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Jogdeo CM, Siddhanta K, Das A, Ding L, Panja S, Kumari N, Oupický D. Beyond Lipids: Exploring Advances in Polymeric Gene Delivery in the Lipid Nanoparticles Era. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2404608. [PMID: 38842816 DOI: 10.1002/adma.202404608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/23/2024] [Indexed: 06/07/2024]
Abstract
The recent success of gene therapy during the COVID-19 pandemic has underscored the importance of effective and safe delivery systems. Complementing lipid-based delivery systems, polymers present a promising alternative for gene delivery. Significant advances have been made in the recent past, with multiple clinical trials progressing beyond phase I and several companies actively working on polymeric delivery systems which provides assurance that polymeric carriers can soon achieve clinical translation. The massive advantage of structural tunability and vast chemical space of polymers is being actively leveraged to mitigate shortcomings of traditional polycationic polymers and improve the translatability of delivery systems. Tailored polymeric approaches for diverse nucleic acids and for specific subcellular targets are now being designed to improve therapeutic efficacy. This review describes the recent advances in polymer design for improved gene delivery by polyplexes and covalent polymer-nucleic acid conjugates. The review also offers a brief note on novel computational techniques for improved polymer design. The review concludes with an overview of the current state of polymeric gene therapies in the clinic as well as future directions on their translation to the clinic.
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Affiliation(s)
- Chinmay M Jogdeo
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kasturi Siddhanta
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ashish Das
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ling Ding
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sudipta Panja
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Neha Kumari
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - David Oupický
- Center for Drug Delivery and Nanomedicine, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
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2
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Singh N, Singh A, Dhanka M, Bhatia D. DNA functionalized programmable hybrid biomaterials for targeted multiplexed applications. J Mater Chem B 2024. [PMID: 38973587 DOI: 10.1039/d4tb00287c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
With the advent of DNA nanotechnology, DNA-based biomaterials have emerged as a unique class of materials at the center of various biological advances. Owing to DNA's high modification capacity via programmable Watson-Crick base-pairing, DNA structures of desired design with increased complexity have been developed. However, the limited scalability, along with poor mechanical properties, high synthesis costs, and poor stability, reduced the adaptability of DNA-based materials to complex biological applications. DNA-based hybrid biomaterials were designed to overcome these limitations by conjugating DNA with functional materials. Today, DNA-based hybrid materials have attracted significant attention in biological engineering with broad application prospects in biomedicine, clinical diagnosis, and nanodevices. Here, we summarize the recent advances in DNA-based hybrid materials with an in-depth understanding of general molecular design principles, functionalities, and applications. Finally, the challenges and prospects associated with DNA-based hybrid materials are discussed at the end of this review.
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Affiliation(s)
- Nihal Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Ankur Singh
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Mukesh Dhanka
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
| | - Dhiraj Bhatia
- Discipline of Bioengineering, Indian Institute of Technology Gandhinagar, Gujarat, India, 382355.
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3
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Mullins N, Alashraf AR, McDermott K, Brown RS, Payne SJ. Polyethylenimine mediated recovery of SARS-CoV-2 and total viral RNA: Impact of aqueous conditions on behaviour and recovery. WATER RESEARCH 2024; 253:121207. [PMID: 38401469 DOI: 10.1016/j.watres.2024.121207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/28/2023] [Accepted: 01/26/2024] [Indexed: 02/26/2024]
Abstract
Wastewater-based epidemiology (WBE) is an emerging, practical surveillance tool for monitoring community levels of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, SC2). However, a paucity of data exists regarding SARS-CoV-2 and viral biomarker behaviour in aqueous and wastewater environments. Therefore, there is a pressing need to develop efficient and robust methods that both improve method sensitivity and reduce time and cost. We present a novel method for SARS-CoV-2, Human Coronavirus 229E (229E), and Pepper Mild Mottle Virus (PMMoV) recovery utilizing surface charge-based attraction via the branched cationic polymer, polyethylenimine (PEI). Initially, dose-optimization experiments demonstrated that low concentrations of PEI (0.001% w/v) proved most effective at flocculating suspended viruses and viral material, including additional unbound SC2 viral fragments and/or RNA from raw wastewater. A design-of-experiments (DOE) approach was used to optimize virus and/or viral material aggregation behaviour and recovery across varying aqueous conditions, revealing pH as a major influence on recoverability in this system, combinatorially due to both a reduction in viral material surface charge and increased protonation of PEI-bound amine groups. Overall, this method has shown great promise in significantly improving quantitative viral recovery, providing a straightforward and effective augmentation to standard centrifugation techniques.
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Affiliation(s)
- Nathan Mullins
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; McMaster University, Department of Chemical Engineering, Hamilton, Ontario, L8S 4L7, Canada
| | - Abdul Rahman Alashraf
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada
| | | | - R Stephen Brown
- Queen's University, Department of Chemistry and School of Environmental Studies, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
| | - Sarah Jane Payne
- Queen's University, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada; Queen's University, Beaty Water Research Centre, Department of Civil Engineering, Kingston, Ontario, K7L 3N6, Canada.
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4
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Jin Z, Al Amili M, Guo S. Tumor Microenvironment-Responsive Drug Delivery Based on Polymeric Micelles for Precision Cancer Therapy: Strategies and Prospects. Biomedicines 2024; 12:417. [PMID: 38398021 PMCID: PMC10886702 DOI: 10.3390/biomedicines12020417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
In clinical practice, drug therapy for cancer is still limited by its inefficiency and high toxicity. For precision therapy, various drug delivery systems, including polymeric micelles self-assembled from amphiphilic polymeric materials, have been developed to achieve tumor-targeting drug delivery. Considering the characteristics of the pathophysiological environment at the drug target site, the design, synthesis, or modification of environmentally responsive polymeric materials has become a crucial strategy for drug-targeted delivery. In comparison to the normal physiological environment, tumors possess a unique microenvironment, characterized by a low pH, high reactive oxygen species concentration, hypoxia, and distinct enzyme systems, providing various stimuli for the environmentally responsive design of polymeric micelles. Polymeric micelles with tumor microenvironment (TME)-responsive characteristics have shown significant improvement in precision therapy for cancer treatment. This review mainly outlines the most promising strategies available for exploiting the tumor microenvironment to construct internal stimulus-responsive drug delivery micelles that target tumors and achieve enhanced antitumor efficacy. In addition, the prospects of TME-responsive polymeric micelles for gene therapy and immunotherapy, the most popular current cancer treatments, are also discussed. TME-responsive drug delivery via polymeric micelles will be an efficient and robust approach for developing clinical cancer therapies in the future.
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Affiliation(s)
- Zhu Jin
- Correspondence: (Z.J.); (S.G.)
| | | | - Shengrong Guo
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
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Selianitis D, Katifelis H, Gazouli M, Pispas S. Novel Multi-Responsive Hyperbranched Polyelectrolyte Polyplexes as Potential Gene Delivery Vectors. Pharmaceutics 2023; 15:1627. [PMID: 37376075 DOI: 10.3390/pharmaceutics15061627] [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: 04/21/2023] [Revised: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
In this work, we investigate the complexation behavior of poly(oligo(ethylene glycol)methyl methacrylate)-co-poly(2-(diisopropylamino)ethyl methacrylate), P(OEGMA-co-DIPAEMA), hyperbranched polyelectrolyte copolymers, synthesized by reversible addition fragmentation chain transfer (RAFT) polymerization, with short-linear DNA molecules. The synthesized hyperbranched copolymers (HBC), having a different chemical composition, are prepared in order to study their ability to bind with a linear nucleic acid at various N/P ratios (amine over phosphate groups). Specifically, the three pH and thermo-responsive P(OEGMA-co-DIPAEMA) hyperbranched copolymers were able to form polyplexes with DNA, with dimensions in the nanoscale. Using several physicochemical methods, such as dynamic and electrophoretic light scattering (DLS, ELS), as well as fluorescence spectroscopy (FS), the complexation process and the properties of formed polyplexes were explored in response to physical and chemical stimuli such as temperature, pH, and ionic strength. The mass and the size of polyplexes are shown to be affected by the hydrophobicity of the copolymer utilized each time, as well as the N/P ratio. Additionally, the stability of polyplexes in the presence of serum proteins is found to be excellent. Finally, the multi-responsive hyperbranched copolymers were evaluated regarding their cytotoxicity via in vitro experiments on HEK 293 non-cancerous cell lines and found to be sufficiently non-toxic. Based on our results, these polyplexes could be useful candidates for gene delivery and related biomedical applications.
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Affiliation(s)
- Dimitrios Selianitis
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
| | - Hector Katifelis
- Laboratory of Biology, Department of Basic Medical Science, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Gazouli
- Laboratory of Biology, Department of Basic Medical Science, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Stergios Pispas
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece
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6
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Li F, Sun X, Yang J, Ren J, Huang M, Wang S, Yang D. A Thermal and Enzymatic Dual-Stimuli Responsive DNA-Based Nanomachine for Controlled mRNA Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204905. [PMID: 36461751 PMCID: PMC9896069 DOI: 10.1002/advs.202204905] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/03/2022] [Indexed: 06/17/2023]
Abstract
The extreme instability of mRNA makes the practical application of mRNA-based vaccines heavily rely on efficient delivery system and cold chain transportation. Herein, a DNA-based nanomachine, which achieves programmed capture, long-term storage without cryopreservation, and efficient delivery of mRNA in cells, is developed. The polythymidine acid (Poly-T) functionalized poly(N-isopropylacrylamide) (DNA-PNIPAM) is synthesized and assembled as the central compartment of the nanomachine. The DNA-PNIPAM nano-assembly exhibits reversible thermal-responsive dynamic property: when lower than the low critical solution temperature (LCST, ≈32 °C) of PNIPAM, the DNA-PNIPAM transforms into extension state to expose the poly-T, facilitating the hybridization with polyadenylic acid (Poly-A) tail of mRNA; when higher than LCST, DNA-PNIPAM re-assembles and achieves an efficient encapsulation of mRNA. It is remarkable that the DNA-PNIPAM nano-assembly realizes long-term storage of mRNA (≈7 days) at 37 °C. Biodegradable 2-hydroxypropyltrimethyl ammonium chloride chitosan is assembled on the outside of DNA-PNIPAM to facilitate the endocytosis of mRNA, RNase-H mediating mRNA release occurs in cytoplasm, and efficient mRNA translation is achieved. This work provides a new disign principle of nanosystem for mRNA delivery.
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Affiliation(s)
- Feng Li
- Frontiers Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)Institute of Biomolecular and Biomedical EngineeringSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300350P. R. China
| | - Xiaolei Sun
- Frontiers Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)Institute of Biomolecular and Biomedical EngineeringSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300350P. R. China
| | - Jing Yang
- Beijing Institute of Microbiology and EpidemiologyBeijing100850P. R. China
| | - Jin Ren
- Beijing Institute of Microbiology and EpidemiologyBeijing100850P. R. China
| | - Mengxue Huang
- Frontiers Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)Institute of Biomolecular and Biomedical EngineeringSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300350P. R. China
| | - Shengqi Wang
- Beijing Institute of Microbiology and EpidemiologyBeijing100850P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic BiologyKey Laboratory of Systems Bioengineering (MOE)Institute of Biomolecular and Biomedical EngineeringSchool of Chemical Engineering and TechnologyTianjin UniversityTianjin300350P. R. China
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7
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Angga MS, Malla B, Raya S, Kitano A, Xie X, Saitoh H, Ohnishi N, Haramoto E. Development of a magnetic nanoparticle-based method for concentrating SARS-CoV-2 in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157613. [PMID: 35901898 PMCID: PMC9310541 DOI: 10.1016/j.scitotenv.2022.157613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Several virus concentration methods have been developed to increase the detection sensitivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater, as part of applying wastewater-based epidemiology. Polyethylene glycol (PEG) precipitation method, a method widely used for concentrating viruses in wastewater, has some limitations, such as long processing time. In this study, Pegcision, a PEG-based method using magnetic nanoparticles (MNPs), was applied to detect SARS-CoV-2 in wastewater, with several modifications to increase its sensitivity and throughput. An enveloped virus surrogate, Pseudomonas phage φ6, and a non-enveloped virus surrogate, coliphage MS2, were seeded into wastewater samples and quantified using reverse transcription-quantitative polymerase chain reaction to assess the recovery performance of the Pegcision. Neither increasing MNP concentration nor reducing the reaction time to 10 min affected the recovery, while adding polyacrylic acid as a polyanion improved the detection sensitivity. The performance of the Pegcision was further compared to that of the PEG precipitation method based on the detection of SARS-CoV-2 and surrogate viruses, including indigenous pepper mild mottle virus (PMMoV), in wastewater samples (n = 27). The Pegcision showed recovery of 14.1 ± 6.3 % and 1.4 ± 1.0 % for φ6 and MS2, respectively, while the PEG precipitation method showed recovery of 20.4 ± 20.2 % and 18.4 ± 21.9 % (n = 27 each). Additionally, comparable PMMoV concentrations were observed between the Pegcision (7.9 ± 0.3 log copies/L) and PEG precipitation methods (8.0 ± 0.2 log copies/L) (P > 0.05) (n = 27). SARS-CoV-2 RNA was successfully detected in 11 (41 %) each of 27 wastewater samples using the Pegcision and PEG precipitation methods. The Pegcision showed comparable performance with the PEG precipitation method for SARS-CoV-2 RNA concentration, suggesting its applicability as a virus concentration method.
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Affiliation(s)
- Made Sandhyana Angga
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sunayana Raya
- Department of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Ayame Kitano
- Yokohama R&D Center, JNC Corporation, 5-1 Okawa, Kanazawa-ku, Yokohama, Kanagawa 236-8605, Japan.
| | - Xiaomao Xie
- Yokohama R&D Center, JNC Corporation, 5-1 Okawa, Kanazawa-ku, Yokohama, Kanagawa 236-8605, Japan.
| | - Hiroshi Saitoh
- Yokohama R&D Center, JNC Corporation, 5-1 Okawa, Kanazawa-ku, Yokohama, Kanagawa 236-8605, Japan.
| | - Noriyuki Ohnishi
- Corporate Research and Development Division, JNC Corporation, 5-1 Goikaigan, Ichihara, Chiba 290-8551, Japan.
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Kaur H, Verma M, Kaur S, Rana B, Singh N, Jena KC. Elucidating the Molecular Structure of Hydrophobically Modified Polyethylenimine Nanoparticles and Its Potential Implications for DNA Binding. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13456-13468. [PMID: 36279506 DOI: 10.1021/acs.langmuir.2c01912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The structural properties of the polyethylenimine (PEI) polymer are generally tuned and selectively modified to reinforce its potential in a broad spectrum of applied domains of medicine, healthcare, material design, sensing, and electronic optimization. The selective modification of the polymer brings about changes in its interfacial characteristics and behavior. The current work involves the synthesis of naphthalimide conjugated polyethylenimine organic nanoparticles (NPEI-ONPs). The interfacial molecular structure of NPEI-ONPs is explored in an aqueous medium at pH 7.4 using surface tensiometry and sum-frequency generation vibrational spectroscopy (SFG-VS). The hydrophobic functionalization rendered a concentration-dependent surface coverage of NPEI-ONPs, where the SFG-VS analysis exhibited the molecular rearrangement of its hydrophobic groups at the interface. The interaction of NPEI-ONPs with double-stranded DNA (dsDNA) is carried out to observe the relevance of the synthesized nanocomposites in the biomedical domain. The bulk-specific studies (i.e., thermal denaturation, viscometry, zeta (ζ) potential, and ATR-FTIR) reveal the condensation of dsDNA in the presence of NPEI-ONPs, making its structure more compact. The interface-sensitive SFG-VS showcased the impact of the dsDNA and NPEI-ONP interaction on the interfacial molecular behavior of NPEI-ONPs at the air-aqueous interface. Our results exhibit the potential of such hydrophobically functionalized ONPs as promising candidates for developing biomedical sealants, substrate coatings, and other biomedical domains.
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Wang RZ, Huang S, Zhang QY, Yu XS, Hong KZ, Cao JR, Xiao H, Wang Y, Shuai XT. Construction of Magnetic Resonance Imaging Visible Polymeric Vector for Efficient Tumor Targeted siRNA Delivery. CHINESE JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1007/s10118-022-2794-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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DNA adsorption on like-charged surfaces mediated by polycations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bindu Ramesan A, Vittala SK, Joseph J. DNA condensation and formation of ultrathin nanosheets via DNA assisted self-assembly of an amphiphilic fullerene derivative. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 226:112352. [PMID: 34798504 DOI: 10.1016/j.jphotobiol.2021.112352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022]
Abstract
DNA nanotechnology propose various assembly strategies to develop novel functional nanostructures utilizing unique interactions of DNA with small molecules, nanoparticles, polymers, and other biomolecules. Although, well defined nanostructures of DNA and amphiphilic small molecules were achieved through hybridization of covalently modified DNA, attaining precise organization of functional moieties through non-covalent interactions remain as a challenging task. Herein, we report mutually assisted assembly of an amphiphilic fullerene derivative and various DNA structures through non-covalent interactions, which leads to initial DNA condensation and subsequent assembly yielding ordered fullerene-DNA nanosheets. The molecular design of the cationic, amphiphilic fullerene derivative (FPy) ensures molecular solubility in the 10% DMSO-PBS buffer system and facile interactions with DNA through groove binding and electrostatic interactions of fullerene moiety and positively charged pyridinium moiety, respectively. The formation of FPy/DNA nanostructures were thoroughly investigated in the presence of λ-DNA, pBR322 plasmid DNA, and single and double stranded 20-mer oligonucleotides using UV-visible spectroscopy, AFM and TEM analysis. λ-DNA and pBR322 plasmid DNA readily condense in presence of FPy leading to micrometer sized few layer nanosheets with significant crystallinity due to ordered arrangement of fullerenes. Similarly, single and double stranded 20-mer oligonucleotides also interact efficiently with FPy and form highly crystalline nanosheets, signifying the role of electrostatic interaction and subsequent charge neutralization in the condensation triggered assembly. However, there is significant differences in the crystallinity and ordered arrangements of fullerenes between these two cases, where longer DNA form condensed structures and less ordered nanosheets while short oligonucleotides lead to more ordered and highly crystalline nanosheets, which could be attributed to the differential DNA condensation. Finally, we have demonstrated the addressability of the assembly using a cyanine modified single strand DNA, which also forms highly crystalline nanosheets and exhibit efficient quenching of the cyanine fluorescence upon self-assembly. These results open up new prospects in the development of functional DNA nanostructures through non-covalent interactions and hence have potential applications in the context of DNA nanotechnology.
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Affiliation(s)
- Anjali Bindu Ramesan
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sandeepa Kulala Vittala
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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12
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Vasiliu T, Craciun BF, Neamtu A, Clima L, Isac DL, Maier SS, Pinteala M, Mocci F, Laaksonen A. In silico study of PEI-PEG-squalene-dsDNA polyplex formation: the delicate role of the PEG length in the binding of PEI to DNA. Biomater Sci 2021; 9:6623-6640. [PMID: 34582532 DOI: 10.1039/d1bm00973g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biocompatible hydrophilic polyethylene glycol (PEG) is widely used in biomedical applications, such as drug or gene delivery, tissue engineering or as an antifouling component in biomedical devices. Experimental studies have shown that the size of PEG can weaken polycation-polyanion interactions, like those between branched polyethyleneimine (b-PEI) and DNA in gene carriers, but details of its cause and underlying interactions on the atomic scale are still not clear. To better understand the interaction mechanisms in the formation of polyplexes between b-PEI-PEG based carriers and DNA, we have used a combination of in silico tools and experiments on three multicomponent systems differing in PEG MW. Using the PEI-PEG-squalene-dsDNA systems of the same size, both in the all-atom MD simulations and in experimental in-gel electrophoresis measurements, we found that the binding between DNA and the vectors is highly influenced by the size of PEG, with the binding efficiency increasing with a shorter PEG length. The mechanism of how PEG interferes with the binding between PEI and DNA is explained using a two-step MD simulation protocol that showed that the DNA-vector interactions are influenced by the PEG length due to the hydrogen bond formation between PEI and PEG. Although computationally demanding we find it important to study molecular systems of the same size both in silico and in a laboratory and to simulate the behaviour of the carrier prior to the addition of bioactive molecules to understand the molecular mechanisms involved in the formation of the polyplex.
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Affiliation(s)
- Tudor Vasiliu
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Bogdan Florin Craciun
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Andrei Neamtu
- Bioinformatics Laboratory, TRANSCEND IRO, Iaşi 700843, Romania
| | - Lilia Clima
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Dragos Lucian Isac
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Stelian S Maier
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania. .,Polymers Research Center, "Gheorghe Asachi" Technical University of Iasi, Iasi, 700487, Romania
| | - Mariana Pinteala
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania.
| | - Francesca Mocci
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania. .,Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Monserrato, 09042 Cagliari, Italy
| | - Aatto Laaksonen
- Center of Advanced Research in Bionanoconjugates and Biopolymers, "Petru Poni" Institute of Macromolecular Chemistry, Iasi 700487, Romania. .,Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, 210009 Nanjing, PR China.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, 97187 Luleå, Sweden
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13
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Whitfield C, Zhang M, Winterwerber P, Wu Y, Ng DYW, Weil T. Functional DNA-Polymer Conjugates. Chem Rev 2021; 121:11030-11084. [PMID: 33739829 PMCID: PMC8461608 DOI: 10.1021/acs.chemrev.0c01074] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 02/07/2023]
Abstract
DNA nanotechnology has seen large developments over the last 30 years through the combination of solid phase synthesis and the discovery of DNA nanostructures. Solid phase synthesis has facilitated the availability of short DNA sequences and the expansion of the DNA toolbox to increase the chemical functionalities afforded on DNA, which in turn enabled the conception and synthesis of sophisticated and complex 2D and 3D nanostructures. In parallel, polymer science has developed several polymerization approaches to build di- and triblock copolymers bearing hydrophilic, hydrophobic, and amphiphilic properties. By bringing together these two emerging technologies, complementary properties of both materials have been explored; for example, the synthesis of amphiphilic DNA-polymer conjugates has enabled the production of several nanostructures, such as spherical and rod-like micelles. Through both the DNA and polymer parts, stimuli-responsiveness can be instilled. Nanostructures have consequently been developed with responsive structural changes to physical properties, such as pH and temperature, as well as short DNA through competitive complementary binding. These responsive changes have enabled the application of DNA-polymer conjugates in biomedical applications including drug delivery. This review discusses the progress of DNA-polymer conjugates, exploring the synthetic routes and state-of-the-art applications afforded through the combination of nucleic acids and synthetic polymers.
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Affiliation(s)
- Colette
J. Whitfield
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Meizhou Zhang
- Hubei
Key Laboratory of Bioinorganic Chemistry and Materia Medica, School
of Chemistry and Chemical Engineering, Huazhong
University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan 430074, People’s Republic of China
| | - Pia Winterwerber
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuzhou Wu
- Hubei
Key Laboratory of Bioinorganic Chemistry and Materia Medica, School
of Chemistry and Chemical Engineering, Huazhong
University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan 430074, People’s Republic of China
| | - David Y. W. Ng
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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14
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Kostritskii AY, Alleva C, Cönen S, Machtens JP. g_elpot: A Tool for Quantifying Biomolecular Electrostatics from Molecular Dynamics Trajectories. J Chem Theory Comput 2021; 17:3157-3167. [PMID: 33914551 DOI: 10.1021/acs.jctc.0c01246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrostatic forces drive a wide variety of biomolecular processes by defining the energetics of the interaction between biomolecules and charged substances. Molecular dynamics (MD) simulations provide trajectories that contain ensembles of structural configurations sampled by biomolecules and their environment. Although this information can be used for high-resolution characterization of biomolecular electrostatics, it has not yet been possible to calculate electrostatic potentials from MD trajectories in a way allowing for quantitative connection to energetics. Here, we present g_elpot, a GROMACS-based tool that utilizes the smooth particle mesh Ewald method to quantify the electrostatics of biomolecules by calculating potential within water molecules that are explicitly present in biomolecular MD simulations. g_elpot can extract the global distribution of the electrostatic potential from MD trajectories and measure its time course in functionally important regions of a biomolecule. To demonstrate that g_elpot can be used to gain biophysical insights into various biomolecular processes, we applied the tool to MD trajectories of the P2X3 receptor, TMEM16 lipid scramblases, the secondary-active transporter GltPh, and DNA complexed with cationic polymers. Our results indicate that g_elpot is well suited for quantifying electrostatics in biomolecular systems to provide a deeper understanding of its role in biomolecular processes.
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Affiliation(s)
- Andrei Y Kostritskii
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062 Aachen, Germany.,Institute of Clinical Pharmacology, RWTH Aachen University, 52062 Aachen, Germany
| | - Claudia Alleva
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Saskia Cönen
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany.,Institute of Clinical Pharmacology, RWTH Aachen University, 52062 Aachen, Germany
| | - Jan-Philipp Machtens
- Institute of Biological Information Processing (IBI-1), Molekular- und Zellphysiologie, and JARA-HPC, Forschungszentrum Jülich, 52425 Jülich, Germany.,Institute of Clinical Pharmacology, RWTH Aachen University, 52062 Aachen, Germany
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15
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Gurtovenko AA. Molecular-Level Insight into the Interactions of DNA/Polycation Complexes with Model Cell Membranes. J Phys Chem B 2019; 123:6505-6514. [DOI: 10.1021/acs.jpcb.9b05110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect V.O. 31, St. Petersburg 199004 Russia
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16
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Jia Z, Ma Y, Yang L, Guo C, Zhou N, Wang M, He L, Zhang Z. NiCo2O4 spinel embedded with carbon nanotubes derived from bimetallic NiCo metal-organic framework for the ultrasensitive detection of human immune deficiency virus-1 gene. Biosens Bioelectron 2019; 133:55-63. [DOI: 10.1016/j.bios.2019.03.030] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/12/2019] [Accepted: 03/17/2019] [Indexed: 01/22/2023]
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17
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Annenkov VV, Krishnan UM, Pal'shin VA, Zelinskiy SN, Kandasamy G, Danilovtseva EN. Design of Oligonucleotide Carriers: Importance of Polyamine Chain Length. Polymers (Basel) 2018; 10:E1297. [PMID: 30961222 PMCID: PMC6401700 DOI: 10.3390/polym10121297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 01/05/2023] Open
Abstract
Amine containing polymers are extensively studied as special carriers for short-chain RNA (13⁻25 nucleotides), which are applied as gene silencing agents in gene therapy of various diseases including cancer. Elaboration of the oligonucleotide carriers requires knowledge about peculiarities of the oligonucleotide⁻polymeric amine interaction. The critical length of the interacting chains is an important parameter which allows us to design sophisticated constructions containing oligonucleotide binding segments, solubilizing, protective and aiming parts. We studied interactions of (TCAG)n, n = 1⁻6 DNA oligonucleotides with polyethylenimine and poly(N-(3-((3-(dimethylamino)propyl)(methyl)amino)propyl)-N-methylacrylamide). The critical length for oligonucleotides in interaction with polymeric amines is 8⁻12 units and complexation at these length can be accompanied by "all-or-nothing" effects. New dimethylacrylamide based polymers with grafted polyamine chains were obtained and studied in complexation with DNA and RNA oligonucleotides. The most effective interaction and transfection activity into A549 cancer cells and silencing efficiency against vascular endothelial growth factor (VEGF) was found for a sample with average number of nitrogens in polyamine chain equal to 27, i.e., for a sample in which all grafted chains are longer than the critical length for polymeric amine⁻oligonucleotide complexation.
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Affiliation(s)
- Vadim V Annenkov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), School of Chemical and Biotechnology, SASTRA University, Thanjavur 613401, Tamil Nadu, India.
| | - Viktor A Pal'shin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
| | - Stanislav N Zelinskiy
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
| | - Gayathri Kandasamy
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), School of Chemical and Biotechnology, SASTRA University, Thanjavur 613401, Tamil Nadu, India.
| | - Elena N Danilovtseva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
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