1
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Maze D, Pichon C, Midoux P. Reversible stabilization of DNA/PEI complexes by reducible click-linkage between DNA and polymer. A new polyplex concept for lowering polymer quantity. Gene Ther 2023; 30:783-791. [PMID: 36755129 DOI: 10.1038/s41434-023-00386-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/18/2023] [Accepted: 01/27/2023] [Indexed: 02/10/2023]
Abstract
Nonviral transfection of mammalian cells can be performed with electrostatic complexes (polyplexes) between a plasmid DNA (pDNA) encoding a foreign gene and a cationic polymer. However, an excess of the cationic polymer is required for pDNA condensation and polyplexes formation, which generate in vivo toxicity. Here, we present a new concept of polyplexes preparation aiming to reduce the polymer quantity. pDNA was functionalized with 3,6,9-trioxaundecan-1- {4 - [(2-chloroethyl) ethylamino)] - benzylamino}, 11-azide, and polyethyleneimine (lPEI) with reducible dibenzocyclooctyl (SS-DBCO) groups allowing azide-alkyne cycloaddition between pDNA and lPEI after condensation. The size of polyplexes with DBCO-SS-lPEI was smaller than with lPEI due to a stronger DNA condensation thanks to linkages between polymer and pDNA preventing dissociation until disulfide bridges reduction. In vitro transfection showed that the amount of DBCO-SS-lPEI leading to the most efficient polyplexes was three times lower than lPEI. As expected, toxicity in mice was significantly reduced upon intravenous injection of DBCO-SS-lPEI polyplexes at doses where the lPEI polyplexes killed mice. This is probably due to the high stability of the DBCO-SS-lPEI polyplexes which prevented their aggregation in the pulmonary capillaries. Overall, this new concept of polyplexes with DBCO-SS-lPEI offering the possibility of administering higher doses of polyplexes than lPEI and their ability to pass the pulmonary barrier could be favorably exploited for transfection of distant organs or tissues, such as tumors.
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Affiliation(s)
- Delphine Maze
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, F-45071, Orléans cedex 02, France
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, F-45071, Orléans cedex 02, France
| | - Patrick Midoux
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, F-45071, Orléans cedex 02, France.
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2
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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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3
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Senapati S, Upadhyaya A, Dhruw S, Giri D, Maiti P. Controlled DNA Delivery Using Poly(lactide) Nanoparticles and Understanding the Binding Interactions. J Phys Chem B 2021; 125:10009-10017. [PMID: 34436883 DOI: 10.1021/acs.jpcb.1c06520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cationic polymer-based gene delivery vectors suffer from several limitations such as low DNA-loading capacity, poor transfection, toxicity, environmental degradations, etc. Again, very limited works are available addressing the binding interactions in detail at the atomic level explaining the loading capacity, protection ability against harsh environments, and controlled release behavior of the DNA-encapsulated vehicles. Here, a poly(l-lactide) (PLA) nanoparticle-based controlled DNA release system is proposed. The developed vehicle possesses a high DNA-loading capacity and can release the loaded DNA in a controlled manner. Spectroscopic, physicochemical, and molecular simulation techniques (AM1 and atomistic molecular dynamics) have been employed to understand the binding interactions between PLA and DNA molecules enabling high DNA loading, protection against external harsh environments, and controlled DNA release behavior. Methyl thiazolyl tetrazolium (MTT) assay experiments confirm the biocompatible nature of the vehicle. Cellular uptake efficiency and endo-lysosomal escape capabilities have been investigated against HeLA cells. This study, therefore, demonstrates the development of a promising nonviral DNA delivery vector and includes a detailed investigation of the atomic-level interaction behavior between PLA and DNA molecules.
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Affiliation(s)
- Sudipta Senapati
- School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Anurag Upadhyaya
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Somnath Dhruw
- School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Debaprasad Giri
- Department of Physics, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
| | - Pralay Maiti
- School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221 005, India
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4
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Kumar R, Santa Chalarca CF, Bockman MR, Bruggen CV, Grimme CJ, Dalal RJ, Hanson MG, Hexum JK, Reineke TM. Polymeric Delivery of Therapeutic Nucleic Acids. Chem Rev 2021; 121:11527-11652. [PMID: 33939409 DOI: 10.1021/acs.chemrev.0c00997] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The advent of genome editing has transformed the therapeutic landscape for several debilitating diseases, and the clinical outlook for gene therapeutics has never been more promising. The therapeutic potential of nucleic acids has been limited by a reliance on engineered viral vectors for delivery. Chemically defined polymers can remediate technological, regulatory, and clinical challenges associated with viral modes of gene delivery. Because of their scalability, versatility, and exquisite tunability, polymers are ideal biomaterial platforms for delivering nucleic acid payloads efficiently while minimizing immune response and cellular toxicity. While polymeric gene delivery has progressed significantly in the past four decades, clinical translation of polymeric vehicles faces several formidable challenges. The aim of our Account is to illustrate diverse concepts in designing polymeric vectors towards meeting therapeutic goals of in vivo and ex vivo gene therapy. Here, we highlight several classes of polymers employed in gene delivery and summarize the recent work on understanding the contributions of chemical and architectural design parameters. We touch upon characterization methods used to visualize and understand events transpiring at the interfaces between polymer, nucleic acids, and the physiological environment. We conclude that interdisciplinary approaches and methodologies motivated by fundamental questions are key to designing high-performing polymeric vehicles for gene therapy.
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Affiliation(s)
- Ramya Kumar
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | - Matthew R Bockman
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Craig Van Bruggen
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rishad J Dalal
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Joseph K Hexum
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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5
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Fliervoet LA, Lisitsyna ES, Durandin NA, Kotsis I, Maas-Bakker RFM, Yliperttula M, Hennink WE, Vuorimaa-Laukkanen E, Vermonden T. Structure and Dynamics of Thermosensitive pDNA Polyplexes Studied by Time-Resolved Fluorescence Spectroscopy. Biomacromolecules 2020; 21:73-88. [PMID: 31500418 PMCID: PMC6961130 DOI: 10.1021/acs.biomac.9b00896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/29/2019] [Indexed: 12/15/2022]
Abstract
Combining multiple stimuli-responsive functionalities into the polymer design is an attractive approach to improve nucleic acid delivery. However, more in-depth fundamental understanding how the multiple functionalities in the polymer structures are influencing polyplex formation and stability is essential for the rational development of such delivery systems. Therefore, in this study the structure and dynamics of thermosensitive polyplexes were investigated by tracking the behavior of labeled plasmid DNA (pDNA) and polymer with time-resolved fluorescence spectroscopy using fluorescence resonance energy transfer (FRET). The successful synthesis of a heterofunctional poly(ethylene glycol) (PEG) macroinitiator containing both an atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain-transfer (RAFT) initiator is reported. The use of this novel PEG macroinitiator allows for the controlled polymerization of cationic and thermosensitive linear triblock copolymers and labeling of the chain-end with a fluorescent dye by maleimide-thiol chemistry. The polymers consisted of a thermosensitive poly(N-isopropylacrylamide) (PNIPAM, N), hydrophilic PEG (P), and cationic poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA, D) block, further referred to as NPD. Polymer block D chain-ends were labeled with Cy3, while pDNA was labeled with FITC. The thermosensitive NPD polymers were used to prepare pDNA polyplexes, and the effect of the N/P charge ratio, temperature, and composition of the triblock copolymer on the polyplex properties were investigated, taking nonthermosensitive PD polymers as the control. FRET was observed both at 4 and 37 °C, indicating that the introduction of the thermosensitive PNIPAM block did not compromise the polyplex structure even above the polymer's cloud point. Furthermore, FRET results showed that the NPD- and PD-based polyplexes have a less dense core compared to polyplexes based on cationic homopolymers (such as PEI) as reported before. The polyplexes showed to have a dynamic character meaning that the polymer chains can exchange between the polyplex core and shell. Mobility of the polymers allow their uniform redistribution within the polyplex and this feature has been reported to be favorable in the context of pDNA release and subsequent improved transfection efficiency, compared to nondynamic formulations.
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Affiliation(s)
- Lies A.
L. Fliervoet
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS),
Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Ekaterina S. Lisitsyna
- Chemistry
and Advanced Materials, Faculty of Engineering and Natural Sciences, Tampere University, FI-33014 Tampere, Finland
| | - Nikita A. Durandin
- Chemistry
and Advanced Materials, Faculty of Engineering and Natural Sciences, Tampere University, FI-33014 Tampere, Finland
| | - Ilias Kotsis
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS),
Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Roel F. M. Maas-Bakker
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS),
Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Marjo Yliperttula
- Division
of Pharmaceutical Biosciences and Drug Research Program, University of Helsinki, P.O. Box 56 (Viikinkaari 5E), 00014 Helsinki, Finland
| | - Wim E. Hennink
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS),
Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Elina Vuorimaa-Laukkanen
- Chemistry
and Advanced Materials, Faculty of Engineering and Natural Sciences, Tampere University, FI-33014 Tampere, Finland
| | - Tina Vermonden
- Department
of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS),
Faculty of Science, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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6
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Tabujew I, Heidari M, Freidel C, Helm M, Tebbe L, Wolfrum U, Nagel-Wolfrum K, Koynov K, Biehl P, Schacher FH, Potestio R, Peneva K. Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental–Computational Approach. Biomacromolecules 2019; 20:4389-4406. [DOI: 10.1021/acs.biomac.9b01061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ilja Tabujew
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743 Jena, Germany
| | - Maziar Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Christoph Freidel
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Lars Tebbe
- Institute of Zoology, Johannes Gutenberg University Mainz, Muellerweg 6, 55099 Mainz, Germany
| | - Uwe Wolfrum
- Institute of Zoology, Johannes Gutenberg University Mainz, Muellerweg 6, 55099 Mainz, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Zoology, Johannes Gutenberg University Mainz, Muellerweg 6, 55099 Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Philip Biehl
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743 Jena, Germany
| | - Felix H. Schacher
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743 Jena, Germany
| | - Raffaello Potestio
- Physics Department, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
| | - Kalina Peneva
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743 Jena, Germany
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7
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Mahajan S, Tang T. Polyethylenimine–DNA Ratio Strongly Affects Their Nanoparticle Formation: A Large-Scale Coarse-Grained Molecular Dynamics Study. J Phys Chem B 2019; 123:9629-9640. [DOI: 10.1021/acs.jpcb.9b07031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Subhamoy Mahajan
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
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8
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Kawagoe Y, Surblys D, Matsubara H, Kikugawa G, Ohara T. Construction of polydisperse polymer model and investigation of heat conduction: A molecular dynamics study of linear and branched polyethylenimine. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.121721] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Gomez JP, Tresset G, Pichon C, Midoux P. Improved histidinylated lPEI polyplexes for skeletal muscle cells transfection. Int J Pharm 2019; 559:58-67. [DOI: 10.1016/j.ijpharm.2019.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/21/2018] [Accepted: 01/08/2019] [Indexed: 01/19/2023]
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10
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Mahajan S, Tang T. Martini coarse-grained model for polyethylenimine. J Comput Chem 2018; 40:607-618. [DOI: 10.1002/jcc.25747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 10/10/2018] [Accepted: 10/13/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Subhamoy Mahajan
- Department of Mechanical Engineering; University of Alberta; Edmonton Alberta Canada
| | - Tian Tang
- Department of Mechanical Engineering; University of Alberta; Edmonton Alberta Canada
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11
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12
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Meneksedag-Erol D, Tang T, Uludağ H. Mechanistic insights into the role of glycosaminoglycans in delivery of polymeric nucleic acid nanoparticles by molecular dynamics simulations. Biomaterials 2018; 156:107-120. [DOI: 10.1016/j.biomaterials.2017.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/02/2017] [Accepted: 11/21/2017] [Indexed: 11/17/2022]
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13
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Study of non-covalent interactions on dendriplex formation: Influence of hydrophobic, electrostatic and hydrogen bonds interactions. Colloids Surf B Biointerfaces 2018; 162:380-388. [DOI: 10.1016/j.colsurfb.2017.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 11/10/2017] [Accepted: 12/07/2017] [Indexed: 11/20/2022]
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14
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Collapse of DNA in packaging and cellular transport. Int J Biol Macromol 2017; 109:36-48. [PMID: 29247730 DOI: 10.1016/j.ijbiomac.2017.12.076] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 01/02/2023]
Abstract
The dawn of molecular biology and recombinant DNA technology arose from our ability to manipulate DNA, including the process of collapse of long extended DNA molecules into nanoparticles of approximately 100 nm diameter. This condensation process is important for the packaging of DNA in the cell and for transporting DNA through the cell membrane for gene therapy. Multivalent cations, such as natural polyamines (spermidine and spermine), were initially recognized for their ability to provoke DNA condensation. Current research is targeted on molecules such as linear and branched polymers, oligopeptides, polypeptides and dendrimers that promote collapse of DNA to nanometric particles for gene therapy and on the energetics of DNA packaging.
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15
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Lisitsyna ES, Ketola TM, Morin-Picardat E, Liang H, Hanzlíková M, Urtti A, Yliperttula M, Vuorimaa-Laukkanen E. Time-Resolved Fluorescence Spectroscopy Reveals Fine Structure and Dynamics of Poly(l-lysine) and Polyethylenimine Based DNA Polyplexes. J Phys Chem B 2017; 121:10782-10792. [DOI: 10.1021/acs.jpcb.7b08394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ekaterina S. Lisitsyna
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| | - Tiia-Maaria Ketola
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| | - Emmanuelle Morin-Picardat
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Huamin Liang
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
| | - Martina Hanzlíková
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Arto Urtti
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Marjo Yliperttula
- Division
of Pharmaceutical Biosciences, Centre for Drug Research, Faculty of
Pharmacy, University of Helsinki, P.O. Box 56, FI-00014 Helsinki, Finland
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, via F. Marzolo, 5, 35131 Padova, Italy
| | - Elina Vuorimaa-Laukkanen
- Department
of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, FI-33101 Tampere, Finland
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16
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Chang PKC, Prestidge CA, Bremmell KE. Interfacial analysis of siRNA complexes with poly-ethylenimine (PEI) or PAMAM dendrimers in gene delivery. Colloids Surf B Biointerfaces 2017; 158:370-378. [PMID: 28719858 DOI: 10.1016/j.colsurfb.2017.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/29/2017] [Accepted: 07/01/2017] [Indexed: 12/29/2022]
Abstract
Solution and interfacial analysis has been employed to gain insight into the complexation of siRNA using either G4 PAMAM dendrimers or 25kDa branched poly-ethylenimine (bPEI). The size, charge and shape/structure of the complexing agents were probed using atomic force microscopy (AFM), circular dichroism spectrometry (CD), dynamic light scattering (DLS), and gel electrophoresis (GE). The binding capability of these cationic polymers to the siRNA molecule, subsequently controls the surface/adsorption behaviour of the complexes to a negatively charged surface. G4 PAMAM dendrimers bind to the major groove of the siRNA structure, while bPEI binds to both major and minor groove. PAMAM-siRNA complexes form a thin uniform surface film with adsorption of monomeric particles, whilst bPEI-siRNA complexes adsorb as particles in random orientations at low bPEI concentration and form network structures across the surface at high charge ratio. This is due to their ability to bind to both regions within siRNA. This new understanding of the interfacial behaviour of siRNA complexes correlates with observations of cellular transfection and can be used in the design of optimal transfection agents.
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Affiliation(s)
- Patrick K C Chang
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Clive A Prestidge
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Kristen E Bremmell
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia.
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17
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Liu Q, Su RC, Yi WJ, Zhao ZG. Biodegradable Poly(Amino Ester) with Aromatic Backbone as Efficient Nonviral Gene Delivery Vectors. Molecules 2017; 22:E566. [PMID: 28362336 PMCID: PMC6154102 DOI: 10.3390/molecules22040566] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 03/25/2017] [Accepted: 03/28/2017] [Indexed: 11/16/2022] Open
Abstract
The development of gene delivery vectors with high efficiency and biocompatibility is one of the critical points of gene therapy. Two biodegradable poly(amino ester)s were synthesized via ring-opening polymerization between low molecular weight (LMW) PEI and diepoxide. The molecular weights of poly(amino ester)s were measured by GPC. Agarose gel retardation assays showed that these materials have good DNA-binding ability and can retard the electrophoretic mobility of plasmid DNA (pDNA) at a weight ratio of 1. The formed polyplexes have proper sizes of around 200 nm and zeta-potential values of about 30-40 mV for cellular uptake. In vitro experiments revealed that polymer P2 gave higher transfection efficiency than PEI 25KDa and Lipofectamine 2000 with less toxicity, especially in 293 cells. Results demonstrate that such a type of degradable poly(amino ester) may serve as a promising non-viral gene vector.
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Affiliation(s)
- Qiang Liu
- College of Chemistry and Environmental Protection Engineering, Southwest Minzu University, Chengdu 610041, China.
| | - Rong-Chuan Su
- College of Chemistry and Environmental Protection Engineering, Southwest Minzu University, Chengdu 610041, China.
| | - Wen-Jing Yi
- College of Chemistry and Environmental Protection Engineering, Southwest Minzu University, Chengdu 610041, China.
| | - Zhi-Gang Zhao
- College of Chemistry and Environmental Protection Engineering, Southwest Minzu University, Chengdu 610041, China.
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18
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Abstract
Gene therapy is an important therapeutic strategy in the treatment of a wide range of genetic disorders. Polymers forming stable complexes with nucleic acids (NAs) are non-viral gene carriers. The self-assembly of polymers and nucleic acids is typically a complex process that involves many types of interaction at different scales. Electrostatic interaction, hydrophobic interaction, and hydrogen bonds are three important and prevalent interactions in the polymer/nucleic acid system. Electrostatic interactions and hydrogen bonds are the main driving forces for the condensation of nucleic acids, while hydrophobic interactions play a significant role in the cellular uptake and endosomal escape of polymer-nucleic acid complexes. To design high-efficiency polymer candidates for the DNA and siRNA delivery, it is necessary to have a detailed understanding of the interactions between them in solution. In this chapter, we survey the roles of the three important interactions between polymers and nucleic acids during the formation of polyplexes and summarize recent understandings of the linear polyelectrolyte-NA interactions and dendrimer-NA interactions. We also review recent progress optimizing the gene delivery system by tuning these interactions.
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19
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Ziebarth JD, Kennetz DR, Walker NJ, Wang Y. Structural Comparisons of PEI/DNA and PEI/siRNA Complexes Revealed with Molecular Dynamics Simulations. J Phys Chem B 2017; 121:1941-1952. [PMID: 28145711 PMCID: PMC5677264 DOI: 10.1021/acs.jpcb.6b10775] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Polyplexes composed of polyethyleneimine (PEI) and DNA or siRNA have attracted great attention for their use in gene therapy. Although many physicochemical characteristics of these polyplexes remain unknown, PEI/DNA complexes have been repeatedly shown to be more stable than their PEI/siRNA counterparts. Here, we examine potential causes for this difference using atomistic molecular dynamics simulations of complexation between linear PEI and DNA or siRNA duplexes containing the same number of bases. The two types of polyplexes are stabilized by similar interactions, as PEI amines primarily interact with nucleic acid phosphate groups but also occasionally interact with groove atoms of both nucleic acids. However, the number of interactions in PEI/DNA complexes is greater than in comparable PEI/siRNA complexes, with interactions between protonated PEI amines and DNA being particularly enhanced. These results indicate that structural differences between DNA and siRNA may play a role in the increased stability of PEI/DNA complexes. In addition, we investigate the binding of PEI chains to polyplexes that have a net positive charge. The binding of PEI to these overcharged complexes involves interactions between PEI and areas on the nucleic acid surface that have maintained a negative electrostatic potential and is facilitated by the release of water from the nucleic acid.
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Affiliation(s)
- Jesse D Ziebarth
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Dennis R Kennetz
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Nyles J Walker
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
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20
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Kou X, Zhang W, Zhang W. Quantifying the Interactions between PEI and Double-Stranded DNA: Toward the Understanding of the Role of PEI in Gene Delivery. ACS APPLIED MATERIALS & INTERFACES 2016; 8:21055-21062. [PMID: 27435435 DOI: 10.1021/acsami.6b06399] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Poly(ethylene imine) (PEI) is one of the most efficient nonviral vectors, and its binding mode/strength with double-stranded DNA (dsDNA), which is still not clear, is a core area of transfection studies. In this work we used the atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS) to detect the interaction between branched PEI and dsDNA quantitatively by using a long chain DNA as a probe. Our results indicate that PEI binds to phosphoric acid skeletons of dsDNA mainly via electrostatic interactions, no obvious groove-binding or intercalation has happened. The interaction strength is about 24-25 pN, and it remains unchanged at pH 5.0 and 7.4, which correspond to the pH values in lysosomes and in the cytoplasmic matrix, respectively. However, the interaction is found to be sensitive to the ionic strength of the environment. In addition, the unbinding force shows no obvious loading rate dependence indicative of equilibrium binding/unbinding.
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Affiliation(s)
- Xiaolong Kou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , Changchun 130012, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University , Changchun 130012, People's Republic of China
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21
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Pigeon L, Gonçalves C, Pichon C, Midoux P. Evidence for plasmid DNA exchange after polyplex mixing. SOFT MATTER 2016; 12:7012-7019. [PMID: 27459887 DOI: 10.1039/c6sm00575f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The self-assembly of a plasmid DNA (pDNA) with cationic polymers or cationic liposomes forms nanosized supramolecular structures called lipoplexes, polyplexes and lipopolyplexes. Here, we report that when two polyplex preparations made using the same polymer and the same pDNA but labelled with two different fluorophores are mixed together, pDNA molecules are exchanged. Indeed, when Flu-pDNA complexed with histidinylated lPEI (Flu-pDNA/His-lPEI) polyplexes are mixed with Cy5-pDNA complexed with histidinylated lPEI (Cy5-pDNA/His-lPEI) polyplexes, a high quantity of polyplexes emitting dual fluorescence is observed and FRET indicates that one single polyplex contains two kinds of fluorescent pDNA molecules. This phenomenon depends on the polymer-type and the strength of the pDNA/polymer interaction. No exchange is observed with polylysine polyplexes, caged His-lPEI polyplexes, lipoplexes, lipopolyplexes or when His-lPEI polyplexes are mixed with lipoplexes. Our results suggest that aggregation or collapse of polyplexes occurs after their interaction leading to their unpackaging followed by the formation of new polyplexes with the exchange of pDNA.
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Affiliation(s)
- L Pigeon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071 Orléans cedex 02, France.
| | - C Gonçalves
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071 Orléans cedex 02, France.
| | - C Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071 Orléans cedex 02, France.
| | - P Midoux
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm and University of Orléans, 45071 Orléans cedex 02, France.
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22
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Mieruszynski S, Briggs C, Digman MA, Gratton E, Jones MR. Live Cell Characterization of DNA Aggregation Delivered through Lipofection. Sci Rep 2015; 5:10528. [PMID: 26013547 PMCID: PMC4444954 DOI: 10.1038/srep10528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 04/17/2015] [Indexed: 01/20/2023] Open
Abstract
DNA trafficking phenomena, such as information on where and to what extent DNA aggregation occurs, have yet to be fully characterised in the live cell. Here we characterise the aggregation of DNA when delivered through lipofection by applying the Number and Brightness (N&B) approach. The N&B analysis demonstrates extensive aggregation throughout the live cell with DNA clusters in the extremity of the cell and peri-nuclear areas. Once within the nucleus aggregation had decreased 3-fold. In addition, we show that increasing serum concentration of cell media results in greater cytoplasmic aggregation. Further, the effects of the DNA fragment size on aggregation was explored, where larger DNA constructs exhibited less aggregation. This study demonstrates the first quantification of DNA aggregation when delivered through lipofection in live cells. In addition, this study has presents a model for alternative uses of this imaging approach, which was originally developed to study protein oligomerization and aggregation.
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Affiliation(s)
- Stephen Mieruszynski
- University of Western Sydney, School of Science and Health, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Candida Briggs
- University of Western Sydney, School of Science and Health, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Michelle A Digman
- 1] Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America; Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, California, United States of America [2] Centre for Bioactive Discovery in Health and Ageing, School of Science &Technology, University of New England, Armidale, Australia
| | - Enrico Gratton
- 1] Department of Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America; Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, California, United States of America [2] Centre for Bioactive Discovery in Health and Ageing, School of Science &Technology, University of New England, Armidale, Australia
| | - Mark R Jones
- University of Western Sydney, School of Science and Health, Hawkesbury Campus, Locked Bag 1797, Penrith NSW 2751, Australia
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23
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Meneksedag-Erol D, Tang T, Uludağ H. Probing the Effect of miRNA on siRNA–PEI Polyplexes. J Phys Chem B 2015; 119:5475-86. [DOI: 10.1021/acs.jpcb.5b00415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deniz Meneksedag-Erol
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
| | - Tian Tang
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department
of Mechanical Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
| | - Hasan Uludağ
- Department of Biomedical Engineering, Faculties of Medicine & Dentistry and Engineering, University of Alberta, Alberta, Canada
- Department of Chemical & Materials Engineering, Faculty of Engineering, University of Alberta, Alberta, Canada
- Faculty
of Pharmacy and Pharmaceutical Sciences, University of Alberta, Alberta, Canada
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24
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Pavan GM. Modeling the Interaction between Dendrimers and Nucleic Acids: a Molecular Perspective through Hierarchical Scales. ChemMedChem 2014; 9:2623-31. [DOI: 10.1002/cmdc.201402280] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 01/02/2023]
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25
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Angelescu DG, Linse P. Branched-linear polyion complexes investigated by Monte Carlo simulations. SOFT MATTER 2014; 10:6047-6058. [PMID: 24999910 DOI: 10.1039/c4sm01055h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Complexes formed by one charged and branched copolymer with an oppositely charged and linear polyion have been investigated by Monte Carlo simulations. A coarse-grained description has been used, in which the main chain of the branched polyion and the linear polyion possess the same absolute charge and charge density. The spatial extension and other structural properties, such as bond-angle orientational correlation function, asphericity, and scaling analysis of formed complexes, at varying branching density and side-chain length of the branched polyion, have been explored. In particular, the balance between cohesive Coulomb attraction and side-chain repulsions resulted in two main structures of a polyion complex. These structures are (i) a globular polyion core surrounded by side chains appearing at low branching density and (ii) an extended polyion core with side chains still being expelled at high branching density. The globule-to-extended transition occurred at a crossover branching density being practically independent of the side chain length.
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Affiliation(s)
- Daniel G Angelescu
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania.
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26
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Bromfield SM, Posocco P, Fermeglia M, Tolosa J, Herreros-López A, Pricl S, Rodríguez-López J, Smith DK. Shape-Persistent and Adaptive Multivalency: Rigid Transgeden (TGD) and Flexible PAMAM Dendrimers for Heparin Binding. Chemistry 2014; 20:9666-74. [DOI: 10.1002/chem.201402237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Indexed: 11/06/2022]
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27
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Bagai S, Sun C, Tang T. Lipid-modified polyethylenimine-mediated DNA attraction evaluated by molecular dynamics simulations. J Phys Chem B 2014; 118:7070-6. [PMID: 24918771 DOI: 10.1021/jp503381r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The effect of lipid modification on polyethylenimine (PEI)-mediated DNA attraction was studied by performing umbrella sampling molecular dynamics simulations that involved PEIs modified with three different types of lipids: oleic acid (OA), linoleic acid (LA), and caprylic acid (CA). The potential of mean force between two DNA molecules in the presence of these lipid-modified PEIs was calculated using the weighted histogram analysis method, and it predicted the stability and size of the DNA aggregate. When compared to native PEI, lipid modification was found to enhance the stability of DNA aggregation in the case of long lipids (LA and OA) but reduce the stability in the case of a short lipid (CA). In addition, LA-substituted PEI was shown to form stronger DNA aggregate than OA-substituted PEI, which correlates positively with previous experimental observations.
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Affiliation(s)
- Sampada Bagai
- Department of Mechanical Engineering, University of Alberta , Edmonton, Alberta, Canada T6G 2G8
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28
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Meneksedag-Erol D, Tang T, Uludağ H. Molecular modeling of polynucleotide complexes. Biomaterials 2014; 35:7068-76. [PMID: 24856107 DOI: 10.1016/j.biomaterials.2014.04.103] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 04/28/2014] [Indexed: 11/30/2022]
Abstract
Delivery of polynucleotides into patient cells is a promising strategy for treatment of genetic disorders. Gene therapy aims to either synthesize desired proteins (DNA delivery) or suppress expression of endogenous genes (siRNA delivery). Carriers constitute an important part of gene therapeutics due to limitations arising from the pharmacokinetics of polynucleotides. Non-viral carriers such as polymers and lipids protect polynucleotides from intra and extracellular threats and facilitate formation of cell-permeable nanoparticles through shielding and/or bridging multiple polynucleotide molecules. Formation of nanoparticulate systems with optimal features, their cellular uptake and intracellular trafficking are crucial steps for an effective gene therapy. Despite the great amount of experimental work pursued, critical features of the nanoparticles as well as their processing mechanisms are still under debate due to the lack of instrumentation at atomic resolution. Molecular modeling based computational approaches can shed light onto the atomic level details of gene delivery systems, thus provide valuable input that cannot be readily obtained with experimental techniques. Here, we review the molecular modeling research pursued on critical gene therapy steps, highlight the knowledge gaps in the field and providing future perspectives. Existing modeling studies revealed several important aspects of gene delivery, such as nanoparticle formation dynamics with various carriers, effect of carrier properties on complexation, carrier conformations in endosomal stages, and release of polynucleotides from carriers. Rate-limiting steps related to cellular events (i.e. internalization, endosomal escape, and nuclear uptake) are now beginning to be addressed by computational approaches. Limitations arising from current computational power and accuracy of modeling have been hindering the development of more realistic models. With the help of rapidly-growing computational power, the critical aspects of gene therapy are expected to be better investigated and direct comparison between more realistic molecular modeling and experiments may open the path for design of next generation gene therapeutics.
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Affiliation(s)
- Deniz Meneksedag-Erol
- Department of Biomedical Engineering, University of Alberta, Edmonton, Canada; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada
| | - Tian Tang
- Department of Biomedical Engineering, University of Alberta, Edmonton, Canada; Department of Mechanical Engineering, University of Alberta, Edmonton, Canada.
| | - Hasan Uludağ
- Department of Biomedical Engineering, University of Alberta, Edmonton, Canada; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada; Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Canada.
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29
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Molecular Dynamics Simulations of Polyplexes and Lipoplexes Employed in Gene Delivery. INTRACELLULAR DELIVERY II 2014. [DOI: 10.1007/978-94-017-8896-0_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Sun C, Tang T, Uludag H. A molecular dynamics simulation study on the effect of lipid substitution on polyethylenimine mediated siRNA complexation. Biomaterials 2013; 34:2822-33. [PMID: 23352043 DOI: 10.1016/j.biomaterials.2013.01.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/02/2013] [Indexed: 01/16/2023]
Abstract
Polycations have been explored as non-viral carriers for effective delivery of small interfering RNA (siRNA). Modifying polycations such as polyethylenimine (PEI) with lipid substitution was found to improve the siRNA delivery efficiency of polycationic carriers. However, the role of such lipid modification is not clear and remains to be probed at the atomistic level. In this work, we elucidate the role of lipid modification through a series of all-atom molecular dynamics simulations on siRNA complexation mediated by a native PEI and four analogous obtained by different lipid modifications. The lipid modification does not affect PEI's capability of neutralizing the siRNA charge, neither does it affect the polyion bridging which plays an important role in siRNA complexation. Significant linkages among the lipid modified PEIs via association of lipid side-groups are observed and this results in more stable and compact PEI/siRNA polyplexes. The lipid associations between short lipids form and break frequently while the lipid associations between long lipids are more stable. For PEIs modified with short lipids, increasing the lipid substitution level results in more compact and stable siRNA structure. For PEIs modified with long lipids, increasing the lipid substitution does not change the amount of PEI linkage via lipid association, and has a reverse effect on compacting siRNA structure due to increased steric hindrance brought by the lipid association on individual PEIs. The simulation results generally correlate well with experimental data and suggest a framework of designing and systematic evaluation of polycation-based siRNA carriers using molecular dynamics simulations.
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Affiliation(s)
- Chongbo Sun
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB T6G 2G8, Canada
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31
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Bagai S, Sun C, Tang T. Potential of Mean Force of Polyethylenimine-Mediated DNA Attraction. J Phys Chem B 2012; 117:49-56. [DOI: 10.1021/jp308132y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sampada Bagai
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8,
Canada
| | - Chongbo Sun
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8,
Canada
| | - Tian Tang
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta, T6G 2G8,
Canada
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32
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Kim H, Man HB, Saha B, Kopacz AM, Lee OS, Schatz GC, Ho D, Liu WK. Multiscale Simulation as a Framework for the Enhanced Design of Nanodiamond-Polyethylenimine-based Gene Delivery. J Phys Chem Lett 2012; 3:3791-3797. [PMID: 23304428 PMCID: PMC3538166 DOI: 10.1021/jz301756e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Nanodiamonds (NDs) are emerging carbon platforms with promise as gene/drug delivery vectors for cancer therapy. Specifically, NDs functionalized with the polymer polyethylenimine (PEI) can transfect small interfering RNAs (siRNA) in vitro with high efficiency and low cytotoxicity. Here we present a modeling framework to accurately guide the design of ND-PEI gene platforms and elucidate binding mechanisms between ND, PEI, and siRNA. This is among the first ND simulations to comprehensively account for ND size, charge distribution, surface functionalization, and graphitization. The simulation results are compared with our experimental results both for PEI loading onto NDs and for siRNA (C-myc) loading onto ND-PEI for various mixing ratios. Remarkably, the model is able to predict loading trends and saturation limits for PEI and siRNA, while confirming the essential role of ND surface functionalization in mediating ND-PEI interactions. These results demonstrate that this robust framework can be a powerful tool in ND platform development, with the capacity to realistically treat other nanoparticle systems.
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Affiliation(s)
- Hansung Kim
- Department of Mechanical Engineering, Robert R. McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208 USA
- Address correspondence to: , ,
| | - Han Bin Man
- Department of Mechanical Engineering, Robert R. McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208 USA
| | - Biswajit Saha
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208 USA
| | - Adrian M. Kopacz
- Department of Mechanical Engineering, Robert R. McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208 USA
| | - One-Sun Lee
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208 USA
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208 USA
- Address correspondence to: , ,
| | - Dean Ho
- Division of Oral Biology and Medicine, Division of Advanced Prosthodontics, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, California NanoSystems Institute, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California 90095, USA
- Address correspondence to: , ,
| | - Wing Kam Liu
- Department of Mechanical Engineering, Robert R. McCormick School of Engineering and Applied Science, Northwestern University, Evanston, Illinois 60208 USA
- Distinguished World Class University Professor, School of Mechanical Engineering, Sungkyunkwan University, Suwon, Kyonggi-do, Republic of Korea
- Address correspondence to: , ,
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33
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Sun C, Tang T, Uludağ H. Probing the Effects of Lipid Substitution on Polycation Mediated DNA Aggregation: A Molecular Dynamics Simulations Study. Biomacromolecules 2012; 13:2982-8. [DOI: 10.1021/bm301045b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Chongbo Sun
- Department
of Mechanical Engineering, ‡Department of Chemical and Materials Engineering, ¶Department of Biomedical
Engineering, and §Faculty of Pharmacy and Pharmaceutical Sciences, University
of Alberta, Edmonton, Canada
| | - Tian Tang
- Department
of Mechanical Engineering, ‡Department of Chemical and Materials Engineering, ¶Department of Biomedical
Engineering, and §Faculty of Pharmacy and Pharmaceutical Sciences, University
of Alberta, Edmonton, Canada
| | - Hasan Uludağ
- Department
of Mechanical Engineering, ‡Department of Chemical and Materials Engineering, ¶Department of Biomedical
Engineering, and §Faculty of Pharmacy and Pharmaceutical Sciences, University
of Alberta, Edmonton, Canada
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34
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Aliabadi HM, Landry B, Sun C, Tang T, Uludağ H. Supramolecular assemblies in functional siRNA delivery: Where do we stand? Biomaterials 2012; 33:2546-69. [DOI: 10.1016/j.biomaterials.2011.11.079] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 11/26/2011] [Indexed: 12/14/2022]
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35
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Sun C, Tang T, Uludaǧ H. Molecular dynamics simulations for complexation of DNA with 2 kDa PEI reveal profound effect of PEI architecture on complexation. J Phys Chem B 2012; 116:2405-13. [PMID: 22292702 DOI: 10.1021/jp211716v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of all-atom molecular dynamics (MD) simulations of the complexation between DNA and 2 kDa branched and linear polyethylenimines (PEIs) are reported in this study. The simulations revealed distinct binding modes of branched and linear PEIs to DNA, with branched PEIs adhering to the DNA surface like beads and linear PEIs adhering to the DNA surface like cords. The dynamics of each PEI's binding state to the DNA during the simulations and how the PEIs neutralize the DNA were quantified. For both branched and linear PEIs, the addition of salt ions similar to physiological conditions were found to have only a small effect on DNA/PEI complexation compared to salt-free conditions. The simulation results reported here will be helpful to understand the mechanism of action for the PEI-based gene carriers.
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Affiliation(s)
- Chongbo Sun
- Department of Mechanical Engineering, University of Alberta, Edmonton, Canada
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