolas Marro
- EaStCHEM School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
| | - Flavio Della Sala
- EaStCHEM School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
| | - Euan R Kay
- EaStCHEM School of Chemistry , University of St Andrews , North Haugh , St Andrews , KY16 9ST , UK .
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Depciuch J, Stec M, Maximenko A, Pawlyta M, Baran J, Parlinska-Wojtan M. Control of Arms of Au Stars Size and its Dependent Cytotoxicity and Photosensitizer Effects in Photothermal Anticancer Therapy. Int J Mol Sci 2019; 20:E5011. [PMID: 31658649 PMCID: PMC6834177 DOI: 10.3390/ijms20205011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 09/28/2019] [Accepted: 10/09/2019] [Indexed: 11/29/2022] Open
Abstract
Gold nanostars (AuS NPs) are a very attractive nanomaterial, which is characterized by high effective transduction of the electromagnetic radiation into heat energy. Therefore, AuS NPs can be used as photosensitizers in photothermal therapy (PTT). However, understanding the photothermal conversion efficiency in nanostars is very important to select the most appropriate shape and size of AuS NPs. Therefore, in this article, the synthesis of AuS NPs with different lengths of star arms for potential application in PTT was investigated. Moreover, the formation mechanism of these AuS NPs depending on the reducer concentration is proposed. Transmission electron microscopy (TEM) with selected area diffraction (SEAD) and X-ray diffraction (X-Ray) showed that all the obtained AuS NPs are crystalline and have cores with similar values of the diagonal (parameter d), from 140 nm to 146 nm. However, the widths of the star arm edges (parameter c) and the lengths of the arms (parameter a) vary between 3.75 nm and 193 nm for AuS1 NPs to 6.25 nm and 356 nm for AuS4 NPs. Ultraviolet-visible (UV-Vis) spectra revealed that, with increasing edge widths and lengths of the star arms, the surface plasmon resonance (SPR) peak is shifted to the higher wavelengths, from 640 nm for AuS1 NPs to 770 nm for AuS4 NPs. Moreover, the increase of temperature in the AuS NPs solutions as well as the values of calculated photothermal efficiency grew with the elongation of the star arms. The potential application of AuS NPs in the PTT showed that the highest decrease of viability, around 75%, of cells cultured with AuS NPs and irradiated by lasers was noticed for AuS4 NPs with the longest arms, while the smallest changes were visible for gold nanostars with the shortest arms. The present study shows that photothermal properties of AuS NPs depend on edge widths and lengths of the star arms and the values of photothermal efficiency are higher with the increase of the arm lengths, which is correlated with the reducer concentration.
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Affiliation(s)
- Joanna Depciuch
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31-342 Krakow, Poland.
| | - Malgorzata Stec
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, PL-30-663 Krakow, Poland.
| | - Alexey Maximenko
- Institute of Nuclear Physics Polish Academy of Sciences, PL-31-342 Krakow, Poland.
| | - Miroslawa Pawlyta
- Institute of Engineering Materials and Biomaterials, Silesian University of Technology, Konarskiego 18A, 44100 Gliwice, Poland.
| | - Jarek Baran
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, PL-30-663 Krakow, Poland.
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20
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Abstract
Proteins are a class of nanoscale building block with remarkable chemical complexity and sophistication: their diverse functions, shapes, and symmetry as well as atomically monodisperse structures far surpass the range of conventional nanoparticles that can be accessed synthetically. The chemical topologies of proteins that drive their assembly into materials are central to their functions in nature. However, despite the importance of protein materials in biology, efforts to harness these building blocks synthetically to engineer new materials have been impeded by the chemical complexity of protein surfaces, making it difficult to reliably design protein building blocks that can be robustly transformed into targeted materials. Here we describe our work aimed at exploiting a simple but important concept: if one could exchange complex protein-protein interactions with well-defined and programmable DNA-DNA interactions, one could control the assembly of proteins into structurally well-defined oligomeric and polymeric materials and three-dimensional crystals. As a class of nanoscale building block, proteins with surface DNA modifications have a vast design space that exceeds what is practically and conceptually possible with their inorganic counterparts: the sequences of the DNA and protein and the chemical nature and position of DNA attachment all play roles in dictating the assembly behavior of protein-DNA conjugates. We summarize how each of these design parameters can influence structural outcome, beginning with proteins with a single surface DNA modification, where energy barriers between protein monomers can be tuned through the sequence and secondary structure of the oligonucleotide. We then explore challenges and progress in designing directional interactions and valency on protein surfaces. The directional binding properties of protein-DNA conjugates are ultimately imposed by the amino acid sequence of the protein, which defines the spatial distribution of DNA modification sites on the protein. Through careful design and mutagenesis, bivalent building blocks that bind directionally to form one-dimensional assemblies can be realized. Finally, we discuss the assembly of proteins densely modified with DNA into crystalline superlattices. At first glance, these protein building blocks display crystallization behavior remarkably similar to that of their DNA-functionalized inorganic nanoparticle counterparts, which allows design principles elucidated for DNA-guided nanoparticle crystallization to be used as predictive tools in determining structural outcomes in protein systems. Proteins additionally offer design handles that nanoparticles do not: unlike nanoparticles, the number and spatial distribution of DNA can be controlled through the protein sequence and DNA modification chemistry. Changing the spatial distributions of DNA can drive otherwise identical proteins down distinct crystallization pathways and yield building blocks with exotic distributions of DNA that crystallize into structures that are not yet attainable using isotropically functionalized particles. We highlight challenges in accessing other classes of architectures and establishing general design rules for DNA-mediated protein assembly. Harnessing surface DNA modifications to build protein materials creates many opportunities to realize new architectures and answer fundamental questions about DNA-modified nanostructures in both materials and biological contexts. Proteins with surface DNA modifications are a powerful class of nanomaterial building blocks for which the DNA and protein sequences and the nature of their conjugation dictate the material structure.
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21
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Huang ZM, Lin MY, Zhang CH, Wu Z, Yu RQ, Jiang JH. Recombinant Fusion Streptavidin as a Scaffold for DNA Nanotetrads for Nucleic Acid Delivery and Telomerase Activity Imaging in Living Cells. Anal Chem 2019; 91:9361-9365. [DOI: 10.1021/acs.analchem.9b02115] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zhi-Mei Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Mei-Ya Lin
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Chong-Hua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
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22
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Dehne H, Reitenbach A, Bausch AR. Transient self-organisation of DNA coated colloids directed by enzymatic reactions. Sci Rep 2019; 9:7350. [PMID: 31089164 PMCID: PMC6517385 DOI: 10.1038/s41598-019-43720-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/16/2019] [Indexed: 11/16/2022] Open
Abstract
Dynamic self-organisation far from equilibrium is a key concept towards building autonomously acting materials. Here, we report the coupling of an antagonistic enzymatic reaction of RNA polymerisation and degradation to the aggregation of micron sized DNA coated colloids into fractal structures. A transient colloidal aggregation process is controlled by competing reactions of RNA synthesis of linker strands by a RNA polymerase and their degradation by a ribonuclease. By limiting the energy supply (NTP) of the enzymatic reactions, colloidal clusters form and subsequently disintegrate without the need of external stimuli. Here, the autonomous colloidal aggregation and disintegration can be modulated in terms of lifetime and cluster size. By restricting the enzyme activity locally, a directed spatial propagation of a colloidal aggregation and disintegration front is realised.
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Affiliation(s)
- H Dehne
- Lehrstuhl für Zellbiophysik, Technische Universität München, James-Franck-Str. 1, D-85748, Garching, Germany.
| | - A Reitenbach
- Lehrstuhl für Zellbiophysik, Technische Universität München, James-Franck-Str. 1, D-85748, Garching, Germany.
| | - A R Bausch
- Lehrstuhl für Zellbiophysik, Technische Universität München, James-Franck-Str. 1, D-85748, Garching, Germany
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23
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Virus capsid assembly across different length scales inspire the development of virus-based biomaterials. Curr Opin Virol 2019; 36:38-46. [PMID: 31071601 DOI: 10.1016/j.coviro.2019.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/12/2019] [Accepted: 02/25/2019] [Indexed: 01/26/2023]
Abstract
In biology, there are an abundant number of self-assembled structures organized according to hierarchical levels of complexity. In some examples, the assemblies formed at each level exhibit unique properties and behaviors not present in individual components. Viruses are an example of such where first individual subunits come together to form a capsid structure, some utilizing a scaffolding protein to template or catalyze the capsid formation. Increasing the level of complexity, the viral capsids can then be used as building blocks of higher-level assemblies. This has inspired scientists to design and construct virus capsid-based functional nano-materials. This review provides some insight into the assembly of virus capsids across several length scales, and certain properties that arise at different levels, providing examples found in naturally occurring systems and those that are synthetically designed.
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24
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Pretti E, Mao R, Mittal J. Modelling and simulation of DNA-mediated self-assembly for superlattice design. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1610951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Evan Pretti
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Runfang Mao
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA, USA
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25
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Brunk NE, Uchida M, Lee B, Fukuto M, Yang L, Douglas T, Jadhao V. Linker-Mediated Assembly of Virus-Like Particles into Ordered Arrays via Electrostatic Control. ACS APPLIED BIO MATERIALS 2019; 2:2192-2201. [DOI: 10.1021/acsabm.9b00166] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Nicholas E. Brunk
- Intelligent Systems Engineering, Indiana University, Bloomington, Indiana 47408, United States
| | - Masaki Uchida
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Byeongdu Lee
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Masafumi Fukuto
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Vikram Jadhao
- Intelligent Systems Engineering, Indiana University, Bloomington, Indiana 47408, United States
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26
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Oh T, Park SS, Mirkin CA. Stabilization of Colloidal Crystals Engineered with DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805480. [PMID: 30370680 DOI: 10.1002/adma.201805480] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/24/2018] [Indexed: 05/23/2023]
Abstract
A postsynthetic method for stabilizing colloidal crystals programmed from DNA is developed. The method relies on Ag+ ions to stabilize the particle-connecting DNA duplexes within the crystal lattice, essentially transforming them from loosely bound structures to ones with very strong interparticle links. Such crystals do not dissociate as a function of temperature like normal DNA or DNA-interconnected superlattices, and they can be moved from water to organic media or the solid state, and stay intact. The Ag+ -stabilization of the DNA bonds is accompanied by a nondestructive ≈25% contraction of the lattice, and both the stabilization and contraction are reversible with the chemical extraction of the Ag+ ions, by AgCl precipitation with NaCl. This synthetic tool is important, since it allows scientists and engineers to study such crystals in environments that are incompatible with structures made by conventional DNA programmable methods and without the influence of a matrix such as silica.
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Affiliation(s)
- Taegon Oh
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
| | - Sarah S Park
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, IL, 60208, USA
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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27
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Diba FS, Boden A, Thissen H, Bhave M, Kingshott P, Wang PY. Binary colloidal crystals (BCCs): Interactions, fabrication, and applications. Adv Colloid Interface Sci 2018; 261:102-127. [PMID: 30243666 DOI: 10.1016/j.cis.2018.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 08/08/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
Abstract
The organization of matter into hierarchical structures is a fundamental characteristic of functional materials and living organisms. Binary colloidal crystal (BCC) systems present a diversified range of nanotopographic structures where large and small colloidal particles simultaneously self-assemble into either 2D monolayer or 3D hierarchical crystal lattices. More importantly, understanding how BCCs form opens up the possibility to fabricate more complex systems such as ternary or quaternary colloidal crystals. Monolayer BCCs can also offer the possibility to achieve surface micro- and nano-topographies with heterogeneous chemistries, which can be challenging to achieve with other traditional fabrication tools. A number of fabrication methods have been reported that enable generation of BCC structures offering high accuracy in growth with controllable stoichiometries; however, it is still a challenge to make uniform BCC structures over large surface areas. Therefore, fully understand the mechanism of binary colloidal self-assembly is crucial and new/combinational methods are needed. In this review, we summarize the recent advances in BCC fabrication using particles made of different materials, shapes, and dispersion medium. Depending on the potential application, the degree of order and efficiency of crystal formation has to be determined in order to induce variability in the intended lattice structures. The mechanisms involved in the formation of highly ordered lattice structures from binary colloidal suspensions and applications are discussed. The generation of BCCs can be controlled by manipulation of their extensive phase behavior, which facilitates a wide range potential applications in the fields of both material and biointerfacial sciences including photonics, biosensors, chromatography, antifouling surfaces, biomedical devices, and cell culture tools.
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28
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Oh T, Ku JC, Lee JH, Hersam MC, Mirkin CA. Density-Gradient Control over Nanoparticle Supercrystal Formation. NANO LETTERS 2018; 18:6022-6029. [PMID: 30101587 DOI: 10.1021/acs.nanolett.8b02910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
With the advent of DNA-directed methods to form "single crystal" nanoparticle superlattices, new opportunities for studying the properties of such structures across many length scales now exist. These structure-property relationships rely on the ability of one to deliberately use DNA to control crystal symmetry, lattice parameter, and microscale crystal habit. Although DNA-programmed colloidal crystals consistently form thermodynamically favored crystal habits with a well-defined symmetry and lattice parameter based upon well-established design rules, the sizes of such crystals often vary substantially. For many applications, especially those pertaining to optics, each crystal can represent a single device, and therefore size variability can significantly reduce their scope of use. Consequently, we developed a new method based upon the density difference between two layers of solvents to control nanoparticle superlattice formation and growth. In a top aqueous layer, the assembling particles form a less viscous and less dense state, but once the particles assemble into well-defined rhombic dodecahedral superlattices of a critical size, they sediment into a higher density and higher viscosity sublayer that does not contain particles (aqueous polysaccharide), thereby arresting growth. As a proof-of-concept, this method was used to prepare a uniform batch of Au nanoparticle (20.0 ± 1.6 nm in diameter) superlattices in the form of 0.95 ± 0.20 μm edge length rhombic dodecahedra with body-centered cubic crystal symmetries and a 49 nm lattice parameter (cf. 1.04 ± 0.38 μm without the sublayer). This approach to controlling and arresting superlattice growth yields structures with a 3-fold enhancement in the polydispersity index.
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Affiliation(s)
- Taegon Oh
- Department of Materials Science and Engineering , Northwestern University , 2220 Campus Drive , Evanston , Illinois 60208 , United States
- International Institute for Nanotechnology , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - Jessie C Ku
- Department of Materials Science and Engineering , Northwestern University , 2220 Campus Drive , Evanston , Illinois 60208 , United States
- International Institute for Nanotechnology , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - Jae-Hyeok Lee
- Department of Materials Science and Engineering , Northwestern University , 2220 Campus Drive , Evanston , Illinois 60208 , United States
- Predictive Model Research Center , Korea Institute of Toxicology (KIT) , Daejeon 34114 , Republic of Korea
| | - Mark C Hersam
- Department of Materials Science and Engineering , Northwestern University , 2220 Campus Drive , Evanston , Illinois 60208 , United States
- International Institute for Nanotechnology , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - Chad A Mirkin
- Department of Materials Science and Engineering , Northwestern University , 2220 Campus Drive , Evanston , Illinois 60208 , United States
- International Institute for Nanotechnology , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
- Department of Chemistry , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
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29
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Pretti E, Zerze H, Song M, Ding Y, Mahynski NA, Hatch HW, Shen VK, Mittal J. Assembly of three-dimensional binary superlattices from multi-flavored particles. SOFT MATTER 2018; 14:6303-6312. [PMID: 30014070 PMCID: PMC7339916 DOI: 10.1039/c8sm00989a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Binary superlattices constructed from nano- or micron-sized colloidal particles have a wide variety of applications, including the design of advanced materials. Self-assembly of such crystals from their constituent colloids can be achieved in practice by, among other means, the functionalization of colloid surfaces with single-stranded DNA sequences. However, when driven by DNA, this assembly is traditionally premised on the pairwise interaction between a single DNA sequence and its complement, and often relies on particle size asymmetry to entropically control the crystalline arrangement of its constituents. The recently proposed "multi-flavoring" motif for DNA functionalization, wherein multiple distinct strands of DNA are grafted in different ratios to different colloids, can be used to experimentally realize a binary mixture in which all pairwise interactions are independently controllable. In this work, we use various computational methods, including molecular dynamics and Wang-Landau Monte Carlo simulations, to study a multi-flavored binary system of micron-sized DNA-functionalized particles modeled implicitly by Fermi-Jagla pairwise interactions. We show how self-assembly of such systems can be controlled in a purely enthalpic manner, and by tuning only the interactions between like particles, demonstrate assembly into various morphologies. Although polymorphism is present over a wide range of pairwise interaction strengths, we show that careful selection of interactions can lead to the generation of pure compositionally ordered crystals. Additionally, we show how the crystal composition changes with the like-pair interaction strengths, and how the solution stoichiometry affects the assembled structures.
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Affiliation(s)
- Evan Pretti
- Lehigh University, Chemical and Biomolecular Engineering, 111 Research Dr., Bethlehem, Pennsylvania 18015-4791, USA.
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30
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Huang DJ, Huang ZM, Xiao HY, Wu ZK, Tang LJ, Jiang JH. Protein scaffolded DNA tetrads enable efficient delivery and ultrasensitive imaging of miRNA through crosslinking hybridization chain reaction. Chem Sci 2018; 9:4892-4897. [PMID: 29910942 PMCID: PMC5982210 DOI: 10.1039/c8sc01001c] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/04/2018] [Indexed: 12/28/2022] Open
Abstract
Efficient intracellular delivery of nucleic acids to achieve sensitive detection and gene regulation is essential for chemistry and biology. Here we developed a novel protein scaffolded DNA tetrad, a four-arm DNA nanostructure constructed using streptavidin (SA) protein and four biotinylated hairpin DNA probes for efficient nucleic acid delivery and ultrasensitive miRNA imaging through crosslinking hybridization chain reaction (cHCR). DNA tetrads were easy to prepare and allowed precise control of the structure of the probes. DNA tetrads showed rapid intracellular delivery of DNA probes and high efficiency in lysosome escape by using confocal images for individual cells and flow cytometry for a large population of cells. cHCR allowed generating clumps of crosslinked hydrogel networks specifically to target miRNA, affording high sensitivity and spatial resolution for imaging. To our knowledge, this is the first time that HCR amplification has been realized in situ on nanostructures. Moreover, the FRET based design of cHCR conferred improved precision with the use of dual-emission ratiometric imaging to avoid false signals in biological systems. Intracellular imaging experiments further showed that DNA tetrad based cHCR could realize ultrasensitive and accurate miRNA imaging in living cells. Moreover, DNA tetrad based cHCR provided a potential tool for quantitative measurement of intracellular miRNA. The results suggested that this developed strategy provided a useful platform for nucleic acid delivery and low level biomarker imaging.
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Affiliation(s)
- Du-Juan Huang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Zhi-Mei Huang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Hu-Yan Xiao
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Zhen-Kun Wu
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Li-Juan Tang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
| | - Jian-Hui Jiang
- Institute of Chemical Biology & Nanomedicine , State Key Laboratory of Chemo/Biosensing & Chemometrics , College of Chemistry & Chemical Engineering , Hunan University , Changsha 410082 , China . ;
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31
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Abstract
Bivalent DNA conjugates of β-galactosidase (βGal), having pairs of oligonucleotides positioned closely on opposing faces of the protein, have been synthesized and characterized. These structures, due to their directional bonding characteristics, allow for the programmable access of one-dimensional protein materials. When conjugates functionalized with complementary oligonucleotides are combined under conditions that support DNA hybridization, periodic wire-type superstructures consisting of aligned proteins form. These structures have been characterized by gel electrophoresis, cryo-transmission electron microscopy, and negative-stain transmission electron microscopy. Significantly, melting experiments of complementary building blocks display narrowed and elevated melting transitions compared to the free duplex DNA, further supporting the formation of the designed binding mode, and unambiguously characterizing their association as DNA-mediated. These novel structures illustrate, for the first time, that directional DNA bonding can be realized with only a pair of DNA modifications, which will allow one to engineer directional interactions and realize new classes of superstructures not possible simply through shape control or isotropically functionalized materials.
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Affiliation(s)
- Janet R McMillan
- Department of Chemistry and International Institute for Nanotechnology , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208 , United States
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32
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Abstract
Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.
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Affiliation(s)
- William M Aumiller
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
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33
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Long C, Lei QL, Ren CL, Ma YQ. Three-Dimensional Non-Close-Packed Structures of Oppositely Charged Colloids Driven by pH Oscillation. J Phys Chem B 2018; 122:3196-3201. [DOI: 10.1021/acs.jpcb.8b00441] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cheng Long
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Qun-li Lei
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
| | - Chun-lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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34
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Uchida M, McCoy K, Fukuto M, Yang L, Yoshimura H, Miettinen HM, LaFrance B, Patterson DP, Schwarz B, Karty JA, Prevelige PE, Lee B, Douglas T. Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis. ACS NANO 2018; 12:942-953. [PMID: 29131580 PMCID: PMC5870838 DOI: 10.1021/acsnano.7b06049] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from an amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. This study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.
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Affiliation(s)
- Masaki Uchida
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Kimberly McCoy
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Masafumi Fukuto
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hideyuki Yoshimura
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
- Department of Physics, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, 214-8571, Japan
| | - Heini M. Miettinen
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717, USA
| | - Ben LaFrance
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA
| | - Dustin P. Patterson
- Department of Chemistry and Biochemistry, University of Texas at Tyler, Tyler, Texas 75799, USA
| | - Benjamin Schwarz
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Jonathan A. Karty
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Byeongdu Lee
- X-ray science division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Ave., Argonne, IL 60439, USA
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Ave., Bloomington, IN 47405, USA
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Xu K, Sukhanov AA, Zhao Y, Zhao J, Ji W, Peng X, Escudero D, Jacquemin D, Voronkova VK. Unexpected Nucleophilic Substitution Reaction of BODIPY: Preparation of the BODIPY-TEMPO Triad Showing Radical-Enhanced Intersystem Crossing. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Kejing Xu
- State Key Laboratory of Fine Chemicals; School of Chemical Engineering; Dalian University of Technology; E-208 West Campus, 2 Ling Gong Rd. 116024 Dalian China
| | - Andrey A. Sukhanov
- Zavoisky Physical-Technical Institute; FIC KazanSC; Russian Academy of Sciences; Sibirsky trakt 10/7 420029 Kazan Russia
| | - Yingjie Zhao
- State Key Laboratory of Fine Chemicals; School of Chemical Engineering; Dalian University of Technology; E-208 West Campus, 2 Ling Gong Rd. 116024 Dalian China
| | - Jianzhang Zhao
- State Key Laboratory of Fine Chemicals; School of Chemical Engineering; Dalian University of Technology; E-208 West Campus, 2 Ling Gong Rd. 116024 Dalian China
| | - Wei Ji
- State Key Laboratory of Fine Chemicals; School of Chemical Engineering; Dalian University of Technology; E-208 West Campus, 2 Ling Gong Rd. 116024 Dalian China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals; School of Chemical Engineering; Dalian University of Technology; E-208 West Campus, 2 Ling Gong Rd. 116024 Dalian China
| | - Daniel Escudero
- CEISAM UMR CNRS 6230; Université de Nantes; 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Denis Jacquemin
- CEISAM UMR CNRS 6230; Université de Nantes; 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
- Institut Universitaire de France; 1, rue Descartes 75005 Paris Cedex 5 France
| | - Violeta K. Voronkova
- Zavoisky Physical-Technical Institute; FIC KazanSC; Russian Academy of Sciences; Sibirsky trakt 10/7 420029 Kazan Russia
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36
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Song M, Ding Y, Zerze H, Snyder MA, Mittal J. Binary Superlattice Design by Controlling DNA-Mediated Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:991-998. [PMID: 29111738 DOI: 10.1021/acs.langmuir.7b02835] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Most binary superlattices created using DNA functionalization rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized micron-sized particles (DFPs), and employ a strategy that leverages the tunable disparity in interparticle interactions, and thus enthalpic driving forces, to open new avenues for design of binary superlattices that do not rely on the ability to tune particle size (i.e., entropic driving forces). Our strategy employs tailored blends of complementary strands of ssDNA to control interparticle interactions between micron-sized silica particles in a binary mixture to create compositionally diverse 2D lattices. We show that the particle arrangement can be further controlled by changing the stoichiometry of the binary mixture in certain cases. With this approach, we demonstrate the ability to program the particle assembly into square, pentagonal, and hexagonal lattices. In addition, different particle types can be compositionally ordered in square checkerboard and hexagonal-alternating string, honeycomb, and Kagome arrangements.
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Affiliation(s)
- Minseok Song
- Department of Chemical and Biomolecular Engineering, Lehigh University , 111 Research Drive, Iacooca Hall, Bethlehem, Pennsylvania 18015, United States
| | - Yajun Ding
- Department of Chemical and Biomolecular Engineering, Lehigh University , 111 Research Drive, Iacooca Hall, Bethlehem, Pennsylvania 18015, United States
| | - Hasan Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University , 111 Research Drive, Iacooca Hall, Bethlehem, Pennsylvania 18015, United States
| | - Mark A Snyder
- Department of Chemical and Biomolecular Engineering, Lehigh University , 111 Research Drive, Iacooca Hall, Bethlehem, Pennsylvania 18015, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University , 111 Research Drive, Iacooca Hall, Bethlehem, Pennsylvania 18015, United States
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37
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Wang MX, Brodin JD, Millan JA, Seo SE, Girard M, Olvera de la Cruz M, Lee B, Mirkin CA. Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion. NANO LETTERS 2017; 17:5126-5132. [PMID: 28731353 DOI: 10.1021/acs.nanolett.7b02502] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior. Specifically, our experimental data coupled with coarse-grained molecular dynamics (MD) simulations reveal that, by changing factors related to NP repulsion, two structurally distinct outcomes can be achieved. When steric repulsion between DNA-AuNPs is significantly greater than that between DNA-proteins, a lower packing density crystal lattice is favored over the structure that is predicted by design rules based on DNA hybridization considerations alone. This is enabled by the large difference in DNA density on AuNPs versus proteins and can be tuned by modulating the flexibility, and thus conformational entropy, of the DNA on the constituent particles. At intermediate ligand flexibility, the crystallization pathways are energetically similar, and the structural outcome can be adjusted using the density of DNA duplexes on DNA-AuNPs and by screening the Coulomb potential between them. Such lattices are shown to undergo dynamic reorganization upon changing the salt concentration. These data help elucidate the structural considerations necessary for understanding repulsive forces in DNA-mediated assembly and lay the groundwork for using them to increase architectural diversity in engineering colloidal crystals.
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Affiliation(s)
| | | | | | | | | | | | - Byeongdu Lee
- X-Ray Science Division, Argonne National Laboratory , 9700 S. Cass Avenue, Argonne, Illinois 60439, United States
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Gao J, Sanchez-Purra M, Huang H, Wang S, Chen Y, Yu X, Luo Q, Hamad-Schifferli K, Liu S. Synthesis of different-sized gold nanostars for Raman bioimaging and photothermal therapy in cancer nanotheranostics. Sci China Chem 2017. [DOI: 10.1007/s11426-017-9088-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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39
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Colloidal crystals with diamond symmetry at optical lengthscales. Nat Commun 2017; 8:14173. [PMID: 28194025 PMCID: PMC5316806 DOI: 10.1038/ncomms14173] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/05/2016] [Indexed: 11/08/2022] Open
Abstract
Future optical materials promise to do for photonics what semiconductors did for electronics, but the challenge has long been in creating the structure they require—a regular, three-dimensional array of transparent microspheres arranged like the atoms in a diamond crystal. Here we demonstrate a simple approach for spontaneously growing double-diamond (or B32) crystals that contain a suitable diamond structure, using DNA to direct the self-assembly process. While diamond symmetry crystals have been grown from much smaller nanoparticles, none of those previous methods suffice for the larger particles needed for photonic applications, whose size must be comparable to the wavelength of visible light. Intriguingly, the crystals we observe do not readily form in previously validated simulations; nor have they been predicted theoretically. This finding suggests that other unexpected microstructures may be accessible using this approach and bodes well for future efforts to inexpensively mass-produce metamaterials for an array of photonic applications. Colloidal crystals arranged in a diamond lattice are desirable for photonic applications, yet are challenging to create. Here, Wang et al. show the self-assembly of a binary system composed of two interlocked diamond structures with lattice spacing comparable to the wavelength of visible light.
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40
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Submillimetre Network Formation by Light-induced Hybridization of Zeptomole-level DNA. Sci Rep 2016; 6:37768. [PMID: 27917861 PMCID: PMC5137144 DOI: 10.1038/srep37768] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/01/2016] [Indexed: 12/17/2022] Open
Abstract
Macroscopic unique self-assembled structures are produced via double-stranded DNA formation (hybridization) as a specific binding essential in biological systems. However, a large amount of complementary DNA molecules are usually required to form an optically observable structure via natural hybridization, and the detection of small amounts of DNA less than femtomole requires complex and time-consuming procedures. Here, we demonstrate the laser-induced acceleration of hybridization between zeptomole-level DNA and DNA-modified nanoparticles (NPs), resulting in the assembly of a submillimetre network-like structure at the desired position with a dramatic spectral modulation within several minutes. The gradual enhancement of light-induced force and convection facilitated the two-dimensional network growth near the air-liquid interface with optical and fluidic symmetry breakdown. The simultaneous microscope observation and local spectroscopy revealed that the assembling process and spectral change are sensitive to the DNA sequence. Our findings establish innovative guiding principles for facile bottom-up production via various biomolecular recognition events.
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41
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Schmitt M, Zhang J, Lee J, Lee B, Ning X, Zhang R, Karim A, Davis RF, Matyjaszewski K, Bockstaller MR. Polymer ligand-induced autonomous sorting and reversible phase separation in binary particle blends. SCIENCE ADVANCES 2016; 2:e1601484. [PMID: 28028538 PMCID: PMC5182054 DOI: 10.1126/sciadv.1601484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/11/2016] [Indexed: 05/15/2023]
Abstract
The tethering of ligands to nanoparticles has emerged as an important strategy to control interactions and organization in particle assembly structures. We demonstrate that ligand interactions in mixtures of polymer-tethered nanoparticles (which are modified with distinct types of polymer chains) can impart upper or lower critical solution temperature (UCST/LCST)-type phase behavior on binary particle mixtures in analogy to the phase behavior of the corresponding linear polymer blends. Therefore, cooling (or heating) of polymer-tethered particle blends with appropriate architecture to temperatures below (or above) the UCST (or LCST) results in the organization of the individual particle constituents into monotype microdomain structures. The shape (bicontinuous or island-type) and lengthscale of particle microdomains can be tuned by variation of the composition and thermal process conditions. Thermal cycling of LCST particle brush blends through the critical temperature enables the reversible growth and dissolution of monoparticle domain structures. The ability to autonomously and reversibly organize multicomponent particle mixtures into monotype microdomain structures could enable transformative advances in the high-throughput fabrication of solid films with tailored and mutable structures and properties that play an important role in a range of nanoparticle-based material technologies.
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Affiliation(s)
- Michael Schmitt
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Jianan Zhang
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Jaejun Lee
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Bongjoon Lee
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Xin Ning
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Ren Zhang
- Department of Polymer Engineering, Polymer Engineering Academic Center, University of Akron, 250 South Forge Street, Akron, OH 44325–0301, USA
| | - Alamgir Karim
- Department of Polymer Engineering, Polymer Engineering Academic Center, University of Akron, 250 South Forge Street, Akron, OH 44325–0301, USA
| | - Robert F. Davis
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
| | - Krzysztof Matyjaszewski
- Chemistry Department, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
- Corresponding author. (M.R.B.); (K.M.)
| | - Michael R. Bockstaller
- Department of Materials Science and Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
- Corresponding author. (M.R.B.); (K.M.)
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42
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Pumpens P, Renhofa R, Dishlers A, Kozlovska T, Ose V, Pushko P, Tars K, Grens E, Bachmann MF. The True Story and Advantages of RNA Phage Capsids as Nanotools. Intervirology 2016; 59:74-110. [DOI: 10.1159/000449503] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
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43
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Song M, Ding Y, Snyder MA, Mittal J. Effect of Nonionic Surfactant on Association/Dissociation Transition of DNA-Functionalized Colloids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10017-10025. [PMID: 27595803 DOI: 10.1021/acs.langmuir.6b02096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We report the effect of nonionic surfactants (Pluronics F127 and F88) on the melting transition of micron-sized colloids confined in two dimensions, mediated by complementary single-stranded DNA as a function of the surfactant concentration. Micron-sized silica particles were functionalized with single-stranded DNA using cyanuric chloride chemistry. The existence of covalently linked DNA on particles was confirmed by fluorescence spectroscopy. The nonionic surfactant not only plays a significant role in stabilization of particles, with minimization of nonspecific binding, but also impacts the melting temperature, which increases as a function of the nonionic surfactant concentration. These results suggest that the melting transition for DNA-mediated assembly is sensitive to commonly used additives in laboratory buffers, and that these common solution components may be exploited as a facile and independent handle for tuning the melting temperature and, thus, the assembly and possibly crystallization within these systems.
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Affiliation(s)
- Minseok Song
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Yajun Ding
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Mark A Snyder
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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44
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Zhang Y, Ardejani MS, Orner BP. Design and Applications of Protein-Cage-Based Nanomaterials. Chem Asian J 2016; 11:2814-2828. [DOI: 10.1002/asia.201600769] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Zhang
- Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals; College of Chemical Engineering; Nanjing Forestry University; Nanjing 210037 P.R. China
| | - Maziar S. Ardejani
- Department of Chemistry; The Scripps Research Institute; La Jolla CA 92037 United States
| | - Brendan P. Orner
- Department of Chemistry; King's College London; London SE1 1DB United Kingdom
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45
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Abstract
The self-organization of colloidal particles is a promising approach to create novel structures and materials, with applications spanning from smart materials to optoelectronics to quantum computation. However, designing and producing mesoscale-sized structures remains a major challenge because at length scales of 10-100 μm equilibration times already become prohibitively long. Here, we extend the principle of rapid diffusion-limited cluster aggregation (DLCA) to a multicomponent system of spherical colloidal particles to enable the rational design and production of finite-sized anisotropic structures on the mesoscale. In stark contrast to equilibrium self-assembly techniques, kinetic traps are not avoided but exploited to control and guide mesoscopic structure formation. To this end the affinities, size, and stoichiometry of up to five different types of DNA-coated microspheres are adjusted to kinetically control a higher-order hierarchical aggregation process in time. We show that the aggregation process can be fully rationalized by considering an extended analytical DLCA model, allowing us to produce mesoscopic structures of up to 26 µm in diameter. This scale-free approach can easily be extended to any multicomponent system that allows for multiple orthogonal interactions, thus yielding a high potential of facilitating novel materials with tailored plasmonic excitation bands, scattering, biochemical, or mechanical behavior.
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Affiliation(s)
- Fabian M Hecht
- Lehrstuhl für Zellbiophysik E27, Technische Universität München, 85748 Garching, Germany
| | - Andreas R Bausch
- Lehrstuhl für Zellbiophysik E27, Technische Universität München, 85748 Garching, Germany
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46
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Wen AM, Steinmetz NF. Design of virus-based nanomaterials for medicine, biotechnology, and energy. Chem Soc Rev 2016; 45:4074-126. [PMID: 27152673 PMCID: PMC5068136 DOI: 10.1039/c5cs00287g] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review provides an overview of recent developments in "chemical virology." Viruses, as materials, provide unique nanoscale scaffolds that have relevance in chemical biology and nanotechnology, with diverse areas of applications. Some fundamental advantages of viruses, compared to synthetically programmed materials, include the highly precise spatial arrangement of their subunits into a diverse array of shapes and sizes and many available avenues for easy and reproducible modification. Here, we will first survey the broad distribution of viruses and various methods for producing virus-based nanoparticles, as well as engineering principles used to impart new functionalities. We will then examine the broad range of applications and implications of virus-based materials, focusing on the medical, biotechnology, and energy sectors. We anticipate that this field will continue to evolve and grow, with exciting new possibilities stemming from advancements in the rational design of virus-based nanomaterials.
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Affiliation(s)
- Amy M Wen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA. and Department of Radiology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Materials Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106, USA and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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47
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Arai N, Yoshimoto Y, Yasuoka K, Ebisuzaki T. Self-assembly behaviours of primitive and modern lipid membrane solutions: a coarse-grained molecular simulation study. Phys Chem Chem Phys 2016; 18:19426-32. [PMID: 27378100 DOI: 10.1039/c6cp02380k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Researchers have studied the origin of life and the process of evolution on early Earth for decades. However, we lack a comprehensive understanding of biogenesis, because there are many stages in the formation and growth of the first cell. We investigate the self-replication processes of coacervate protocells using computer simulations of single-chain lipid and phospholipid aqueous mixtures. Based on a morphological phase diagram, we develop a model of prebiotic self-replication driven by only environmental factors (i.e. temperature and lipid concentrations) without any external force. Moreover, we investigate high concentration structures during the process of self-replication. These structures have an advantage in fusion and repair of cell membranes. Therefore, lipid hot spots may have existed in primordial soup.
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Affiliation(s)
- Noriyoshi Arai
- Department of Mechanical Engineering, Kindai University, Higashiosaka, Osaka, Japan.
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48
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Abstract
X-ray scattering is a structural characterization tool that has impacted diverse fields of study. It is unique in its ability to examine materials in real time and under realistic sample environments, enabling researchers to understand morphology at nanometer and angstrom length scales using complementary small and wide angle X-ray scattering (SAXS, WAXS), respectively. Herein, we focus on the use of SAXS to examine nanoscale particulate systems. We provide a theoretical foundation for X-ray scattering, considering both form factor and structure factor, as well as the use of correlation functions, which may be used to determine a particle's size, size distribution, shape, and organization into hierarchical structures. The theory is expanded upon with contemporary use cases. Both transmission and reflection (grazing incidence) geometries are addressed, as well as the combination of SAXS with other X-ray and non-X-ray characterization tools. We conclude with an examination of several key areas of research where X-ray scattering has played a pivotal role, including in situ nanoparticle synthesis, nanoparticle assembly, and operando studies of catalysts and energy storage materials. Throughout this review we highlight the unique capabilities of X-ray scattering for structural characterization of materials in their native environment.
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Affiliation(s)
- Tao Li
- X-ray Science Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Andrew J Senesi
- X-ray Science Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
| | - Byeongdu Lee
- X-ray Science Division, Argonne National Laboratory , 9700 South Cass Avenue, Lemont, Illinois 60439, United States
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49
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Dong B, Huang Z, Chen H, Yan LT. Chain-Stiffness-Induced Entropy Effects Mediate Interfacial Assembly of Janus Nanoparticles in Block Copolymers: From Interfacial Nanostructures to Optical Responses. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01290] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Bojun Dong
- Key Laboratory
of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Zihan Huang
- Key Laboratory
of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Honglin Chen
- Key Laboratory
of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Li-Tang Yan
- Key Laboratory
of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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50
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Hong BJ, Eryazici I, Bleher R, Thaner RV, Mirkin CA, Nguyen ST. Directed Assembly of Nucleic Acid-Based Polymeric Nanoparticles from Molecular Tetravalent Cores. J Am Chem Soc 2015; 137:8184-91. [PMID: 25980315 PMCID: PMC5493157 DOI: 10.1021/jacs.5b03485] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complementary tetrahedral small molecule-DNA hybrid (SMDH) building blocks have been combined to form nucleic acid-based polymeric nanoparticles without the need for an underlying template or scaffold. The sizes of these particles can be tailored in a facile fashion by adjusting assembly conditions such as SMDH concentration, assembly time, and NaCl concentration. Notably, these novel particles can be stabilized and transformed into functionalized spherical nucleic acid (SNA) structures through the incorporation of capping DNA strands conjugated with functional groups. These results demonstrate a systematic, efficient strategy for the construction and surface functionalization of well-defined, size-tunable nucleic acid particles from readily accessible molecular building blocks. Furthermore, because these nucleic acid-based polymeric nanoparticles exhibited enhanced cellular internalization and resistance to DNase I compared to free synthetic nucleic acids, they should have a plethora of applications in diagnostics and therapeutics.
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Affiliation(s)
- Bong Jin Hong
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Ibrahim Eryazici
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Reiner Bleher
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208-3108, United States
- NUANCE Center, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208-3108, United States
| | - Ryan V. Thaner
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - SonBinh T. Nguyen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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