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Airinei A, Isac DL, Fifere N, Maftei D, Rusu E. Computational and experimental investigation of photoresponsive behavior of 4,4′-dihydroxyazobenzene diglycidyl ether. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2022.100709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Coroaba A, Al-Matarneh C, Vasiliu T, Ibanescu SA, Zonda R, Esanu I, Isac DL, Pinteala M. Revealing the supramolecular interactions of the bis(azopyrenyl) dibenzo-18-crown-6-ether system. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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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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