1
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Zeng C, Jian Y, Zhuo C, Li A, Zeng C, Zhao Y. Evaluation of DNA-protein complex structures using the deep learning method. Phys Chem Chem Phys 2023; 26:130-143. [PMID: 38063012 DOI: 10.1039/d3cp04980a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Biological processes such as transcription, repair, and regulation require interactions between DNA and proteins. To unravel their functions, it is imperative to determine the high-resolution structures of DNA-protein complexes. However, experimental methods for this purpose are costly and technically demanding. Consequently, there is an urgent need for computational techniques to identify the structures of DNA-protein complexes. Despite technological advancements, accurately identifying DNA-protein complexes through computational methods still poses a challenge. Our team has developed a cutting-edge deep-learning approach called DDPScore that assesses DNA-protein complex structures. DDPScore utilizes a 4D convolutional neural network to overcome limited training data. This approach effectively captures local and global features while comprehensively considering the conformational changes arising from the flexibility during the DNA-protein docking process. DDPScore consistently outperformed the available methods in comprehensive DNA-protein complex docking evaluations, even for the flexible docking challenges. DDPScore has a wide range of applications in predicting and designing structures of DNA-protein complexes.
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Affiliation(s)
- Chengwei Zeng
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China.
| | - Yiren Jian
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
| | - Chen Zhuo
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China.
| | - Anbang Li
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China.
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington, DC 20052, USA
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, 430079, China.
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2
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McCarthy DR, Remington JM, Ferrell JB, Schneebeli ST, Li J. Nano-Bio Interactions between DNA Nanocages and Human Serum Albumin. J Chem Theory Comput 2023; 19:7873-7881. [PMID: 37877553 PMCID: PMC11070245 DOI: 10.1021/acs.jctc.3c00720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
DNA nanostructures have emerged as promising nanomedical tools due to their biocompatibility and tunable behavior. Recent work has shown that DNA nanocages decorated with organic dendrimers strongly bind human serum albumin (HSA), yet the dynamic structures of these complexes remain uncharacterized. This theoretical and computational investigation elucidates the fuzzy interactions between dendritically functionalized cubic DNA nanocages and HSA. The dendrimer-HSA interactions occur via nonspecific binding with the protein thermodynamically and kinetically free to cross the open faces of the cubic scaffold. However, the rigidity of the DNA scaffold prevents the binding energetics from scaling with the number of dendrimers. These discoveries not only provide a useful framework by which to model general interactions of DNA nanostructures complexed with serum proteins but also give valuable molecular insight into the design of next-generation DNA nanomedicines.
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Affiliation(s)
| | | | | | - Severin T. Schneebeli
- Department of Chemistry, University of Vermont, Burlington, VT 05405
- Department of Industrial and Physical Pharmacy and Department of Chemistry, Purdue University, West Lafayette, IN 47907
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT 05405
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907
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3
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Raj A, Thomas RK, Vidya L, Neelima S, Aparna VM, Sudarsanakumar C. A Minor Groove Binder with Significant Cytotoxicity on Human Lung Cancer Cells: The Potential of Hesperetin Functionalised Silver Nanoparticles. J Fluoresc 2023:10.1007/s10895-023-03409-7. [PMID: 37721707 DOI: 10.1007/s10895-023-03409-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023]
Abstract
Natural drug functionalised silver (Ag) nanoparticles (NPs) have gained significant interest in pharmacology related applications due to their therapeutic efficiency. We have synthesised silver nanoparticle using hesperetin as a reducing and capping agent. This work aims to discuss the relevance of the hesperetin functionalised silver nanoparticles (H-AgNPs) in the field of nano-medicine. The article primarily investigates the anticancer activity of H-AgNPs and then their interactions with calf thymus DNA (ctDNA) through spectroscopic and thermodynamic techniques. The green synthesised H-AgNPs are stable, spherical in shape and size of 10 ± 3 nm average diameter. The complex formation of H-AgNPs with ctDNA was established by UV-Visible absorption, fluorescent dye displacement assay, isothermal calorimetry and viscosity measurements. The binding constants obtained from these experiments were consistently in the order of 104 Mol-1. The melting temperature analysis and FTIR measurements confirmed that the structural alterations of ctDNA by the presence of H-AgNPs are minimal. All the thermodynamic variables and the endothermic binding nature were acquired from ITC experiments. All these experimental outcomes reveal the formation of H-AgNPs-ctDNA complex, and the results consistently verify the minor groove binding mode of H-AgNPs. The binding constant and limit of detection of 1.8 μM found from the interaction studies imply the DNA detection efficiency of H-AgNPs. The cytotoxicity of H-AgNPs against A549 and L929 cell lines were determined by in vitro MTT cell viability assay and lactate dehydrogenase (LDH) assay. The cell viability and LDH enzyme release are confirmed that the H-AgNPs has high anticancer activity. Moreover, the calculated LD50 value for H-AgNPs against lung cancer cells is 118.49 µl/ml, which is a low value comparing with the value for fibroblast cells (269.35 µl/ml). In short, the results of in vitro cytotoxicity assays revealed that the synthesised nanoparticles can be considered in applications related to cancer treatments. Also, we have found that, H-AgNPs is a minor groove binder, and having high DNA detection efficiency.
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Affiliation(s)
- Aparna Raj
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - Riju K Thomas
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
- Bharata Mata College, Thrikkakara, Ernakulam, Kerala, 682032, India
| | - L Vidya
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - S Neelima
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - V M Aparna
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India
| | - C Sudarsanakumar
- School of Pure & Applied Physics, Mahatma Gandhi University, P.D Hills (P.O), Kottayam, Kerala, 686 560, India.
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4
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Lysne D, Hachigian T, Thachuk C, Lee J, Graugnard E. Leveraging Steric Moieties for Kinetic Control of DNA Strand Displacement Reactions. J Am Chem Soc 2023. [PMID: 37487322 PMCID: PMC10401717 DOI: 10.1021/jacs.3c04344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
DNA strand displacement networks are a critical part of dynamic DNA nanotechnology and are proven primitives for implementing chemical reaction networks. Precise kinetic control of these networks is important for their use in a range of applications. Among the better understood and widely leveraged kinetic properties of these networks are toehold sequence, length, composition, and location. While steric hindrance has been recognized as an important factor in such systems, a clear understanding of its impact and role is lacking. Here, a systematic investigation of steric hindrance within a DNA toehold-mediated strand displacement network was performed through tracking kinetic reactions of reporter complexes with incremental concatenation of steric moieties near the toehold. Two subsets of steric moieties were tested with systematic variation of structures and reaction conditions to isolate sterics from electrostatics. Thermodynamic and coarse-grained computational modeling was performed to gain further insight into the impacts of steric hindrance. Steric factors yielded up to 3 orders of magnitude decrease in the reaction rate constant. This pronounced effect demonstrates that steric moieties can be a powerful tool for kinetic control in strand displacement networks while also being more broadly informative of DNA structural assembly in both DNA-based therapeutic and diagnostic applications that possess elements of steric hindrance through DNA functionalization with an assortment of chemistries.
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Affiliation(s)
- Drew Lysne
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Tim Hachigian
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Chris Thachuk
- Paul G Allen School of Computer Science and Engineering, University of Washington, Paul G. Allen Center, Box 352350, 185 E Stevens Way NE, Seattle, Washington 98195-2350, United States
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
- Department of Chemistry and Biochemistry, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States
- Center for Advanced Energy Studies, Idaho Falls, Idaho 83401, United States
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5
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Ge L, Shi X, Li B, Gong K. Fluctuation-induced dispersion forces on thin DNA films. Phys Rev E 2023; 107:064402. [PMID: 37464699 DOI: 10.1103/physreve.107.064402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/15/2023] [Indexed: 07/20/2023]
Abstract
In this work, the calculation of Casimir forces across thin DNA films is carried out based on the Lifshitz theory. The variations of Casimir forces due to the DNA thicknesses, volume fractions of containing water, covering media, and substrates are investigated. For a DNA film suspended in air or water, the Casimir force is attractive, and its magnitude increases with decreasing thickness of DNA films and the water volume fraction. For DNA films deposited on a dielectric (silica) substrate, the Casimir force is attractive for the air environment. However, the Casimir force shows unusual features in a water environment. Under specific conditions, switching sign of the Casimir force from attractive to repulsive can be achieved by increasing the DNA-film thickness. Finally, the Casimir force for DNA films deposited on a metallic substrate is investigated. The Casimir force is dominated by the repulsive interactions at a small DNA-film thickness for both the air and water environments. In a water environment, the Casimir force turns out to be attractive for a large DNA-film thickness, and a stable Casimir equilibrium can be found. The influences of electrolyte screening on the Casimir pressure of DNA films are also discussed at the end. In addition to the adhesion stability, our finding could be applicable to the problems of condensation and decondensation of DNA, due to fluctuation-induced dispersion forces.
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Affiliation(s)
- Lixin Ge
- School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Xi Shi
- Department of Physics, Shanghai Normal University, Shanghai 200234, China
| | - Bingzhong Li
- School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, China
| | - Ke Gong
- School of Physics and Electronic Engineering, Xinyang Normal University, Xinyang 464000, China
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6
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Polymeric DNA Hydrogels and Their Applications in Drug Delivery for Cancer Therapy. Gels 2023; 9:gels9030239. [PMID: 36975688 PMCID: PMC10048489 DOI: 10.3390/gels9030239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/22/2023] Open
Abstract
The biomolecule deoxyribonucleic acid (DNA), which acts as the carrier of genetic information, is also regarded as a block copolymer for the construction of biomaterials. DNA hydrogels, composed of three-dimensional networks of DNA chains, have received considerable attention as a promising biomaterial due to their good biocompatibility and biodegradability. DNA hydrogels with specific functions can be prepared via assembly of various functional sequences containing DNA modules. In recent years, DNA hydrogels have been widely used for drug delivery, particularly in cancer therapy. Benefiting from the sequence programmability and molecular recognition ability of DNA molecules, DNA hydrogels prepared using functional DNA modules can achieve efficient loading of anti-cancer drugs and integration of specific DNA sequences with cancer therapeutic effects, thus achieving targeted drug delivery and controlled drug release, which are conducive to cancer therapy. In this review, we summarized the assembly strategies for the preparation of DNA hydrogels on the basis of branched DNA modules, hybrid chain reaction (HCR)-synthesized DNA networks and rolling circle amplification (RCA)-produced DNA chains, respectively. The application of DNA hydrogels as drug delivery carriers in cancer therapy has been discussed. Finally, the future development directions of DNA hydrogels in cancer therapy are prospected.
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7
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Esmaeeli R, Bauzá A, Perez A. Structural predictions of protein-DNA binding: MELD-DNA. Nucleic Acids Res 2023; 51:1625-1636. [PMID: 36727436 PMCID: PMC9976882 DOI: 10.1093/nar/gkad013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/27/2022] [Accepted: 01/30/2023] [Indexed: 02/03/2023] Open
Abstract
Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein-DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein-DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein-DNA interactions).
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Affiliation(s)
- Reza Esmaeeli
- Department of Chemistry, Quantum theory project, University of Florida, Gainesville, FL 32611, USA
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Palma de Mallorca (Baleares), 07122, Spain
| | - Alberto Perez
- Department of Chemistry, Quantum theory project, University of Florida, Gainesville, FL 32611, USA
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8
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Han LT, Sun GG, Ruan LS, Li X. Structured Aptamers: A Flourishing Nanomaterial for Tumor Targeting. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structured aptamers are nucleic acid systems produced using DNA nano self-assembly technology and can be constructed in a programmable manner. These aptamers are widely used in biomedical fields because of their low biological toxicity, weak immunogenicity, good cytocompatibility and
biocompatibility, stability, and facile modification ability. Additionally, structured aptamers achieve nano precision in spatial configuration and can be directly internalized into targets without the assistance of transfection reagents. They exhibit higher stability, rigidity, and binding
efficiency than aptamers alone. Therefore, structured aptamers have been universally applied in the tumor-targeting field and have emerged as a current research hotspot. Here, we introduce the assembly principle, assembly methods, and characterization methods of structured aptamers. Moreover,
the application status of structured aptamers for tumor detection and targeted therapy is summarized to provide new research directions for early diagnosis and drug research in the field of oncology.
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Affiliation(s)
- Li-Ting Han
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ge-Ge Sun
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Luo-Shan Ruan
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xin Li
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
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9
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Hu P, Dong Y, Yao C, Yang D. Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering. Chem Asian J 2022; 17:e202200310. [PMID: 35468254 DOI: 10.1002/asia.202200310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/23/2022] [Indexed: 11/08/2022]
Abstract
Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.
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Affiliation(s)
- Pin Hu
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Yuhang Dong
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Chi Yao
- Tianjin University, School of Chemical Engineering and Technology, CHINA
| | - Dayong Yang
- Tianjin University, Chemistry Department, Room 328, Building 54, 300350, Tianjin, CHINA
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10
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Zamoskovtseva AA, Golyshev VM, Kizilova VA, Shevelev GY, Pyshnyi DV, Lomzov AA. Pairing nanoarchitectonics of oligodeoxyribonucleotides with complex diversity: concatemers and self-limited complexes. RSC Adv 2022; 12:6416-6431. [PMID: 35424594 PMCID: PMC8981972 DOI: 10.1039/d2ra00155a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
The development of approaches to the design of two- and three-dimensional self-assembled DNA-based nanostructures with a controlled shape and size is an essential task for applied nanotechnology, therapy, biosensing, and bioimaging. We conducted a comprehensive study on the formation of various complexes from a pair of oligonucleotides with two transposed complementary blocks that can be linked through a nucleotide or non-nucleotide linker. A methodology is proposed to prove the formation of a self-limited complex and to determine its molecularity. It is based on the "opening" of a self-limited complex with an oligonucleotide that effectively binds to a duplex-forming block. The complexes assembled from a pair of oligonucleotides with different block length and different linker sizes and types were investigated by theoretical analysis, several experimental methods (a gel shift assay, atomic force microscopy, and ultraviolet melting analysis), and molecular dynamics simulations. The results showed a variety of complexes formed by only a pair of oligonucleotides. Self-limited associates, concatemer complexes, or mixtures thereof can arise if we change the length of a duplex and loop-forming blocks in oligonucleotides or via introduction of overhangs and chemical modifications. We postulated basic principles of rational design of native self-limited DNA complexes of desired structure, shape, and molecularity. Our foundation makes self-limited complexes useful tools for nanotechnology, biological studies, and therapeutics.
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Affiliation(s)
- Anastasia A Zamoskovtseva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
- Moscow Institute of Physics and Technology 9 Institutskiy per., Dolgoprudny 141701 Russia
| | - Victor M Golyshev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Valeria A Kizilova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS 8 Lavrentiev Avenue Novosibirsk 630090 Russia
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11
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Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
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Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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12
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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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13
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Jiang Z, Thayumanavan S. Non-cationic Material Design for Nucleic Acid Delivery. ADVANCED THERAPEUTICS 2020; 3:1900206. [PMID: 34164572 PMCID: PMC8218910 DOI: 10.1002/adtp.201900206] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Indexed: 12/16/2022]
Abstract
Nucleic acid delivery provides effective options to control intracellular gene expression and protein production. Efficient delivery of nucleic acid typically requires delivery vehicles to facilitate the entry of nucleic acid into cells. Among non-viral delivery vehicles, cationic materials are favored because of their high loading capacity of nucleic acids and prominent cellular uptake efficiency through electrostatic interaction. However, cationic moieties at high dosage tend to induce severe cytotoxicity due to the interference on cell membrane integrity. In contrast, non-cationic materials present alternative delivery approaches with less safety concerns than cationic materials. In this Progress Report, principles of non-cationic material design for nucleic acid delivery are discussed. Examples of such non-cationic platforms are highlighted, including complexation or conjugation with nucleic acids and self-assembled nucleic acid structures.
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Affiliation(s)
- Ziwen Jiang
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA
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14
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Pan G, Mou Q, Ma Y, Ding F, Zhang J, Guo Y, Huang X, Li Q, Zhu X, Zhang C. pH-Responsive and Gemcitabine-Containing DNA Nanogel To Facilitate the Chemodrug Delivery. ACS APPLIED MATERIALS & INTERFACES 2019; 11:41082-41090. [PMID: 31603313 DOI: 10.1021/acsami.9b14892] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Herein, we construct a structure-switchable gemcitabine (Ge)-containing DNA nanogel that can respond to the intracellular acidic environment, subsequently facilitating the chemodrug release inside the cells. Based on the structural similarity between Ge and deoxycytidine (dC), dC nucleotides in the component DNA strands used for nanogel assembly are fully replaced by Ge during their synthesis. By changing the designed sequences, two Ge-containing Y-shaped motifs with different sticky ends are first assembled and then associated together to form nanogel by sticky-end hybridizations. In particular, one of the sticky-end sequences is arbitrarily designed to be rich of Ge and the other is designed to be partially complementary to the first Ge-rich sticky end. At the neutral or basic condition, the Ge-rich sticky ends hybridize with the partially complementary sticky ends on the second Y motifs, keeping the assembled nanogel stable. Upon being exposed to the acidic condition, Ge-rich sticky ends intend to form intramolecular i-motif-like quadruplex structures, resulting in the disassembly of the nanogel. On the one hand, the nanosized feature enables the Ge-containing nanogel with rapid cellular uptake behavior. On the other hand, the pH-responsive feature endows the rapid disassembly of the nanogel to facilitate the enzymatic drug release inside the cell, resulting in the enhanced anticancer activity of the DNA-based drug delivery system.
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Affiliation(s)
- Gaifang Pan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Quanbing Mou
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Yuan Ma
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Fei Ding
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Jiao Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Yuanyuan Guo
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Xiangang Huang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Qifeng Li
- Department of Paediatric Neurosurgery, Xinhua Hospital , Shanghai Jiao Tong University, School of Medicine , Shanghai 200092 , China
| | - Xinyuan Zhu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Key Laboratory of Electrical Insulation and Thermal Ageing , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
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15
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Maysinger D, Ji J. Nanostructured Modulators of Neuroglia. Curr Pharm Des 2019; 25:3905-3916. [PMID: 31512994 DOI: 10.2174/1381612825666190912163339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/08/2019] [Indexed: 01/08/2023]
Abstract
Biological and synthetic nanostructures can influence both glia and neurons in the central nervous system. Neurons represent only a small proportion (about 10%) of cells in the brain, whereas glial cells are the most abundant cell type. Non-targeted nanomedicines are mainly internalized by glia, in particular microglia, and to a lesser extent by astrocytes. Internalized nanomedicines by glia indirectly modify the functional status of neurons. The mechanisms of biochemical, morphological and functional changes of neural cells exposed to nanomedicines are still not well-understood. This minireview provides a cross-section of morphological and biochemical changes in glial cells and neurons exposed to different classes of hard and soft nanostructures.
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Affiliation(s)
- Dusica Maysinger
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec H3AOG4, Canada
| | - Jeff Ji
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec H3AOG4, Canada
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16
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Wang F, Zhang X, Liu X, Fan C, Li Q. Programming Motions of DNA Origami Nanomachines. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900013. [PMID: 30908896 DOI: 10.1002/smll.201900013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/27/2019] [Indexed: 05/15/2023]
Abstract
DNA nanotechnology enables the precise fabrication of DNA-based machines with nanoscale dimensions. A wide range of DNA nanomachines are designed, which can be activated by specific inputs to perform various movement and functions. The excellent rigidity and unprecedented addressability of DNA origami have made it an excellent platform for manipulating and investigating the motion behaviors of DNA machines at single-molecule level. In this Concept, power supply, machine actuation, and motion behavior of DNA machines on origami platforms are summarized and classified. The strategies utilized for programming motion behavior of DNA machines on DNA origami are also discussed with representative examples. The challenges and outlook for future development of manipulating DNA nanomachines at the single molecule level are presented and discussed.
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Affiliation(s)
- Fei Wang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University and Affiliated Sixth People's Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201499, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueli Zhang
- Joint Research Center for Precision Medicine, Shanghai Jiao Tong University and Affiliated Sixth People's Hospital South Campus, Southern Medical University Affiliated Fengxian Hospital, Shanghai, 201499, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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17
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Tan X, Lu H, Sun Y, Chen X, Wang D, Jia F, Zhang K. Expanding the materials space of DNA via organic-phase ring-opening metathesis polymerization. Chem 2019; 5:1584-1596. [PMID: 31903440 DOI: 10.1016/j.chempr.2019.03.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Herein, we develop a facile route to bring DNA to the organic phase, which greatly expands the types of structures accessible using DNA macromonomers. Phosphotriester- and exocyclic amine-protected DNA was synthesized and further modified with a norbornene moiety, which enables homopolymerization via ring-opening metathesis to produce brush-type DNA graft polymers in high yields. Subsequent deprotection cleanly reveals the natural phosphodiester DNA. The method not only achieves high molecular weight DNA graft polymers but when carried out at low monomer:catalyst ratios, yields oligomers that can be further fractionated to molecularly pure, monodisperse entities with one through ten DNA strands per molecule. In addition, we demonstrate substantial simplification in the preparation of traditionally difficult DNA-containing structures, such as DNA/poly(ethylene glycol) diblock graft copolymers and DNA amphiphiles. We envision that the marriage of oligonucleotides with the vast range of organic-phase polymerizations will result in many new classes of materials with yet unknown properties.
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Affiliation(s)
- Xuyu Tan
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States
| | - Hao Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States
| | - Yehui Sun
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States
| | - Xiaoying Chen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States
| | - Dali Wang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States
| | - Fei Jia
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States
| | - Ke Zhang
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States
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18
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Biniuri Y, Albada B, Willner I. Probing ATP/ATP-Aptamer or ATP-Aptamer Mutant Complexes by Microscale Thermophoresis and Molecular Dynamics Simulations: Discovery of an ATP-Aptamer Sequence of Superior Binding Properties. J Phys Chem B 2018; 122:9102-9109. [PMID: 30188731 DOI: 10.1021/acs.jpcb.8b06802] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microscale thermophoresis (MST) is used to follow the dissociation constants corresponding to ATTO 488-labeled adenosine triphosphate (ATP) and the ATP-aptamer or ATP-aptamer mutants that include two binding sites for the ATP ligand. A set of eight ATP-aptamer mutants, where the thymidine bases, within the reported ATP binding aptamer sites, are substituted with cytosine bases, are examined. The MST-derived dissociation constant of ATP to the reported aptamer is Kd = 31 ± 3 μM, whereas most of the aptamer mutants show lower affinity (higher Kd values) toward the ATP ligand. One aptamer mutant reveals, however, a higher affinity toward the ATP ligand, as compared to the reported ATP-aptamer. Molecular dynamics and docking simulations identify the structural features that control the affinities of binding of the ATP ligand to the two binding sites associated with the ATP-aptamer or the ATP-aptamer mutants. The simulated structures suggest that H-bonds between the ATP ligand and G9 and G11 bases, within one binding domain, and the π-π interactions between G6 and the ATP purine moiety and the pyrimidine ring, in the second binding domain, control the affinity of binding interactions between the ATP ligand and the ATP-aptamer or ATP-aptamer mutant. Very good correlation between the computed Kd values and the MST-derived Kd values is found. The ATP-aptamer mutant (consisting of A1→ G, T4 → C, T12 → C, A24 → G, and T27 → C mutations) reveals superior binding affinities toward the ATP ligands ( Kd = 15 ± 1 μM) as compared to the binding affinity of ATP to the reported aptamer. These features of the mutant are supported by molecular dynamics simulations.
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Affiliation(s)
- Yonatan Biniuri
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Bauke Albada
- Laboratory of Organic Chemistry , Wageningen University & Research , Stippeneng 4 , 6708 WE , The Netherlands
| | - Itamar Willner
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
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19
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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20
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Wang Y, Zhu Y, Hu Y, Zeng G, Zhang Y, Zhang C, Feng C. How to Construct DNA Hydrogels for Environmental Applications: Advanced Water Treatment and Environmental Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1703305. [PMID: 29450972 DOI: 10.1002/smll.201703305] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 11/23/2017] [Indexed: 06/08/2023]
Abstract
With high binding affinity, porous structures, safety, green, programmability, etc., DNA hydrogels have gained increasing recognition in the environmental field, i.e., advanced treatment technology of water and analysis of specific pollutants. DNA hydrogels have been demonstrated as versatile potential adsorbents, immobilization carriers of bioactive molecules, catalysts, sensors, etc. Moreover, altering components or choosing appropriate functional DNA optimizes environment-oriented hydrogels. However, the lack of comprehensive information hinders the continued optimization. The principle used to fabricate the most suitable hydrogels in terms of the requirements is the focus of this Review. First, different fabrication strategies are introduced and the ideal characteristic for environmental applications is in focus. Subsequently, recent environmental applications and the development of diverse DNA hydrogels regarding their synthesis mechanism are summarized. Finally, the Review provides an insight into the remaining challenging and future perspectives in environmental applications.
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Affiliation(s)
- Yingrong Wang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yuan Zhu
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yi Hu
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Guangming Zeng
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Yi Zhang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
- Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Chang Zhang
- College of Environmental Science and Engineering, Hunan University, Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Lushan South Road, Changsha, 410082, P. R. China
| | - Chongling Feng
- Research Center of Environmental Science and Engineering, Center South University of Forestry and Technology, Shaoshan South Road, Changsha, 410004, China
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21
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Norouzi A, Ravan H, Mohammadi A, Hosseinzadeh E, Norouzi M, Fozooni T. Aptamer-integrated DNA nanoassembly: A simple and sensitive DNA framework to detect cancer cells. Anal Chim Acta 2018. [PMID: 29534792 DOI: 10.1016/j.aca.2018.02.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions. While an aptamer moiety guided the nanoassembly to the target cancer cell, the peroxidase-mimicking DNAzymes embedded in the nanoassemblies were used as the sensing element to produce colorimetric signals. As proof-of-concept, as low as 175 cancer cells were detected by the assay, and color change was clearly distinguished by the naked eyes. The proposed system enjoys potential applications for point-of-care cancer diagnosis, with its excellent sensitivity and selectivity.
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Affiliation(s)
- Akram Norouzi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Abbas Mohammadi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Elyas Hosseinzadeh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahdieh Norouzi
- Department of Nursing, Islamic Azad University of Kerman, Kerman, Iran
| | - Tahereh Fozooni
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
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22
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Yu X, Gou X, Wu P, Han L, Tian D, Du F, Chen Z, Liu F, Deng G, Chen AT, Ma C, Liu J, Hashmi SM, Guo X, Wang X, Zhao H, Liu X, Zhu X, Sheth K, Chen Q, Fan L, Zhou J. Activatable Protein Nanoparticles for Targeted Delivery of Therapeutic Peptides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:10.1002/adma.201705383. [PMID: 29315863 PMCID: PMC5812013 DOI: 10.1002/adma.201705383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Indexed: 05/06/2023]
Abstract
Clinical translation of therapeutic peptides, particularly those that require penetration of the cell membrane or are cytolytic, is a major challenge. A novel approach based on a complementary mechanism, which has been widely used for guided synthesis of DNA or RNA nanoparticles, for de novo design of activatable protein nanoparticles (APNPs) for targeted delivery of therapeutic peptides is described. APNPs are formed through self-assembly of three independent polypeptides based on pairwise coiled-coil dimerization. They are capable of long circulation in the blood and can be engineered to target diseases. Peptides to be delivered are incorporated into APNPs and released into the disease microenvironment by locally enriched proteases. It is demonstrated that APNPs mediate efficient delivery of NR2B9c, a neuroprotective peptide that functions after cell penetration, and melittin, a cytolytic peptide that perturbs the lipid bilayer, for effective treatment of stroke and cancer, respectively. Due to their robust properties, simple design, and economic costs, APNPs have great potential to serve as a versatile platform for controlled delivery of therapeutic peptides.
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Affiliation(s)
- Xi Yu
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Xingchun Gou
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, 710021, China
| | - Peng Wu
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Liang Han
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Daofeng Tian
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Fengyi Du
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Zeming Chen
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Fuyao Liu
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Gang Deng
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Ann T Chen
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Chao Ma
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Jun Liu
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Sara M Hashmi
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, 06511, USA
| | - Xing Guo
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Xiaolong Wang
- Shaanxi Key Laboratory of Brain Disorders & Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, 710021, China
| | - Haitian Zhao
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
| | - Xinran Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Xudong Zhu
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Kevin Sheth
- Department of Neurology, Yale University, New Haven, CT, 06510, USA
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Louzhen Fan
- Department of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale University, New Haven, CT, 06511, USA
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23
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Zheng Y, Wang Q, Yang X, Li Z, Gao L, Zhang H, Nie W, Geng X, Wang K. Investigation of the interactions between aptamer and misfolded proteins: From monomer and oligomer to fibril by single-molecule force spectroscopy. J Mol Recognit 2017; 31. [PMID: 29143447 DOI: 10.1002/jmr.2686] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/10/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Abstract
Increasing knowledge on the understanding interactions of aptamer with misfolded proteins (including monomer, oligomer, and amyloid fibril) is crucial for development of aggregation inhibitors and diagnosis of amyloid diseases. Herein, the interactions of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer were investigated using single-molecule force spectroscopy. The results revealed that the aptamer screened against lysozyme monomer could also bind to oligomer and amyloid fibril, in spite of the recognition at a lower binding probability. It may be attributed to the inherent structural differences of misfolded proteins and the flexible conformation of aptamer. In addition, dynamic force spectra showed that there were similar dissociation paths in the dissociation process of lysozyme monomer-, oligomer-, and amyloid fibril-aptamer complexes. It showed that the dissociation only passed 1 energy barrier from the binding state to the detachment. However, the dynamic parameters suggested that the oligomer- and amyloid fibril-aptamer were more stable than lysozyme monomer-aptamer. The phenomena may result from the exposure of aptamer-recognized sequences on the surface and the electrostatic interactions. This work demonstrated that single-molecule force spectroscopy could be a powerful tool to study the binding behavior of the aptamer with misfolded proteins at single-molecule level, providing abundant information for researches and comprehensive applications of aptamer probes in diagnosis of amyloid diseases.
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Affiliation(s)
- Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Zhiping Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Lei Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Hua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Wenyan Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Xiuhua Geng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, China
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24
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Rozenfeld JHK, Duarte EL, Oliveira TR, Lamy MT. Structural insights on biologically relevant cationic membranes by ESR spectroscopy. Biophys Rev 2017; 9:633-647. [PMID: 28836112 PMCID: PMC5662045 DOI: 10.1007/s12551-017-0304-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 07/28/2017] [Indexed: 12/26/2022] Open
Abstract
Cationic bilayers have been used as models to study membrane fusion, templates for polymerization and deposition of materials, carriers of nucleic acids and hydrophobic drugs, microbicidal agents and vaccine adjuvants. The versatility of these membranes depends on their structure. Electron spin resonance (ESR) spectroscopy is a powerful technique that employs hydrophobic spin labels to probe membrane structure and packing. The focus of this review is the extensive structural characterization of cationic membranes prepared with dioctadecyldimethylammonium bromide or diC14-amidine to illustrate how ESR spectroscopy can provide important structural information on bilayer thermotropic behavior, gel and fluid phases, phase coexistence, presence of bilayer interdigitation, membrane fusion and interactions with other biologically relevant molecules.
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Affiliation(s)
- Julio H K Rozenfeld
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Botucatu 862, São Paulo, SP, 04023-062, Brazil
| | - Evandro L Duarte
- Instituto de Física, Universidade de São Paulo, R. do Matão 1371, São Paulo, SP, 05508-090, Brazil
| | - Tiago R Oliveira
- Centro de Engenharia, Modelagem e Ciências Sociais Aplicadas, Universidade Federal do ABC, R. Arcturus (Jd Antares), São Bernardo do Campo, SP, Brazil
| | - M Teresa Lamy
- Instituto de Física, Universidade de São Paulo, R. do Matão 1371, São Paulo, SP, 05508-090, Brazil.
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25
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Wu Y, Yao X, Chen Y, Li Y, Tian W. Advance of DNA and CCPs-based nanocarriers in drug delivery systems. Biomed Mater Eng 2017; 28:S255-S261. [PMID: 28372302 DOI: 10.3233/bme-171648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Development of smart and functional polymeric carriers, which enable controlled or timed release of a bioactive material, thereby providing a better dosing pattern and minimizing side effects, becomes a new requirement in the field of drug delivery. In the recent few decades, a great many advancements of polymer synthetic methods have led to a new generation of bioactive polymers' applications as drug controlled release carriers. In this review, we focus on the use of bioactive polymers for drug delivery system, with a particular in the utility of DNA-based nanocarriers and cell-penetrating peptides (CCPs)-based nanocarriers to provide precision control for drug targeting or stimuli responsive systems.
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Affiliation(s)
- Yu Wu
- Department of Biomedical Engineering, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xihui Yao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yun Chen
- Department of Biomedical Engineering, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yinping Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Weiqun Tian
- Department of Biomedical Engineering, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
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26
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Xing Y, Liu B, Chao J, Wang L. DNA-based nanoscale walking devices and their applications. RSC Adv 2017. [DOI: 10.1039/c7ra09781f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Herein we review DNA-based nanoscale walking devices including unipedal, bipedal, multipedal, and other novel walking devices and their applications.
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Affiliation(s)
- Yikang Xing
- Institute of Advanced Materials (IAM)
- Jiangsu National Syngerstic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Bing Liu
- Institute of Advanced Materials (IAM)
- Jiangsu National Syngerstic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Jie Chao
- Institute of Advanced Materials (IAM)
- Jiangsu National Syngerstic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
| | - Lianhui Wang
- Institute of Advanced Materials (IAM)
- Jiangsu National Syngerstic Innovation Center for Advanced Materials (SICAM)
- Nanjing University of Posts & Telecommunications
- Nanjing 210023
- China
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27
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Niu L, Yang X, Pan W, Zhou T, Liu D, Mao C, Liang D. Effects of Structural Flexibility on the Kinetics of DNA Y-Junction Assembly and Gelation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12862-12868. [PMID: 27934533 DOI: 10.1021/acs.langmuir.6b03299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The kinetics of DNA assembly is determined not only by temperature but also by the flexibility of the DNA tiles. In this work, the flexibility effect was studied with a model system of Y-junctions, which contain single-stranded thymine (T) loops in the center. It was demonstrated that the incorporation of a loop with only one thymine prominently improved the assembly rate and tuned the final structure of the assembly, whereas the incorporation of a loop of two thymines exhibited the opposite effect. These observations could be explained by the conformation adjustment rate and the intermotif binding strength. Increasing DNA concentration hindered the conformational adjustment rate of DNA strands, leading to the formation of hydrogels in which the network was connected by ribbons. Therefore, the gel can be treated as a metastable state during the phase transition.
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Affiliation(s)
- Lin Niu
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Xuyan Yang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Wei Pan
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
| | - Tao Zhou
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Chengde Mao
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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28
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Xing P, Zhao Y. Multifunctional Nanoparticles Self-Assembled from Small Organic Building Blocks for Biomedicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:7304-7339. [PMID: 27273862 DOI: 10.1002/adma.201600906] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/17/2016] [Indexed: 06/06/2023]
Abstract
Supramolecular self-assembly shows significant potential to construct responsive materials. By tailoring the structural parameters of organic building blocks, nanosystems can be fabricated, whose performance in catalysis, energy storage and conversion, and biomedicine has been explored. Since small organic building blocks are structurally simple, easily modified, and reproducible, they are frequently employed in supramolecular self-assembly and materials science. The dynamic and adaptive nature of self-assembled nanoarchitectures affords an enhanced sensitivity to the changes in environmental conditions, favoring their applications in controllable drug release and bioimaging. Here, recent significant research advancements of small-organic-molecule self-assembled nanoarchitectures toward biomedical applications are highlighted. Functionalized assemblies, mainly including vesicles, nanoparticles, and micelles are categorized according to their topological morphologies and functions. These nanoarchitectures with different topologies possess distinguishing advantages in biological applications, well incarnating the structure-property relationship. By presenting some important discoveries, three domains of these nanoarchitectures in biomedical research are covered, including biosensors, bioimaging, and controlled release/therapy. The strategies regarding how to design and characterize organic assemblies to exhibit biomedical applications are also discussed. Up-to-date research developments in the field are provided and research challenges to be overcome in future studies are revealed.
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Affiliation(s)
- Pengyao Xing
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore
- School of Chemistry and Chemical Engineering and Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, Shandong University, Jinan, 250100, P. R. China
| | - Yanli Zhao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371, Singapore.
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
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29
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Maver U, Velnar T, Gaberšček M, Planinšek O, Finšgar M. Recent progressive use of atomic force microscopy in biomedical applications. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.03.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Liu J, Wei T, Zhao J, Huang Y, Deng H, Kumar A, Wang C, Liang Z, Ma X, Liang XJ. Multifunctional aptamer-based nanoparticles for targeted drug delivery to circumvent cancer resistance. Biomaterials 2016; 91:44-56. [PMID: 26994877 DOI: 10.1016/j.biomaterials.2016.03.013] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/29/2016] [Accepted: 03/06/2016] [Indexed: 12/14/2022]
Abstract
By its unique advantages over traditional medicine, nanomedicine has offered new strategies for cancer treatment. In particular, the development of drug delivery strategies has focused on nanoscale particles to improve bioavailability. However, many of these nanoparticles are unable to overcome tumor resistance to chemotherapeutic agents. Recently, new opportunities for drug delivery have been provided by oligonucleotides that can self-assemble into three-dimensional nanostructures. In this work, we have designed and developed functional DNA nanostructures to deliver the chemotherapy drug doxorubicin (Dox) to resistant cancer cells. These nanostructures have two components. The first component is a DNA aptamer, which forms a dimeric G-quadruplex nanostructure to target cancer cells by binding with nucleolin. The second component is double-stranded DNA (dsDNA), which is rich in -GC- base pairs that can be applied for Dox delivery. We demonstrated that Dox was able to efficiently intercalate into dsDNA and this intercalation did not affect the aptamer's three-dimensional structure. In addition, the Aptamer-dsDNA (ApS) nanoparticle showed good stability and protected the dsDNA from degradation in bovine serum. More importantly, the ApS&Dox nanoparticle efficiently reversed the resistance of human breast cancer cells to Dox. The mechanism circumventing doxorubicin resistance by ApS&Dox nanoparticles may be predominantly by cell cycle arrest in S phase, effectively increased cell uptake and decreased cell efflux of doxorubicin. Furthermore, the ApS&Dox nanoparticles could effectively inhibit tumor growth, while less cardiotoxicity was observed. Overall, this functional DNA nanostructure provides new insights into the design of nanocarriers to overcome multidrug resistance through targeted drug delivery.
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Affiliation(s)
- Juan Liu
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Tuo Wei
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Jing Zhao
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yuanyu Huang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Hua Deng
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Anil Kumar
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Chenxuan Wang
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zicai Liang
- Laboratory of Nucleic Acid Technology, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaowei Ma
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China.
| | - Xing-Jie Liang
- CAS Center for Excellence in Nanoscience, Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, and Laboratory of Controllable Nanopharmaceuticals, National Center for Nanoscience and Technology of China, Beijing 100190, China.
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31
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Zhao J, Feng SS. Nanocarriers for delivery of siRNA and co-delivery of siRNA and other therapeutic agents. Nanomedicine (Lond) 2016. [PMID: 26214357 DOI: 10.2217/nnm.15.61] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
A major problem in cancer treatment is the multidrug resistance. siRNA inhibitors have great advantages to solve the problem, if the bottleneck of their delivery could be well addressed by the various nanocarriers. Moreover, co-delivery of siRNA together with the various anticancer agents in one nanocarrier may maximize their additive or synergistic effect. This review provides a comprehensive summary on the state-of-the-art of the nanocarriers, which may include prodrugs, micelles, liposomes, dendrimers, nanohydrogels, solid lipid nanoparticles, nanoparticles of biodegradable polymers and nucleic acid nanocarriers for delivery of siRNA and co-delivery of siRNA together with anticancer agents with focus on synthesis of the nanocarrier materials, design and characterization, in vitro and in vivo evaluation, and prospect and challenges of nanocarriers.
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Affiliation(s)
- Jing Zhao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117576, Singapore
| | - Si-Shen Feng
- Department of Chemical & Biomolecular Engineering, Faculty of Engineering, National University of Singapore, Singapore 117576, Singapore.,International Joint Cancer Institute, Second Military Medical University, Shanghai 200433, China
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32
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Chen Z, Tan L, Hu L, Zhang Y, Wang S, Lv F. Real Colorimetric Thrombin Aptasensor by Masking Surfaces of Catalytically Active Gold Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2016; 8:102-108. [PMID: 26558607 DOI: 10.1021/acsami.5b08975] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We presented a simple, cost-effective, and ultrasensitive colorimetric approach for visually detecting thrombin by the catalytic amplification of gold nanoparticles (AuNPs) and aptamer-thrombin recognition. Thrombin can be quantified in the presence of catalytic AuNP surface by using color-change time of 4-nitrophenol. Without thrombin, yellow 4-nitrophenol can freely access the surface of AuNP and becomes colorless 4-aminophenol. With the addition of thrombin, aptamer-thrombin with large size interaction masks the partial surfaces of AuNPs, and increases the reduction time of 4-nitrophenol to 4-aminophenol. The maximum number of bound thrombin fully mask the catalytic AuNP surface, and thus 4-nitrophenol cannot approach to AuNP surface, the color of the solution remains yellow. The limit of detection (LOD) of 0.1 nM can be achieved with naked eyes. Of note, the method was further applied for the detection of thrombin in human serum samples, showing the results in agreement with those values obtained in an immobilization buffer by the colorimetric method.
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Affiliation(s)
- Zhengbo Chen
- Department of Chemistry, Capital Normal University , Beijing 100048, China
| | - Lulu Tan
- Department of Chemistry, Capital Normal University , Beijing 100048, China
| | - Liangyu Hu
- Department of Chemistry, Capital Normal University , Beijing 100048, China
| | - Yimeng Zhang
- Department of Chemistry, Capital Normal University , Beijing 100048, China
| | - Shaoxiong Wang
- Department of Chemistry, Capital Normal University , Beijing 100048, China
| | - Fanyi Lv
- Department of Chemistry, Capital Normal University , Beijing 100048, China
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33
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Du K, Yang M, Zhang Q, Dan S. Highly Porous Polymer Monolith Immobilized with Aptamer (RNA) Anchored Grafted Tentacles and Its Potential for the Purification of Lysozyme. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.5b02793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Kaifeng Du
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Min Yang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Qi Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Shunmin Dan
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China
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34
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Efficient amplification of self-gelling polypod-like structured DNA by rolling circle amplification and enzymatic digestion. Sci Rep 2015; 5:14979. [PMID: 26462616 PMCID: PMC4604513 DOI: 10.1038/srep14979] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/15/2015] [Indexed: 01/19/2023] Open
Abstract
The application of DNA as a functional material such as DNA hydrogel has attracted much attention. Despite an increasing interest, the high cost of DNA synthesis is a limiting factor for its utilization. To reduce the cost, we report here a highly efficient amplification technique for polypod-like structured DNA (polypodna) with adhesive ends that spontaneously forms DNA hydrogel. Two types of polypodna with three (tripodna) and four (tetrapodna) pods were selected, and a template oligodeoxynucleotide, containing a tandem sequence of a looped tripodna or tetrapodna, respectively, along with restriction enzyme (TspRI) sites, was designed. The template was circularized using T4 DNA ligase, and amplified by rolling circle amplification (RCA). The RCA product was highly viscous and resistant to restriction digestion. Observation under an electron microscope revealed microflower-like structures. These structures were composed of long DNA and magnesium pyrophosphate, and their treatment with EDTA followed by restriction digestion with TspRI resulted in numerous copies of polypodna with adhesive ends, which formed a DNA hydrogel. Thus, we believe this technique provides a new approach to produce DNA nanostructures, and helps in expanding their practical applications.
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35
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Fernández MS, Misko VR, Peeters FM. Self-assembly of Janus particles into helices with tunable pitch. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042309. [PMID: 26565242 DOI: 10.1103/physreve.92.042309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 06/05/2023]
Abstract
Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. In this work we consider a three-dimensional model of Janus spheres that contain one hydrophobic and one charged hemisphere. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment. The interplay between the attractive and repulsive forces on each particle gives rise to a rich phase space where the relative orientation of each particle plays a dominant role in the formation of large-scale clusters. The interest in this system is primarily due to the fact that it could give a better understanding of the mechanisms of the formation of polar membranes. A variety of ordered membranelike morphologies is found consisting of single and multiple connected chain configurations. The helicity of these chains can be chosen by simply changing the salt concentration of the solution. Special attention is given to the formation of Bernal spirals. These helices are composed of regular tetrahedra and are known to exhibit nontrivial translational and rotational symmetry.
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Affiliation(s)
| | - V R Misko
- Departement Fysica, Universiteit Antwerpen, B-2020 Antwerpen, Belgium
| | - F M Peeters
- Departement Fysica, Universiteit Antwerpen, B-2020 Antwerpen, Belgium
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36
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Computational docking simulations of a DNA-aptamer for argininamide and related ligands. J Comput Aided Mol Des 2015; 29:643-54. [PMID: 25877490 DOI: 10.1007/s10822-015-9844-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
Abstract
The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes. In the present study we apply molecular docking simulations to probe the features of an experimentally documented L-argininamide aptamer complex. The docking simulations were performed using AutoDock 4.0 and YASARA Structure software, a well-suited program for following intermolecular interactions and structures of biomolecules, including DNA. We explored the binding features of a DNA aptamer to L-argininamide and to a series of arginine derivatives or arginine-like ligands. We find that the best docking results are obtained after an energy-minimization of the parent ligand-aptamer complexes. The calculated binding energies of all mono-substituted guanidine-containing ligands show a good correlation with the experimentally determined binding constants. The results provide valuable guidelines for the application of docking simulations for the prediction of aptamer-ligand structures, and for the design of novel features of ligand-aptamer complexes.
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37
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Niu L, Yang X, Zhou J, Mao C, Liang H, Liang D. Mechanism of DNA assembly as revealed by energy barriers. Chem Commun (Camb) 2015; 51:7717-20. [DOI: 10.1039/c5cc00783f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA assembly is determined by the conformation adjustment rate of strands and the spreading rate of strands on the nuclei surface.
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Affiliation(s)
- Lin Niu
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
| | - Xuyan Yang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
| | - Jihan Zhou
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
| | - Chengde Mao
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Haojun Liang
- Department of Polymer Science and Engineering
- University of Science and Technology of China
- Hefei
- P. R. China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences and the Key Laboratory of Polymer Chemistry and Physics of Ministry of Education
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- P. R. China
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38
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Structure and blood compatibility of highly oriented poly(l-lactic acid) chain extended by ethylene glycol diglycidyl ether. POLYMER 2015. [DOI: 10.1016/j.polymer.2014.11.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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39
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Escorihuela J, González-Martínez MÁ, López-Paz JL, Puchades R, Maquieira Á, Gimenez-Romero D. Dual-Polarization Interferometry: A Novel Technique To Light up the Nanomolecular World. Chem Rev 2014; 115:265-94. [DOI: 10.1021/cr5002063] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jorge Escorihuela
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - Miguel Ángel González-Martínez
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - José Luis López-Paz
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - Rosa Puchades
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - Ángel Maquieira
- Department
of Chemistry, Institute of Molecular Recognition and Technological
Development, Universitat Politècnica de València, Camino
de Vera s/n, 46022 València, Spain
| | - David Gimenez-Romero
- Physical
Chemistry Department, Faculty of Chemistry, Universitat de València, Avenida Dr. Moliner 50, 46100 Burjassot, València, Spain
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40
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Tao Y, Ju E, Ren J, Qu X. Immunostimulatory oligonucleotides-loaded cationic graphene oxide with photothermally enhanced immunogenicity for photothermal/immune cancer therapy. Biomaterials 2014; 35:9963-9971. [PMID: 25224368 DOI: 10.1016/j.biomaterials.2014.08.036] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 08/23/2014] [Indexed: 02/08/2023]
Abstract
Graphene oxide (GO) has attracted tremendous research interest due to its excellent electrical, thermal, and mechanical properties. Here, we apply the polyethylene glycol (PEG) and polyethylenimine (PEI) dual-polymer-functionalized GO (GO-PEG-PEI) as the carrier for efficient CpG delivery. GO-PEG-PEI can significantly promote the production of proinflammatory cytokines and enhance the immunostimulatory effect of CpG. In addition, the NIR optical absorbance of GO-PEG-PEI has been further applied to control the immunostimulatory activity of CpG ODNs, showing remarkably enhanced immunostimulation responses under NIR laser irradiation, owing to the photothermally induced local heating that accelerated intracellular trafficking of nanovectors. This is the first demonstration of using the photothermally enhanced intracellular transportation of nanocarriers for light-controllable CpG delivery. In vivo assay demonstrates that the GO-PEG-PEI-CpG complex provides synergistic photothermal and immunological effects under laser irradiation for cancer treatment, which shows the highest efficiency in tumor reduction, implying the excellent therapeutic efficacy of the GO-PEG-PEI-CpG complex in cancer therapy.
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Affiliation(s)
- Yu Tao
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Enguo Ju
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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41
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Facile route to versatile nanoplatforms for drug delivery by one-pot self-assembly. Acta Biomater 2014; 10:2630-42. [PMID: 24486911 DOI: 10.1016/j.actbio.2014.01.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/18/2013] [Accepted: 01/21/2014] [Indexed: 12/17/2022]
Abstract
There is still unmet demand for developing powerful approaches to produce polymeric nanoplatforms with versatile functions and broad applications, which are essential for the successful bench-to-bedside translation of polymeric nanotherapeutics developed in the laboratory. We have discovered a facile, convenient, cost-effective and easily scalable one-pot strategy to assemble various lipophilic therapeutics bearing carboxyl groups into nanomedicines, through which highly effective cargo loading and nanoparticle formation can be achieved simultaneously. Besides dramatically improving water solubility, the assembled nanopharmaceuticals showed significantly higher bioavailability and much better therapeutic activity. These one-pot assemblies may also serve as nanocontainers to effectively accommodate other highly hydrophobic drugs such as paclitaxel (PTX). PTX nanomedicines thus formulated display strikingly enhanced in vitro antitumor activity and can reverse the multidrug resistance of tumor cells to PTX therapy. The special surface chemistry offers these assembled entities the additional capability of efficiently packaging and efficaciously transfecting plasmid DNA, with a transfection efficiency markedly higher than that of commonly used positive controls. Consequently, this one-pot assembly approach provides a facile route to multifunctional nanoplatforms for simultaneous delivery of multiple therapeutics with improved therapeutic significance.
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42
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Muro S. A DNA-Device that Mediates Selective Endosomal Escape and Intracellular Delivery of Drugs and Biologicals. ADVANCED FUNCTIONAL MATERIALS 2014; 24:2899-2906. [PMID: 25018687 PMCID: PMC4091764 DOI: 10.1002/adfm.201303188] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Design of materials to aid intracellular delivery of agents can greatly improve medical treatments. While DNA is a molecule difficult to introduce into cells, DNA can be engineered into devices capable of intracellular delivery. Yet, transport mediated by DNA-devices void of other structural material, with size greater than that associated with non-specific penetration, and with targeting capacity enough to overcome non-specific pathways has not been achived. This study demonstrates that this is possible. Submicrometer (200-nm) dendrimers built of DNA (nucleodendrimers (NDs)) are coupled to antibodies against selected cell-surface receptors and compared to polymer nanoparticles (NPs). NDs and NPs bind specifically to cells expressing these targets and efficiently enter cells via the pathway associated with the selected receptor. While NPs traffic to perinuclear endo-lysosomes, NDs remain scattered throughout the cell, suggesting endosomal escape. This is confirmed in vitro, where NDs disrupt membranous vesicles at endosomal-like pH and in cell culture, where they: provide endosomal escape of model drugs, sugars, proteins, and nucleic acids; allow access to other intracellular compartments; result in measurable effects of cargoes; and do not cause cytotoxicity. Therefore, these DNA-nanodevices can be used to selectively overcome intracellular barriers, underscoring the growing range of applications of DNA materials.
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Affiliation(s)
- Silvia Muro
- S. M. Institute for Bioscience and Biotechnology Resarch & Fischell Department of Bioengineering, University of Maryland College Park, 5115 Plant Sciences Building, College Park, MD 20742, USA
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43
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Sengupta E, Yan Y, Wang X, Munechika K, Ginger DS. Dynamic force spectroscopy of photoswitch-modified DNA. ACS NANO 2014; 8:2625-2631. [PMID: 24502655 DOI: 10.1021/nn406334b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We apply a combination of photoswitch-modified DNA and AFM-based pulling measurements to study the force-induced melting of double-stranded DNA in the unzipping geometry. We measure the differences in peak rupture force for azobenzene-modified DNA, as the incorporated azobenzenes are photoswitched reversibly between the trans and the cis form. Fitting our rupture force versus loading rate data, we obtain off rate (koff) at zero force values in the range of ∼10 s(-1). We show that the change in peak rupture force and koff induced by destabilizing the DNA duplex depends on the position of the destabilizing azobenzene photoswitch relative to the force-loading site. When the azobenzenes are proximal to the unzipping end, the decrease in peak force and koff upon azobenzene photoisomerization is significantly larger than when the azobenzene is distal to the site of force loading. We interpret these results as experimental evidence supporting the picture that the destabilization of a double-stranded DNA by a photoswitch isomerization is localized to a small bubble around the photoswitch.
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Affiliation(s)
- Esha Sengupta
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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44
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Sobrino Fernández M, Misko VR, Peeters FM. Self-assembly of Janus particles confined in a channel. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022306. [PMID: 25353471 DOI: 10.1103/physreve.89.022306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Indexed: 06/04/2023]
Abstract
Janus particles present an important class of building blocks for directional assembly. These are compartmentalized colloids with two different hemispheres. Here, we consider a two-dimensional model of Janus disks consisting of a hydrophobic semicircle and an electro-negatively charged one. Placed in a solution, the hydrophobic sides will attract each other while the charged sides will give rise to a repulsive force. Using molecular dynamics simulations, we study the morphology of these particles when confined in a channel-like environment using a one dimensional harmonic confinement potential. The interest to this system is first of all due to the fact that it could serve as a simple model for membrane formation. Indeed, the recently synthesized new class of artificial amphiphiles, known as Janus dendrimers, were shown to self-assemble in bilayer structures mimicking biological membranes. In turn, Janus particles that combine the amphiphilicity and colloidal rigidity serve as a good model for Janus dendrimers. A variety of ordered membrane-like morphologies are found consisting of single and multiple chain configurations with different orientations of the particles with respect to each other that we summarize in a phase diagram.
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Affiliation(s)
| | - V R Misko
- Departement Fysica, Universiteit Antwerpen, B-2020 Antwerpen, Belgium
| | - F M Peeters
- Departement Fysica, Universiteit Antwerpen, B-2020 Antwerpen, Belgium
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45
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Holowka EP, Bhatia SK. Controlled-Release Systems. Drug Deliv 2014. [DOI: 10.1007/978-1-4939-1998-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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46
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Fakhoury JJ, McLaughlin CK, Edwardson TW, Conway JW, Sleiman HF. Development and Characterization of Gene Silencing DNA Cages. Biomacromolecules 2013; 15:276-82. [DOI: 10.1021/bm401532n] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Johans J. Fakhoury
- Department
of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Christopher K. McLaughlin
- Department
of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Donnelly Centre, Department of Chemical Engineering & Applied Chemistry, Institute of Biomaterials & Biomedical Engineering, University of, Toronto, Room 514, 160 College Street, Toronto, Ontario, M5S 3E1, Canada
| | - Thomas W. Edwardson
- Department
of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Justin W. Conway
- Department
of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department
of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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47
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de Vries JW, Zhang F, Herrmann A. Drug delivery systems based on nucleic acid nanostructures. J Control Release 2013; 172:467-83. [DOI: 10.1016/j.jconrel.2013.05.022] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/23/2013] [Accepted: 05/24/2013] [Indexed: 01/26/2023]
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48
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Wang Y, Mo L, Wei W, Shi X. Efficacy and safety of dendrimer nanoparticles with coexpression of tumor necrosis factor-α and herpes simplex virus thymidine kinase in gene radiotherapy of the human uveal melanoma OCM-1 cell line. Int J Nanomedicine 2013; 8:3805-16. [PMID: 24124368 PMCID: PMC3795008 DOI: 10.2147/ijn.s48950] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human uveal melanoma is the most common primary intraocular tumor, and brachytherapy is one of the most common and effective treatment strategies. In order to find a safer and more effective way to increase the radio sensitivity of the tumor, we tried to use the dendrimer nanoparticle performing coexpression gene radiotherapy. In this study, we constructed recombinant DNA plasmids (early growth response-1 tumor necrosis factor-α [pEgr1-TNFα], pEgr1 thymidine kinase [TK], and pEgr1-TNFα-TK) according to the Egr1 promoter sequence. The sequences of human TNFα and herpes simplex virus (HSV) TK that were published by GenBank. Agarose gel electrophoresis and DNA sequencing had proven that we constructed the double-gene recombined plasmids pEgr1-TNF-TK correctly, as well as the plasmids pEgr1-TNFα and pEgr1-TK. The dendrimer nanoparticles combined with plasmid DNA as dendriplexes were verified with agarose gel electrophoresis and observed by transmission electron microscopy (TEM) and scanning electron microscopy to define size and shape. Zeta potential was measured using a Zetasizer analyzer. Optimal size and neutral zeta-potential characteristics of dendriplexes were achieved for the transfection studies. DNase I examination proved that the dendriplexes could protect plasmid DNA for at least 6 hours. The recombinant plasmids were transfected with dendrimer nanoparticles into the human choroidal melanoma OCM-1 cell line, followed by exposure to iodine-125 ((125)I) after transfection. After transfection with dendrimer nanoparticles and the irradiation of (125)I, the gene expressions of TNFα and HSV1-TK were significantly increased at the protein level by enzyme-linked immunosorbent assay and Western blot analysis in OCM-1 cells. The cellular morphology of OCM-1 cells altering was observed by TEM, and a decrease in cell proliferation was revealed in cell-growth curves. Flow cytometry of annexin V/propidium iodide double-dyeing apoptosis and caspase-3 fluorescence staining showed that this treatment method could turn transfected OCM-1 cells into apoptosis and necrosis by the effects of the gene expression. This study indicated that the dendrimer nanoparticles with coexpression of TNF-α and HSV1-TK gene therapy are effective and safe and can provide us with a novel strategy to treat human uveal melanoma in the future.
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Affiliation(s)
- Yingchih Wang
- Beijing Tongren Eye Center, Capital Medical University, Beijing, People's Republic of China
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BMP7 gene transfer via gold nanoparticles into stroma inhibits corneal fibrosis in vivo. PLoS One 2013; 8:e66434. [PMID: 23799103 PMCID: PMC3682981 DOI: 10.1371/journal.pone.0066434] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/07/2013] [Indexed: 12/25/2022] Open
Abstract
This study examined the effects of BMP7 gene transfer on corneal wound healing and fibrosis inhibition in vivo using a rabbit model. Corneal haze in rabbits was produced with the excimer laser performing -9 diopters photorefractive keratectomy. BMP7 gene was introduced into rabbit keratocytes by polyethylimine-conjugated gold nanoparticles (PEI2-GNPs) transfection solution single 5-minute topical application on the eye. Corneal haze and ocular health in live animals was gauged with stereo- and slit-lamp biomicroscopy. The levels of fibrosis [α-smooth muscle actin (αSMA), F-actin and fibronectin], immune reaction (CD11b and F4/80), keratocyte apoptosis (TUNEL), calcification (alizarin red, vonKossa and osteocalcin), and delivered-BMP7 gene expression in corneal tissues were quantified with immunofluorescence, western blotting and/or real-time PCR. Human corneal fibroblasts (HCF) and in vitro experiments were used to characterize the molecular mechanism mediating BMP7’s anti-fibrosis effects. PEI2-GNPs showed substantial BMP7 gene delivery into rabbit keratocytes in vivo (2×104 gene copies/ug DNA). Localized BMP7 gene therapy showed a significant corneal haze decrease (1.68±0.31 compared to 3.2±0.43 in control corneas; p<0.05) in Fantes grading scale. Immunostaining and immunoblot analyses detected significantly reduced levels of αSMA (46±5% p<0.001) and fibronectin proteins (48±5% p<0.01). TUNEL, CD11b, and F4/80 assays revealed that BMP7 gene therapy is nonimmunogenic and nontoxic for the cornea. Furthermore, alizarin red, vonKossa and osteocalcin analyses revealed that localized PEI2-GNP-mediated BMP7 gene transfer in rabbit cornea does not cause calcification or osteoblast recruitment. Immunofluorescence of BMP7-transefected HCFs showed significantly increased pSmad-1/5/8 nuclear localization (>88%; p<0.0001), and immunoblotting of BMP7-transefected HCFs grown in the presence of TGFβ demonstrated significantly enhanced pSmad-1/5/8 (95%; p<0.001) and Smad6 (53%, p<0.001), and decreased αSMA (78%; p<0.001) protein levels. These results suggest that localized BMP7 gene delivery in rabbit cornea modulates wound healing and inhibits fibrosis in vivo by counter balancing TGFβ1-mediated profibrotic Smad signaling.
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Qu ZG, He XC, Lin M, Sha BY, Shi XH, Lu TJ, Xu F. Advances in the understanding of nanomaterial–biomembrane interactions and their mathematical and numerical modeling. Nanomedicine (Lond) 2013; 8:995-1011. [DOI: 10.2217/nnm.13.81] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The widespread application of nanomaterials (NMs), which has accompanied advances in nanotechnology, has increased their chances of entering an organism, for example, via the respiratory system, skin absorption or intravenous injection. Although accumulating experimental evidence has indicated the important role of NM–biomembrane interaction in these processes, the underlying mechanisms remain unclear. Computational techniques, as an alternative to experimental efforts, are effective tools to simulate complicated biological behaviors. Computer simulations can investigate NM–biomembrane interactions at the nanoscale, providing fundamental insights into dynamic processes that are challenging to experimental observation. This paper reviews the current understanding of NM–biomembrane interactions, and existing mathematical and numerical modeling methods. We highlight the advantages and limitations of each method, and also discuss the future perspectives in this field. Better understanding of NM–biomembrane interactions can benefit various fields, including nanomedicine and diagnosis.
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Affiliation(s)
- Zhi Guo Qu
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy & Power Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering & Biomechanics Center, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xiao Cong He
- Key Laboratory of Thermo-Fluid Science & Engineering, Ministry of Education, School of Energy & Power Engineering, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering & Biomechanics Center, Xi’an Jiaotong University, Xi’an 710049, China
| | - Min Lin
- Bioinspired Engineering & Biomechanics Center, Xi’an Jiaotong University, Xi’an 710049, China
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science & Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Bao Yong Sha
- Bioinspired Engineering & Biomechanics Center, Xi’an Jiaotong University, Xi’an 710049, China
- Laboratory of Cell Biology & Translational Medicine, Xi’an Medical University, Xi’an 710021, China
| | - Xing Hua Shi
- The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
| | - Tian Jian Lu
- Bioinspired Engineering & Biomechanics Center, Xi’an Jiaotong University, Xi’an 710049, China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science & Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Bioinspired Engineering & Biomechanics Center, Xi’an Jiaotong University, Xi’an 710049, China.
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