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Mahajan S, Tang T. Polyethylenimine-DNA Nanoparticles under Endosomal Acidification and Implication to Gene Delivery. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8382-8397. [PMID: 35759612 DOI: 10.1021/acs.langmuir.2c00952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Non-viral gene delivery using polyethylenimine (PEI) has shown tremendous promise as a therapeutic technique. Through the formation of nanoparticles (NPs), PEIs protect genetic material such as DNA from degradation. Escape of the NPs from endosomes and lysosomes is facilitated by PEI's buffering capacity over a wide range of pH. However, little is known about the effects of endosomal acidification on the morphology of the NPs. In this work, large-scale coarse-grained simulations performed to mimic endosomal acidification reveal that NPs undergo a resizing process that is highly dependent on the N/P ratio (ratio of PEI nitrogen to DNA phosphate) at which they are prepared. With a low N/P ratio, NPs further aggregate after endosomal acidification, whereas with a high N/P ratio they dissociate. The mechanisms behind such NP resizing and its consequences on endosomal escape and nuclear trafficking are discussed. Based on the findings, suggestions are made on the PEI architecture that may enhance NP dissociation driven by endosomal acidification.
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Affiliation(s)
- Subhamoy Mahajan
- Department of Mechanical Engineering, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton T6G 2R3, Alberta, Canada
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2
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Ge H, Du J, Long S, Xia X, Zheng J, Xu N, Yao Q, Fan J, Peng X. Near-Infrared Light Triggered H 2 Generation for Enhanced Photothermal/Photodynamic Therapy against Hypoxic Tumor. Adv Healthc Mater 2022; 11:e2101449. [PMID: 34879433 DOI: 10.1002/adhm.202101449] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/01/2021] [Indexed: 01/09/2023]
Abstract
The principle of photochemical transformation has shown significant inspiration on phototherapy of solid tumors. However, both photodynamic therapy (PDT) and photothermal therapy (PTT) can induce stress response of tumor cells, which draw the attention in recent. Herein, an asymmetric and lollipop like nanostructure consisting of gold nanorod/titanium dioxide (l-TiO2 -GNR) is developed by controlling single head growth of titanium dioxide (TiO2 ) on gold nanorods (GNR). Through the reasonable utilization of hot electrons of GNR by 808 nm light irradiation, l-TiO2 -GNR perform type I-PDT, mild PTT (48 °C), and H2 therapy which is efficient for hypoxic tumors. In particular, H2 can downregulate both triphosadenine and heat shock protein which are found to be main source of tumor stress response. l-TiO2 -GNR opens a new window for treatment of hypoxic tumor by the perfect synergy of type I-PDT, mild PTT, and H2 therapy.
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Affiliation(s)
- Haoying Ge
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
| | - Jianjun Du
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
- Ningbo Institute of Dalian University of Technology 26 Yucai Road, Jiangbei District Ningbo 315016 China
| | - Saran Long
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
- Ningbo Institute of Dalian University of Technology 26 Yucai Road, Jiangbei District Ningbo 315016 China
| | - Xiang Xia
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
| | - Jiazhu Zheng
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
| | - Ning Xu
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
| | - Qichao Yao
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
- Ningbo Institute of Dalian University of Technology 26 Yucai Road, Jiangbei District Ningbo 315016 China
| | - Jiangli Fan
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
- Ningbo Institute of Dalian University of Technology 26 Yucai Road, Jiangbei District Ningbo 315016 China
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals Dalian University of Technology Dalian 116024 China
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3
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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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4
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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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Dey A, Kamat A, Nayak S, Danino D, Kesselman E, Dandekar P, Jain R. Role of proton balance in formation of self-assembled chitosan nanoparticles. Colloids Surf B Biointerfaces 2018; 166:127-134. [PMID: 29558703 DOI: 10.1016/j.colsurfb.2018.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/08/2018] [Accepted: 03/13/2018] [Indexed: 11/17/2022]
Abstract
Researchers have explored the ability of chitosan to form nanoparticles, to suit varying applications, ranging from wound-healing to gene delivery. Ionic gelation is a widely used method for formulating chitosan nanoparticles, where self-assembly plays a crucial role. This self-assembly is initially promoted by hydrophilic-hydrophobic parity amongst individual chitosan residues, along with electrostatic and Van der Waals interactions with the cross-linker. However, until now the intrinsic ability of chitosan to self-assemble is not widely studied; hence, we investigate the self-assembly of chitosan, based on proton balance between its protonated and deprotonated residues, to promote facile nanoparticle synthesis. This is one of the first reports that highlights subtle but critical influence of proton balance in the chitosan polymer on the formation of chitosan nanoparticles.
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Affiliation(s)
- Anomitra Dey
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Aditya Kamat
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Sonal Nayak
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Dganit Danino
- Department of Biotechnology & Food Engineering, Technion - Israel Institute of Technology, Hafia 3200003, Israel
| | - Ellina Kesselman
- Department of Biotechnology & Food Engineering, Technion - Israel Institute of Technology, Hafia 3200003, Israel
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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7
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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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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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9
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Jorge AF, Nunes SC, Cova TF, Pais AA. Cooperative action in DNA condensation. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Shakya A, Al-Hashimi HM, Banaszak Holl MM. Three RNA Microenvironments Detected in Fluxional Gene Delivery Polyplex Nanoassemblies. ACS Macro Lett 2016; 5:1104-1108. [PMID: 35658189 DOI: 10.1021/acsmacrolett.6b00668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Prototropic and solvatochromatic properties of fluorescein (FL) were employed to detect the presence of microenvironments in polyplexes consisting of polycationic polymer (POCP) and a fluorescein-conjugated RNA, the HIV-1 transactivation response element (TAR-FL). Results reveal new aspects of polyplex structure with respect to polyplex-bound RNA existing in the following local microenvironments: (a) RNA associated with the polyplex that experiences local pH changes in a manner dependent on POCP nitrogen to RNA phosphate ratio (N:P), (b) RNA experiencing relatively acidic local pH environment that remains constant in polyplexes formed after a charge-neutral ratio, and (c) RNA packed close enough to mediate fluorophore/fluorophore quenching. The magnitude of these changes observed as a function of POCP to nucleic acid N:P ratio is polymer dependent. Assessment of the different microenvironments can help elucidate the functional hierarchy of polyplex-bound oligonucleotides and additionally characterize POCPs based on the resulting local pH and solvent properties upon polyplex formation.
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Affiliation(s)
| | - Hashim M. Al-Hashimi
- Department
of Biochemistry and Chemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
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11
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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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12
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Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions. Int J Mol Sci 2016; 17:ijms17050692. [PMID: 27171075 PMCID: PMC4881518 DOI: 10.3390/ijms17050692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 04/26/2016] [Accepted: 04/26/2016] [Indexed: 11/16/2022] Open
Abstract
Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35). The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD) variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg) presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes.
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13
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Ramezanpour M, Leung SSW, Delgado-Magnero KH, Bashe BYM, Thewalt J, Tieleman DP. Computational and experimental approaches for investigating nanoparticle-based drug delivery systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1688-709. [PMID: 26930298 DOI: 10.1016/j.bbamem.2016.02.028] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 12/21/2022]
Abstract
Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- M Ramezanpour
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - S S W Leung
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - K H Delgado-Magnero
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - B Y M Bashe
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - J Thewalt
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - D P Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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15
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Gaspar VM, Gonçalves C, de Melo-Diogo D, Costa EC, Queiroz JA, Pichon C, Sousa F, Correia IJ. Poly(2-ethyl-2-oxazoline)-PLA-g-PEI amphiphilic triblock micelles for co-delivery of minicircle DNA and chemotherapeutics. J Control Release 2014; 189:90-104. [PMID: 24984013 DOI: 10.1016/j.jconrel.2014.06.040] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/21/2014] [Accepted: 06/21/2014] [Indexed: 12/24/2022]
Abstract
The design of nanocarriers for the delivery of drugs and nucleic-acids remains a very challenging goal due to their physicochemical differences. In addition, the reported accelerated clearance and immune response of pegylated nanomedicines highlight the necessity to develop carriers using new materials. Herein, we describe the synthesis of amphiphilic triblock poly(2-ethyl-2-oxazoline)-PLA-g-PEI (PEOz-PLA-g-PEI) micelles for the delivery of minicircle DNA (mcDNA) vectors. In this copolymer the generally used PEG moieties are replaced by the biocompatible PEOz polymer backbone that assembles the hydrophilic shell. The obtained results show that amphiphilic micelles have low critical micellar concentration, are hemocompatible and exhibit stability upon incubation in serum. The uptake in MCF-7 cells was efficient and the nanocarriers achieved 2.7 fold higher expression than control particles. Moreover, mcDNA-loaded micelleplexes penetrated into 3D multicellular spheroids and promoted widespread gene expression. Additionally, to prove the concept of co-delivery, mcDNA and doxorubicin (Dox) were simultaneously encapsulated in PEOz-PLA-g-PEI carriers, with high efficiency. Dox-mcDNA micelleplexes exhibited extensive cellular uptake and demonstrated anti-tumoral activity. These findings led us to conclude that this system has a potential not only for the delivery of novel mcDNA vectors, but also for the co-delivery of drug-mcDNA combinations without PEG functionalization.
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Affiliation(s)
- Vítor M Gaspar
- CICS-UBI, Health Sciences Research Center, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Cristine Gonçalves
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm et Université d'Orléans, 45071 Orléans cedex 02, France
| | - Duarte de Melo-Diogo
- CICS-UBI, Health Sciences Research Center, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Elisabete C Costa
- CICS-UBI, Health Sciences Research Center, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - João A Queiroz
- CICS-UBI, Health Sciences Research Center, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, CNRS UPR4301, Inserm et Université d'Orléans, 45071 Orléans cedex 02, France
| | - Fani Sousa
- CICS-UBI, Health Sciences Research Center, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Ilídio J Correia
- CICS-UBI, Health Sciences Research Center, University of Beira Interior, 6200-506 Covilhã, Portugal.
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16
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Zhou S. Effects of discreteness of surface charges on the effective electrostatic interactions. J Chem Phys 2014; 140:234704. [PMID: 24952557 DOI: 10.1063/1.4881601] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Shiqi Zhou
- School of Physics and Electronics, Central South University, Changsha, Hunan 410083, China
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17
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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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18
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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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19
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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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20
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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