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Zhang Y, Giunta G, Liang H, Dijkstra M. Shape-induced crystallization of binary DNA-functionalized nanocubes. J Chem Phys 2023; 158:2890487. [PMID: 37172219 DOI: 10.1063/5.0148139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/21/2023] [Indexed: 05/14/2023] Open
Abstract
Leveraging the anisotropic shape of DNA-functionalized nanoparticles holds potential for shape-directed crystallization of a wide collection of superlattice structures. Using coarse-grained molecular dynamics simulations, we study the self-assembly of a binary mixture of cubic gold nanoparticles, which are functionalized by complementary DNA strands. We observe the spontaneous self-assembly of simple cubic (SC), plastic body-centered tetragonal (pBCT), and compositionally disordered plastic body-centered tetragonal (d-pBCT) phases due to hybridization of the DNA strands. We systematically investigate the effect of length, grafting density, as well as rigidity of the DNA strands on the self-assembly behavior of cubic nanoparticles. We measure the potential of mean force between DNA-functionalized nanocubes for varying rigidity of the DNA strands and DNA lengths. Using free-energy calculations, we find that longer and flexible DNA strands can lead to a phase transformation from SC to the pBCT phase due to a gain in entropy arising from the orientational degrees of freedom of the nanocubes in the pBCT phase. Our results may serve as a guide for self-assembly experiments on DNA-functionalized cubic nanoparticles.
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Affiliation(s)
- Yunhan Zhang
- Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Giuliana Giunta
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Haojun Liang
- Department of Polymer Science and Engineering, CAS Key Laboratory of Soft Matter Chemistry, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
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2
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Kumar R, Santa Chalarca CF, Bockman MR, Bruggen CV, Grimme CJ, Dalal RJ, Hanson MG, Hexum JK, Reineke TM. Polymeric Delivery of Therapeutic Nucleic Acids. Chem Rev 2021; 121:11527-11652. [PMID: 33939409 DOI: 10.1021/acs.chemrev.0c00997] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The advent of genome editing has transformed the therapeutic landscape for several debilitating diseases, and the clinical outlook for gene therapeutics has never been more promising. The therapeutic potential of nucleic acids has been limited by a reliance on engineered viral vectors for delivery. Chemically defined polymers can remediate technological, regulatory, and clinical challenges associated with viral modes of gene delivery. Because of their scalability, versatility, and exquisite tunability, polymers are ideal biomaterial platforms for delivering nucleic acid payloads efficiently while minimizing immune response and cellular toxicity. While polymeric gene delivery has progressed significantly in the past four decades, clinical translation of polymeric vehicles faces several formidable challenges. The aim of our Account is to illustrate diverse concepts in designing polymeric vectors towards meeting therapeutic goals of in vivo and ex vivo gene therapy. Here, we highlight several classes of polymers employed in gene delivery and summarize the recent work on understanding the contributions of chemical and architectural design parameters. We touch upon characterization methods used to visualize and understand events transpiring at the interfaces between polymer, nucleic acids, and the physiological environment. We conclude that interdisciplinary approaches and methodologies motivated by fundamental questions are key to designing high-performing polymeric vehicles for gene therapy.
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Affiliation(s)
- Ramya Kumar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | - Matthew R Bockman
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Craig Van Bruggen
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rishad J Dalal
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Joseph K Hexum
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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3
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Mei Y, Tang L, Xiao Q, Zhang Z, Zhang Z, Zang J, Zhou J, Wang Y, Wang W, Ren M. Reconstituted high density lipoprotein (rHDL), a versatile drug delivery nanoplatform for tumor targeted therapy. J Mater Chem B 2021; 9:612-633. [PMID: 33306079 DOI: 10.1039/d0tb02139c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
rHDL is a synthesized drug delivery nanoplatform exhibiting excellent biocompatibility, which possesses most of the advantages of HDL. rHDL shows almost no toxicity and can be degraded to non-toxic substances in vivo. The severe limitation of the application of various antitumor agents is mainly due to their low bioavailability, high toxicity, poor stability, etc. Favorably, antitumor drug-loaded rHDL nanoparticles (NPs), which are known as an important drug delivery system (DDS), help to change the situation a lot. This DDS shows an outstanding active-targeting ability towards tumor cells and improves the therapeutic effect during antitumor treatment while overcoming the shortcomings mentioned above. In the following text, we will mainly focus on the various applications of rHDL in tumor targeted therapy by describing the properties, preparation, receptor active-targeting ability and antitumor effects of antineoplastic drug-loaded rHDL NPs.
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Affiliation(s)
- Yijun Mei
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China.
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4
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Mao R, Mittal J. Self-Assembly of DNA-Functionalized Nanoparticles Guided by Binding Kinetics. J Phys Chem B 2020; 124:11593-11599. [PMID: 33296210 DOI: 10.1021/acs.jpcb.0c08225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We use a coarse-grained model of DNA-functionalized particles (DFPs) to understand the role of DNA strand length on their self-assembly. We find that the increasing strand length for a given particle size decreases the propensity to form ordered crystalline assemblies within the simulation time. Instead, disordered structures form when the strand length exceeds a certain threshold, consistent with the previous experiments. Analysis of the simulation data based on a pair of DFPs suggests weakening interparticle interactions with increasing strand length, thereby shifting the suitable assembly conditions to lower temperatures. We find that DNA (un)hybridization kinetics at these lower temperatures becomes significantly slower, preventing systems with longer DNA strands from crystallizing successfully. We suggest that a suitable strategy to overcome this kinetic barrier is to enhance interparticle interactions for DFPs with longer DNA strands, which is achieved by increasing the DNA grafting density. We directly test this hypothesis and show successful crystallization within the simulation time for DFPs with longer strands with higher grafting densities. Our results highlight the power of computational modeling in elucidating the fundamental design principles and guiding the assembly of nanoparticles to form complex nanostructures in cases where experiments alone have not been able to do so.
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Affiliation(s)
- Runfang Mao
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015-4791, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015-4791, United States
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5
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Zhang J, Jin J, Du Y, Zhou X, Liang H, Jiang W. Enhancing the stability of single-stranded DNA on gold nanoparticles as molecular machines through salt and acid regulation. J Mater Chem B 2020; 7:5554-5562. [PMID: 31465072 DOI: 10.1039/c9tb01238a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-functionalized gold nanoparticles (DNA-AuNPs) have shown great potential and exciting opportunities for constructing machine-like nanodevices. Nonthiolated DNA can be grafted onto gold surfaces via DNA bases, such as polyadenine (polyA)-DNA. The colloidal stability of polyA-DNA-AuNPs has a significant dependency on salt and pH that affects the assembly of AuNPs and their application in polyA-DNA molecular machines. High salt and low pH value contribute to the stabilization of polyA-DNA-AuNPs. In acid conditions, adenine can be protonated and becomes positively-charged, thus enhancing the adsorption of polyA-DNA onto the gold surface by electrostatic interactions; coordination of multiple interactions achieves a high DNA grafting density and colloidal stability. In addition, the length of adenine has an important effect on the efficiency of the DNA machine, while the length of thymine has little effect when the thymine length is less than or equal to seven. The assembly of AuNPs driven by dynamic polyA-DNA molecular machines was successfully accomplished with A5-DNA and A9-DNA. A moderate concentration of catalyst oligomer (50 nM) could improve the DNA hybridization efficiency. The A9-DNA based molecular machine is more efficient than the A5-DNA based one because of the larger amount of A9-DNA on the AuNPs, which increases the probability of collisions between complementary DNA strands. Therefore, polyA-DNA functionalized nanoparticles can be used as a basic unit to construct assembly-ordering structures and achieve dynamic molecular machines to be applied in the molecular diagnostics field.
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Affiliation(s)
- Jianing Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
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6
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He Z, Yang Y, Liang HW, Liu JW, Yu SH. Nanowire Genome: A Magic Toolbox for 1D Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902807. [PMID: 31566828 DOI: 10.1002/adma.201902807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/07/2019] [Indexed: 06/10/2023]
Abstract
1D nanomaterials with high aspect ratio, i.e., nanowires and nanotubes, have inspired considerable research interest thanks to the fact that exotic physical and chemical properties emerge as their diameters approach or fall into certain length scales, such as the wavelength of light, the mean free path of phonons, the exciton Bohr radius, the critical size of magnetic domains, and the exciton diffusion length. On the basis of their components, aspect ratio, and properties, there may be imperceptible connections among hundreds of nanowires prepared by different strategies. Inspired by the heredity system in life, a new concept termed the "nanowire genome" is introduced here to clarify the relationships between hundreds of nanowires reported previously. As such, this approach will not only improve the tools incorporating the prior nanowires but also help to precisely synthesize new nanowires and even assist in the prediction on the properties of nanowires. Although the road from start-ups to maturity is long and fraught with challenges, the genetical syntheses of more than 200 kinds of nanostructures stemming from three mother nanowires (Te, Ag, and Cu) are summarized here to demonstrate the nanowire genome as a versatile toolbox. A summary and outlook on future challenges in this field are also presented.
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Affiliation(s)
- Zhen He
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yuan Yang
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Hai-Wei Liang
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Jian-Wei Liu
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Shu-Hong Yu
- Division of Nanomaterials and Chemistry, Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, Hefei Science Center of CAS, Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
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7
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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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8
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Xu L, Zhang P, Liu Y, Fang X, Zhang Z, Liu Y, Peng L, Liu J. Continuously Tunable Nucleotide/Lanthanide Coordination Nanoparticles for DNA Adsorption and Sensing. ACS OMEGA 2018; 3:9043-9051. [PMID: 31459038 PMCID: PMC6644583 DOI: 10.1021/acsomega.8b01217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/07/2018] [Indexed: 05/02/2023]
Abstract
Metal-organic coordination polymers (CPs) have attracted great research interest because they are easy to prepare, porous, flexible in composition, and designable in structure. Their applications in biosensor development, drug delivery, and catalysis have been explored. Lanthanides and nucleotides can form interesting CPs, although most previous works have focused on a single type of metal ligand. In this work, we explored mixed nucleotides and studied their DNA adsorption properties using fluorescently labeled oligonucleotides. Adenosine monophosphate (AMP) and guanosine monophosphate (GMP) formed negatively charged CP nanoparticles with most lanthanides, and thus a salt was required to adsorb negatively charged DNA. DNA adsorption was faster and reached a higher capacity with lighter lanthanides. Desorption of pre-adsorbed DNA by inorganic phosphates, urea, proteins, surfactants, and competing DNA was successively carried out. The results suggested the importance of the DNA phosphate backbone, although hydrogen bonding and DNA bases also contributed to adsorption. The AMP CPs adsorbed DNA more strongly than the GMP ones, and using mixtures of AMP and GMP, continuous tuning of DNA adsorption affinity was achieved. Such CPs were also used as a sensor for DNA detection based on the different affinities of single- and double-stranded DNA, and a detection limit of 0.9 nM target DNA was achieved. Instead of tuning DNA adsorption by varying the length and sequence of DNA, the composition of CPs can also be controlled to achieve this goal.
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Affiliation(s)
- Li Xu
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Peipei Zhang
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Yan Liu
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Xiaoqiang Fang
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Zijie Zhang
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Yibo Liu
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Lulu Peng
- School of Chemistry
and Chemical Engineering, Guangdong Pharmaceutical
University, Zhongshan 528458, P. R. China
| | - Juewen Liu
- Department
of Chemistry and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
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9
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Yu Q, Hu J, Hu Y, Wang R. Significance of DNA bond strength in programmable nanoparticle thermodynamics and dynamics. SOFT MATTER 2018; 14:2665-2670. [PMID: 29561032 DOI: 10.1039/c7sm02456h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Assembly of nanoparticles (NPs) coated with complementary DNA strands leads to novel crystals with nanosized basic units rather than classic atoms, ions or molecules. The assembly process is mediated by hybridization of DNA via specific base pairing interaction, and is kinetically linked to the disassociation of DNA duplexes. DNA-level physiochemical quantities, both thermodynamic and kinetic, are key to understanding this process and essential for the design of DNA-NP crystals. The melting transition properties are helpful to judge the thermostability and sensitivity of relative DNA probes or other applications. Three different cases are investigated by changing the linker length and the spacer length on which the melting properties depend using the molecular dynamics method. Melting temperature is determined by sigmoidal melting curves based on hybridization percentage versus temperature and the Lindemann melting rule simultaneously. We provide a computational strategy based on a coarse-grained model to estimate the hybridization enthalpy, entropy and free energy from percentages of hybridizations which are readily accessible in experiments. Importantly, the lifetime of DNA bond dehybridization based on temperature and the activation energy depending on DNA bond strength are also calculated. The simulation results are in good agreement with the theoretical analysis and the present experimental data. Our study provides a good strategy to predict the melting temperature which is important for the DNA-directed nanoparticle system, and bridges the dynamics and thermodynamics of DNA-directed nanoparticle systems by estimating the equilibrium constant from the hybridization of DNA bonds quantitatively.
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Affiliation(s)
- Qiuyan Yu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Jinglei Hu
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Yi Hu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Rong Wang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210023, China.
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10
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Oligonucleotide-conjugated nanoparticles for targeted drug delivery via scavenger receptors class A: An in vitro assessment for proof-of-concept. Int J Pharm 2017; 532:647-655. [PMID: 28827202 DOI: 10.1016/j.ijpharm.2017.08.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/26/2017] [Accepted: 08/12/2017] [Indexed: 12/11/2022]
Abstract
Spherical nucleic acid gold nanoparticles represent a unique nanotechnology in which the spherical arrangement of oligonucleotides enables the nanoparticles to be efficiently internalized into cells expressing scavenger receptors class A (SR-A). Herein, we seek to replace the gold core with a biodegradable polymeric construct and explore their potential applications in targeted drug delivery. Oligonucleotide-conjugated poly(ethylene glycol)-block-poly(ε-caprolactone) was synthesized and characterized by 1H NMR and gel electrophoresis. This polymer was applied to fabricate micellar nanoparticles (OLN-NPs) by an anti-solvent method. These nanoparticles have a mean particle size about 58.1nm with a narrow size distribution (PDI <0.2) and they were also non-cytotoxic. Relative to non-targeted NPs, OLN-NPs exhibited substantially better uptake (3.94×) in a mouse endothelial cell line (C166), attributing to lipid-raft-mediated endocytosis via SR-A. To explore the potential applications of OLN-NPs as drug carriers, paclitaxel, a poorly soluble anti-angiogenic compound, was selected as the model. OLN-NPs increased the solubility of paclitaxel by at least 300×. The boosted drug solubility in conjunction with improved cellular uptake translated into enhanced in vitro efficacy in the inhibition of angiogenesis. In conclusions, OLN-NPs show considerable promise in targeted drug delivery and their potential applications should be further investigated.
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11
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Yu Q, Zhang X, Hu Y, Zhang Z, Wang R. Dynamic Properties of DNA-Programmable Nanoparticle Crystallization. ACS NANO 2016; 10:7485-7492. [PMID: 27409362 DOI: 10.1021/acsnano.6b02067] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The dynamics of DNA hybridization is very important in DNA-programmable nanoparticle crystallization. Here, coarse-grained molecular dynamics is utilized to explore the structural and dynamic properties of DNA hybridizations for a self-complementary DNA-directed nanoparticle self-assembly system. The hexagonal close-packed (HCP) and close-packed face-centered cubic (FCC) ordered structures are identified for the systems of different grafted DNA chains per nanoparticle, which are in good agreement with the experimental results. Most importantly, the dynamic crystallization processes of DNA hybridizations are elucidated by virtue of the mean square displacement, the percentage of hybridizations, and the lifetime of DNA bonds. The lifetime can be modeled by the DNA dehybridization, which has an exponential form. The lifetime of DNA bonds closely depends on the temperature. A suitable temperature for the DNA-nanoparticle crystallization is obtained in the work. Moreover, a too large volume fraction hinders the self-assembly process due to steric effects. This work provides some essential information for future design of nanomaterials.
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Affiliation(s)
- Qiuyan Yu
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Xuena Zhang
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Yi Hu
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Zhihao Zhang
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Rong Wang
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210023, China
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12
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Sharma V, Mohammad A, Mishra V, Chaudhary A, Kapoor K, Mobin SM. Fabrication of innovative ZnO nanoflowers showing drastic biological activity. NEW J CHEM 2016. [DOI: 10.1039/c5nj02391b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The present article highlights a facile approach towards the synthesis of ZnO nanoflowers using designed single molecular precursors (1 and 2) at room temperature. The relative biological activities of 1, 2 and ZnO nanoflowers have also been demonstrated.
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Affiliation(s)
- Vinay Sharma
- Centre for Biosciences and Bio-Medical Engineering
- Indian Institute of Technology Indore
- Indore 452017
- India
| | - Akbar Mohammad
- School of Basic Sciences
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore 452017
- India
| | - Veenu Mishra
- School of Basic Sciences
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore 452017
- India
| | - Archana Chaudhary
- School of Basic Sciences
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore 452017
- India
| | - Kshipra Kapoor
- School of Basic Sciences
- Discipline of Chemistry
- Indian Institute of Technology Indore
- Indore 452017
- India
| | - Shaikh M. Mobin
- Centre for Biosciences and Bio-Medical Engineering
- Indian Institute of Technology Indore
- Indore 452017
- India
- School of Basic Sciences
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13
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Zhang X, Wang R, Xue G. Programming macro-materials from DNA-directed self-assembly. SOFT MATTER 2015; 11:1862-70. [PMID: 25687673 DOI: 10.1039/c4sm02649g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
DNA is a powerful tool that can be attached to nano- and micro-objects and direct the self-assembly through base pairing. Since the strategy of DNA programmable nanoparticle self-assembly was first introduced in 1996, it has remained challenging to use DNA to make powerful diagnostic tools and to make designed materials with novel properties and highly ordered crystal structures. In this review, we summarize recent experimental and theoretical developments of DNA-programmable self-assembly into three-dimensional (3D) materials. Various types of aggregates and 3D crystal structures obtained from an experimental DNA-driven assembly are introduced. Furthermore, theoretical calculations and simulations for DNA-mediated assembly systems are described and we highlight some typical theoretical models for Monte Carlo and Molecular Dynamics simulations.
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Affiliation(s)
- Xuena Zhang
- Department of Polymer Science and Engineering, Key Laboratory of High Performance Polymer Materials and Technology of Ministry of Education, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China.
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14
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Qian C, Siler T, Ozin GA. Exploring the possibilities and limitations of a nanomaterials genome. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:64-69. [PMID: 25244158 DOI: 10.1002/smll.201402197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/25/2014] [Indexed: 06/03/2023]
Abstract
What are we going to do with the cornucopia of nanomaterials appearing in the open and patent literature, every day? Imagine the benefits of an intelligent and convenient means of categorizing, organizing, sifting, sorting, connecting, and utilizing this information in scientifically and technologically innovative ways by building a Nanomaterials Genome founded upon an all-purpose Periodic Table of Nanomaterials. In this Concept article, inspired by work on the Human Genome project, which began in 1989 together with motivation from the recent emergence of the Materials Genome project initiated in 2011 and the Nanoinformatics Roadmap 2020 instigated in 2010, we envision the development of a Nanomaterials Genome (NMG) database with the most advanced data-mining tools that leverage inference engines to help connect and interpret patterns of nanomaterials information. It will be equipped with state-of-the-art visualization techniques that rapidly organize and picture, categorize and interrelate the inherited behavior of complex nanomatter from the information programmed in its constituent nanomaterials building blocks. A Nanomaterials Genome Initiative (NMGI) of the type imagined herein has the potential to serve the global nanoscience community with an opportunity to speed up the development continuum of nanomaterials through the innovation process steps of discovery, structure determination and property optimization, functionality elucidation, system design and integration, certification and manufacturing to deployment in technologies that apply these versatile nanomaterials in environmentally responsible ways. The possibilities and limitations of this concept are critically evaluated in this article.
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Affiliation(s)
- Chenxi Qian
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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15
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Zhang C, Macfarlane RJ, Young KL, Choi CHJ, Hao L, Auyeung E, Liu G, Zhou X, Mirkin CA. A general approach to DNA-programmable atom equivalents. NATURE MATERIALS 2013; 12:741-746. [PMID: 23685863 DOI: 10.1038/nmat3647] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/02/2013] [Indexed: 06/02/2023]
Abstract
Nanoparticles can be combined with nucleic acids to programme the formation of three-dimensional colloidal crystals where the particles' size, shape, composition and position can be independently controlled. However, the diversity of the types of material that can be used is limited by the lack of a general method for preparing the basic DNA-functionalized building blocks needed to bond nanoparticles of different chemical compositions into lattices in a controllable manner. Here we show that by coating nanoparticles protected with aliphatic ligands with an azide-bearing amphiphilic polymer, followed by the coupling of DNA to the polymer using strain-promoted azide-alkyne cycloaddition (also known as copper-free azide-alkyne click chemistry), nanoparticles bearing a high-density shell of nucleic acids can be created regardless of nanoparticle composition. This method provides a route to a virtually endless class of programmable atom equivalents for DNA-based colloidal crystallization.
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Affiliation(s)
- Chuan Zhang
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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16
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Li TING, Sknepnek R, Olvera de la Cruz M. Thermally active hybridization drives the crystallization of DNA-functionalized nanoparticles. J Am Chem Soc 2013; 135:8535-41. [PMID: 23662638 DOI: 10.1021/ja312644h] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The selectivity of DNA recognition inspires an elegant protocol for designing versatile nanoparticle (NP) assemblies. We use molecular dynamics simulations to analyze dynamic aspects of the assembly process and identify ingredients that are key to a successful assembly of NP superlattices through DNA hybridization. A scale-accurate coarse-grained model faithfully captures the relevant contributions to the kinetics of the DNA hybridization process and is able to recover all experimentally reported to date binary superlattices (BCC, CsCl, AlB2, Cr3Si, and Cs6C60). We study the assembly mechanism in systems with up to 10(6) degrees of freedom and find that the crystallization process is accompanied with a slight decrease of enthalpy. Furthermore, we find that the optimal range of the DNA linker interaction strengths for a successful assembly is 12-16kBT, and the optimal mean lifetime of a DNA hybridization event is 10(-4)-10(-3) of the total time it takes to form a crystal. We also obtain the optimal percentage of hybridized DNA pairs for different binary systems. On the basis of these results, we propose suitable linker sequences for future nanomaterials design.
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Affiliation(s)
- Ting I N G Li
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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17
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Li W, Chakrabarti A, Gunton JD. Self-assembly of a bipolar model of biomacromolecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4470-4476. [PMID: 23484544 DOI: 10.1021/la4002994] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Extending recent work on a generic bipolar model proposed to study the nanochain formation of amelogenin molecules, we conduct a systematic investigation in this paper on the self-assembly of such a model via sweeping the relative parameter space. The bipolar model consists of a short-range attraction and an off-center Coulomb repulsion for the supermolecule. Through the Brownian dynamics simulation of both translational and rotational motions, we study the kinetics of the self-assembly and the structure of clusters formed within the system for various interaction settings. From the results of structure factor and cluster analysis, we find that the range of the repulsive interaction has a sensitive impact in controlling the cluster size, while the strength of the attractive interaction dominates the cluster morphology such that the greater the attraction among particles, the more elongated the cluster formed.
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Affiliation(s)
- Wei Li
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA.
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18
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Von White G, Chen Y, Roder-Hanna J, Bothun GD, Kitchens CL. Structural and thermal analysis of lipid vesicles encapsulating hydrophobic gold nanoparticles. ACS NANO 2012; 6:4678-85. [PMID: 22632177 DOI: 10.1021/nn2042016] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The structure and stability of hybrid lipid vesicles containing bilayer-encapsulated hydrophobic nanoparticles is dependent upon lipid phase behavior. By embedding stearylamine-stabilized gold nanoparticles in dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylglycerol vesicles, we show that encapsulation at lipid to nanoparticle ratios from 10,000:1 to 5000:1 leads to bilayer thickening and hydrophobic mismatch, favoring nanoparticle inclusion in gel phase vesicles. High loadings lead to large increases in the gel to fluid melting temperature upon heating and significant hysteresis on cooling, which cannot be attributed solely to excess free ligand. This behavior is due to a cooperative effect of excess free SA ligand and nanoparticle embedment. Nanoparticle clustering was observed during lipid melting and could be reversed upon lipid freezing owing to lateral capillary forces within the bilayer. The impact of nanoparticle embedment on vesicle structure and properties at such low concentrations is reminiscent of hydrophobic proteins, suggesting that the underlying lipid biophysics between proteins and nanoparticle are similar and may provide a predictive design tool for therapeutic applications.
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Affiliation(s)
- Gregory Von White
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, USA
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19
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Li TING, Sknepnek R, Macfarlane RJ, Mirkin CA, de la Cruz MO. Modeling the crystallization of spherical nucleic acid nanoparticle conjugates with molecular dynamics simulations. NANO LETTERS 2012; 12:2509-2514. [PMID: 22458569 DOI: 10.1021/nl300679e] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We use molecular dynamics simulations to study the crystallization of spherical nucleic-acid (SNA) gold nanoparticle conjugates, guided by sequence-specific DNA hybridization events. Binary mixtures of SNA gold nanoparticle conjugates (inorganic core diameter in the 8-15 nm range) are shown to assemble into BCC, CsCl, AlB(2), and Cr(3)Si crystalline structures, depending upon particle stoichiometry, number of immobilized strands of DNA per particle, DNA sequence length, and hydrodynamic size ratio of the conjugates involved in crystallization. These data have been used to construct phase diagrams that are in excellent agreement with experimental data from wet-laboratory studies.
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Affiliation(s)
- Ting I N G Li
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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20
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Baeissa A, Moghimi N, Liu J. Hydrogel porosity controlling DNA-directed immobilization of gold nanoparticles revealed by DNA melting and scanning helium ion microscopy. RSC Adv 2012. [DOI: 10.1039/c2ra01252a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Zhang X, Sun D, Sue HJ, Nishimura R. Colloidal crystallization of surfactant-free ZnO quantum dots. Chemphyschem 2011; 12:3533-8. [PMID: 22069245 DOI: 10.1002/cphc.201100579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Indexed: 01/26/2023]
Affiliation(s)
- Xi Zhang
- Materials Science and Engineering Program, Texas A&M University, College Station, Texas 77843, USA
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22
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Crew E, Rahman S, Razzak-Jaffar A, Mott D, Kamundi M, Yu G, Tchah N, Lee J, Bellavia M, Zhong CJ. MicroRNA Conjugated Gold Nanoparticles and Cell Transfection. Anal Chem 2011; 84:26-9. [DOI: 10.1021/ac202749p] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Elizabeth Crew
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Sharaara Rahman
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Asma Razzak-Jaffar
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Derrick Mott
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Martha Kamundi
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Gang Yu
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Nuri Tchah
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Jehwan Lee
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Michael Bellavia
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
| | - Chaun-Jian Zhong
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York, 13902,
United States
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23
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Li W, Liu Y, Perez T, Gunton JD, Sorensen CM, Chakrabarti A. Kinetics of nanochain formation in a simplified model of amelogenin biomacromolecules. Biophys J 2011; 101:2502-6. [PMID: 22098749 PMCID: PMC3218329 DOI: 10.1016/j.bpj.2011.09.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/25/2011] [Accepted: 09/02/2011] [Indexed: 10/15/2022] Open
Abstract
We show that the kinetics of nanochain formation of amelogenin molecules is well described by a combination of translational and rotational diffusion of a simplified anisotropic bipolar model consisting of hydrophobic spherical colloid particles and a point charge located on each particle surface. The colloid particles interact via a standard depletion attraction whereas the point charges interact through a screened Coulomb repulsion. We study the kinetics via a Brownian dynamics simulation of both translational and rotational motions and show that the anisotropy brought in by the charge dramatically affects the kinetic pathway of cluster formation and our simple model captures the main features of the experimental observations.
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Affiliation(s)
- Wei Li
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania, USA.
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24
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Rybtchinski B. Adaptive supramolecular nanomaterials based on strong noncovalent interactions. ACS NANO 2011; 5:6791-818. [PMID: 21870803 DOI: 10.1021/nn2025397] [Citation(s) in RCA: 345] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Noncovalent systems are adaptive and allow facile processing and recycling. Can they be at the same time robust? How can one rationally design such systems? Can they compete with high-performance covalent materials? The recent literature reveals that noncovalent systems can be robust yet adaptive, self-healing, and recyclable, featuring complex nanoscale structures and unique functions. We review such systems, focusing on the rational design of strong noncovalent interactions, kinetically controlled pathway-dependent processes, complexity, and function. The overview of the recent examples points at the emergent field of noncovalent nanomaterials that can represent a versatile, multifunctional, and environmentally friendly alternative to conventional covalent systems.
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Affiliation(s)
- Boris Rybtchinski
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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25
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Luthi AJ, Patel PC, Ko CH, Mutharasan RK, Mirkin CA, Thaxton CS. Nanotechnology for synthetic high-density lipoproteins. Trends Mol Med 2010; 16:553-60. [PMID: 21087901 PMCID: PMC4076051 DOI: 10.1016/j.molmed.2010.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 10/12/2010] [Accepted: 10/12/2010] [Indexed: 01/04/2023]
Abstract
Atherosclerosis is the disease mechanism responsible for coronary heart disease (CHD), the leading cause of death worldwide. One strategy to combat atherosclerosis is to increase the amount of circulating high-density lipoproteins (HDL), which transport cholesterol from peripheral tissues to the liver for excretion. The process, known as reverse cholesterol transport, is thought to be one of the main reasons for the significant inverse correlation observed between HDL blood levels and the development of CHD. This article highlights the most common strategies for treating atherosclerosis using HDL. We further detail potential treatment opportunities that utilize nanotechnology to increase the amount of HDL in circulation. The synthesis of biomimetic HDL nanostructures that replicate the chemical and physical properties of natural HDL provides novel materials for investigating the structure-function relationships of HDL and for potential new therapeutics to combat CHD.
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Affiliation(s)
- Andrea J. Luthi
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Pinal C. Patel
- Interdepartmental Biological Sciences, Northwestern University, 2145 Sheridan Road, Evanston, Il 60203, USA
| | - Caroline H. Ko
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - R. Kannan Mutharasan
- Feinberg Cardiovascular Research Institute, Northwestern University, 303 E. Chicago Avenue, Chicago, IL 60611
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - C. Shad Thaxton
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Feinberg School of Medicine, Department of Urology, 303 E. Chicago Avenue, Tarry 16-703, Chicago, IL 60611, USA
- Institute for BioNanotechnology and Medicine, Northwestern University, 303 E. Superior, Suite 11-131, Chicago, IL 60611, USA
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