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Fokina A, Poletaeva Y, Dukova S, Klabenkova K, Rad’kova Z, Bakulina A, Zatsepin T, Ryabchikova E, Stetsenko D. Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides. Int J Mol Sci 2023; 24:15978. [PMID: 37958961 PMCID: PMC10650595 DOI: 10.3390/ijms242115978] [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] [Received: 07/31/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.
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Affiliation(s)
- Alesya Fokina
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yulia Poletaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (Y.P.); (E.R.)
| | | | - Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Zinaida Rad’kova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia; (Z.R.); (A.B.)
| | - Anastasia Bakulina
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia; (Z.R.); (A.B.)
| | - Timofei Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (Y.P.); (E.R.)
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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Zhou P, Ding L, Yan Y, Wang Y, Su B. Recent advances in label-free imaging of cell-matrix adhesions. Chem Commun (Camb) 2023; 59:2341-2351. [PMID: 36744880 DOI: 10.1039/d2cc06499e] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Cell-matrix adhesions play an essential role in mediating and regulating many biological processes. The adhesion receptors, typically transmembrane integrins, provide dynamic correlations between intracellular environments and extracellular matrixes (ECMs) by bi-directional signaling. In-depth investigations of cell-matrix adhesion and integrin-mediated cell adhesive force are of great significance in biology and medicine. The emergence of advanced imaging techniques and principles has facilitated the understanding of the molecular composition and structure dynamics of cell-matrix adhesions, especially the label-free imaging methods that can be used to study living cell dynamics without immunofluorescence staining. This highlight article aims to give an overview of recent developments in imaging cell-matrix adhesions in a label-free manner. Electrochemiluminescence microscopy (ECLM) and surface plasmon resonance microscopy (SPRM) are briefly introduced and their applications in imaging analysis of cell-matrix adhesions are summarized. Then we highlight the advances in mapping cell-matrix adhesion force based on molecular tension probes and fluorescence microscopy (collectively termed as MTFM). The biomaterials including polyethylene glycol (PEG), peptides and DNA for constructing tension probes in MTFM are summarized. Finally, the outlook and perspectives on the further developments of cell-matrix adhesion imaging are presented.
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Affiliation(s)
- Ping Zhou
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Lurong Ding
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Yajuan Yan
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Yafeng Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
| | - Bin Su
- Key Laboratory of Excited-State Materials of Zhejiang Province, Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, China.
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Baig MMFA, Fatima A, Gao X, Farid A, Ajmal Khan M, Zia AW, Wu H. Disrupting biofilm and eradicating bacteria by Ag-Fe 3O 4@MoS 2 MNPs nanocomposite carrying enzyme and antibiotics. J Control Release 2022; 352:98-120. [PMID: 36243235 DOI: 10.1016/j.jconrel.2022.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/07/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022]
Abstract
In this study, novel multilayered magnetic nanoparticles (ML-MNPs) loaded with DNase and/or vancomycin (Vanc) were fabricated for eliminating multispecies biofilms. Iron-oxide MNPs (IO-core) (500-800 nm) were synthesized via co-precipitation; further, the IO-core was coated with heavy-metal-based layers (Ag and MoS2 NPs) using solvent evaporation. DNase and Vanc were loaded onto the outermost layer of the ML-MNP formed by nanoporous MoS2 NPs through physical deposition and adsorption. The biofilms of S. mutans or E. faecalis (or both) were formed in a brain-heart-infusion broth (BHI) for 3 days, followed by treatment with ML-MNPs for 24 h. The results revealed that coatings of Ag (200 nm) and ultrasmall MoS2 (20 nm) were assembled as outer layers of ML-MNPs successfully, and they formed Ag-Fe3O4@MoS2 MNPs (3-5 μm). The DNase-Vanc-loaded MNPs caused nanochannels digging and resulted in the enhanced penetration of MNPs towards the bottom layers of biofilm, which resulted in a decrease in the thickness of the 72-h biofilm from 48 to 58 μm to 0-4 μm. The sustained release of Vanc caused a synergistic bacterial killing up to 96%-100%. The heavy-metal-based layers of MNPs act as nanozymes to interfere with bacterial metabolism and proliferation, which adversely affects biofilm integrity. Further, loading DNase/Vanc onto the nanoporous-MoS2-layer of ML-MNPs promoted nanochannel creation through the biofilm. Therefore, DNase-and Vanc-loaded ML-MNPs exhibited potent effects on biofilm disruption and bacterial killing.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China.
| | - Arshia Fatima
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Xiuli Gao
- Microbiology and Biochemical Pharmaceutical Engineering Research Center of Guizhou Provincial Department of Education, State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang 550025, China.
| | - Awais Farid
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Muhammad Ajmal Khan
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Abdul Wasy Zia
- Department of Mechanical and Construction Engineering, Marie Curie Research Unit, Northumbria University, Newcastle, United Kingdom
| | - Hongkai Wu
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China; Department of Chemical and Biological Engineering, Division of Biomedical Engineering, School of Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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Mundekkad D, Cho WC. Nanoparticles in Clinical Translation for Cancer Therapy. Int J Mol Sci 2022; 23:ijms23031685. [PMID: 35163607 PMCID: PMC8835852 DOI: 10.3390/ijms23031685] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 02/07/2023] Open
Abstract
The advent of cancer therapeutics brought a paradigm shift from conventional therapy to precision medicine. The new therapeutic modalities accomplished through the properties of nanomaterials have extended their scope in cancer therapy beyond conventional drug delivery. Nanoparticles can be channeled in cancer therapy to encapsulate active pharmaceutical ingredients and deliver them to the tumor site in a more efficient manner. This review enumerates various types of nanoparticles that have entered clinical trials for cancer treatment. The obstacles in the journey of nanodrug from clinic to market are reviewed. Furthermore, the latest developments in using nanoparticles in cancer therapy are also highlighted.
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Affiliation(s)
- Deepa Mundekkad
- Centre for NanoBioTechnology (CNBT), Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India;
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China
- Correspondence: or
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Singh A, Bhatia D. DNA hydrogels: Principles, synthesis, characterization and applications to cell biology. Methods Cell Biol 2022; 169:323-346. [DOI: 10.1016/bs.mcb.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Baig MMFA, Dissanayaka WL, Zhang C. 2D DNA nanoporous scaffold promotes osteogenic differentiation of pre-osteoblasts. Int J Biol Macromol 2021; 188:657-669. [PMID: 34371047 DOI: 10.1016/j.ijbiomac.2021.07.198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/23/2021] [Accepted: 07/31/2021] [Indexed: 01/06/2023]
Abstract
Biofunctional materials with nanomechanical parameters similar to bone tissue may promote the adherence, migration, proliferation, and differentiation of pre-osteoblasts. In this study, deoxyribonucleic acid (DNA) nanoporous scaffold (DNA-NPS) was synthesized by the polymerization of rectangular and double-crossover (DX) DNA tiles. The diagonally precise polymerization of nanometer-sized DNA tiles (A + B) through sticky end cohesion gave rise to a micrometer-sized porous giant-sheet material. The synthesized DNA-NPS exhibited a uniformly distributed porosity with a size of 25 ± 20 nm. The morphology, dimensions, sectional profiles, 2-dimensional (2D) layer height, texture, topology, pore size, and mechanical parameters of DNA-NPS have been characterized by atomic force microscopy (AFM). The size and zeta potential of DNA-NPS have been characterized by the zeta sizer. Cell biocompatibility, proliferation, and apoptosis have been evaluated by flow cytometry. The AFM results confirmed that the fabricated DNA-NPS was interconnected and uniformly porous, with a surface roughness of 0.125 ± 0.08035 nm. The elastic modulus of the DNA-NPS was 22.45 ± 8.65 GPa, which was comparable to that of native bone tissue. DNA-NPS facilitated pre-osteoblast adhesion, proliferation, and osteogenic differentiation. These findings indicated the potential of 2D DNA-NPS in promoting bone tissue regeneration.
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Affiliation(s)
| | - Waruna Lakmal Dissanayaka
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, China
| | - Chengfei Zhang
- Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, China.
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Fokina AA, Poletaeva YE, Burakova EA, Bakulina AY, Zatsepin TS, Ryabchikova EI, Stetsenko DA. Template-Assisted Assembly of DNA Nanostructures from Branched Oligonucleotides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041885] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.
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Mabrouk M, Das DB, Salem ZA, Beherei HH. Nanomaterials for Biomedical Applications: Production, Characterisations, Recent Trends and Difficulties. Molecules 2021; 26:1077. [PMID: 33670668 PMCID: PMC7922738 DOI: 10.3390/molecules26041077] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Designing of nanomaterials has now become a top-priority research goal with a view to developing specific applications in the biomedical fields. In fact, the recent trends in the literature show that there is a lack of in-depth reviews that specifically highlight the current knowledge based on the design and production of nanomaterials. Considerations of size, shape, surface charge and microstructures are important factors in this regard as they affect the performance of nanoparticles (NPs). These parameters are also found to be dependent on their synthesis methods. The characterisation techniques that have been used for the investigation of these nanomaterials are relatively different in their concepts, sample preparation methods and obtained results. Consequently, this review article aims to carry out an in-depth discussion on the recent trends on nanomaterials for biomedical engineering, with a particular emphasis on the choices of the nanomaterials, preparation methods/instruments and characterisations techniques used for designing of nanomaterials. Key applications of these nanomaterials, such as tissue regeneration, medication delivery and wound healing, are also discussed briefly. Covering this knowledge gap will result in a better understanding of the role of nanomaterial design and subsequent larger-scale applications in terms of both its potential and difficulties.
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Affiliation(s)
- Mostafa Mabrouk
- Refractories, Ceramics and Building Materials Department, National Research Centre, 33El Bohouth St (former EL Tahrir St), Dokki, Giza P.O. 12622, Egypt;
- Department of Chemical Engineering, Loughborough University, Loughborough LE113TU, Leicestershire, UK
| | - Diganta B. Das
- Department of Chemical Engineering, Loughborough University, Loughborough LE113TU, Leicestershire, UK
| | - Zeinab A. Salem
- Department of Oral Biology, Faculty of Dentistry, Cairo University, Giza P.O. 12613, Egypt;
- Faculty of Oral and Dental Medicine, Ahram Canadian University, 6 October City P.O. 12573, Egypt
| | - Hanan H. Beherei
- Refractories, Ceramics and Building Materials Department, National Research Centre, 33El Bohouth St (former EL Tahrir St), Dokki, Giza P.O. 12622, Egypt;
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Baig MMFA, Zou T, Neelakantan P, Zhang C. Development and functionalization of
DNA
nanostructures for biomedical applications. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202000373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Biomedical Engineering and Biofunctional Materials Theme, Restorative Dental Sciences, Faculty of Dentistry The University of Hong Kong Hong Kong SAR China
| | - Ting Zou
- Biomedical Engineering and Biofunctional Materials Theme, Restorative Dental Sciences, Faculty of Dentistry The University of Hong Kong Hong Kong SAR China
| | - Prasanna Neelakantan
- Biomedical Engineering and Biofunctional Materials Theme, Restorative Dental Sciences, Faculty of Dentistry The University of Hong Kong Hong Kong SAR China
| | - Chengfei Zhang
- Biomedical Engineering and Biofunctional Materials Theme, Restorative Dental Sciences, Faculty of Dentistry The University of Hong Kong Hong Kong SAR China
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