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Vahid H, Scacchi A, Sammalkorpi M, Ala-Nissila T. Adsorption of polyelectrolytes in the presence of varying dielectric discontinuity between solution and substrate. J Chem Phys 2024; 161:134907. [PMID: 39360687 DOI: 10.1063/5.0223124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
We examine the interactions between polyelectrolytes (PEs) and uncharged substrates under conditions corresponding to a dielectric discontinuity between the aqueous solution and the substrate. To this end, we vary the relevant system characteristics, in particular the substrate dielectric constant ɛs under different salt conditions. We employ coarse-grained molecular dynamics simulations with rodlike PEs in salt solutions with explicit ions and implicit water solvent with dielectric constant ɛw = 80. As expected, at low salt concentrations, PEs are repelled from the substrates with ɛs < ɛw but are attracted to substrates with a high dielectric constant due to image charges. This attraction considerably weakens for high salt and multivalent counterions due to enhanced screening. Furthermore, for monovalent salt, screening enhances adsorption for weakly charged PEs, but weakens it for strongly charged ones. Meanwhile, multivalent counterions have little effect on weakly charged PEs, but prevent adsorption of highly charged PEs, even at low salt concentrations. We also find that correlation-induced charge inversion of a PE is enhanced close to the low dielectric constant substrates, but suppressed when the dielectric constant is high. To explore the possibility of a PE monolayer formation, we examine the interaction of a pair of like-charged PEs aligned parallel to a high dielectric constant substrate with ɛs = 8000. Our main conclusion is that monolayer formation is possible only for weakly charged PEs at high salt concentrations of both monovalent and multivalent counterions. Finally, we also consider the energetics of a PE approaching the substrate perpendicular to it, in analogy to polymer translocation. Our results highlight the complex interplay between electrostatic and steric interactions and contribute to a deeper understanding of PE-substrate interactions and adsorption at substrate interfaces with varying dielectric discontinuities from solution, ubiquitous in biointerfaces, PE coating applications, and designing adsorption setups.
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Affiliation(s)
- Hossein Vahid
- Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Mechanical and Materials Engineering, University of Turku, Vesilinnantie 5, FI-20014 Turku, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 15600, FI-00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough Leicestershire LE11 3TU, United Kingdom
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2
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Dai Y, Zhou Z, Yu W, Ma Y, Kim K, Rivera N, Mohammed J, Lantelme E, Hsu-Kim H, Chilkoti A, You L. Biomolecular condensates regulate cellular electrochemical equilibria. Cell 2024:S0092-8674(24)00909-7. [PMID: 39260373 DOI: 10.1016/j.cell.2024.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/22/2024] [Accepted: 08/09/2024] [Indexed: 09/13/2024]
Abstract
Control of the electrochemical environment in living cells is typically attributed to ion channels. Here, we show that the formation of biomolecular condensates can modulate the electrochemical environment in bacterial cells, which affects cellular processes globally. Condensate formation generates an electric potential gradient, which directly affects the electrochemical properties of a cell, including cytoplasmic pH and membrane potential. Condensate formation also amplifies cell-cell variability of their electrochemical properties due to passive environmental effect. The modulation of the electrochemical equilibria further controls cell-environment interactions, thus directly influencing bacterial survival under antibiotic stress. The condensate-mediated shift in intracellular electrochemical equilibria drives a change of the global gene expression profile. Our work reveals the biochemical functions of condensates, which extend beyond the functions of biomolecules driving and participating in condensate formation, and uncovers a role of condensates in regulating global cellular physiology.
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Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Zhengqing Zhou
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Wen Yu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Yuefeng Ma
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Nelson Rivera
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Javid Mohammed
- Department of Immunology, Duke University, Durham, NC 27705, USA
| | - Erica Lantelme
- Department of Pathology and Immunology, Washington University in St. Louis, Saint Louis, MO 63110, USA
| | - Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Immunology, Duke University, Durham, NC 27705, USA.
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Immunology, Duke University, Durham, NC 27705, USA; Center for Quantitative Biodesign, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
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3
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Zhang H, Liu D, Zhang J, Adams E, Gong J, Li W, Wang B, Liu X, Yang R, Wei F, Allen HC. GMP affected assembly behaviors of phosphatidylethanolamine monolayers elucidated by multi-resolved SFG-VS and BAM. Colloids Surf B Biointerfaces 2024; 241:113995. [PMID: 38870647 DOI: 10.1016/j.colsurfb.2024.113995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/18/2024] [Accepted: 05/26/2024] [Indexed: 06/15/2024]
Abstract
The interaction between nucleotide molecules and lipid molecules plays important roles in cell activities, but the molecular mechanism is very elusive. In the present study, a small but noticeable interaction between the negatively charged phosphatidylethanolamine (PE) and Guanosine monophosphate (GMP) molecules was observed from the PE monolayer at the air/water interface. As shown by the sum frequency generation (SFG) spectra and Pi-A isotherm of the PE monolayer, the interaction between the PE and GMP molecules imposes very small changes to the PE molecules. However, the Brewster angle microscopy (BAM) technique revealed that the assembly conformations of PE molecules are significantly changed by the adsorption of GMP molecules. By comparing the SFG spectra of PE monolayers after the adsorption of GMP, guanosine and guanine, it is also shown that the hydrogen bonding effect plays an important role in the nucleotide-PE interactions. These results provide fundamental insight into the structure changes during the nucleotide-lipid interaction, which may shed light on the molecular mechanism of viral infection, DNA drug delivery, and cell membrane curvature control in the brain or neurons.
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Affiliation(s)
- Hongjuan Zhang
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Dongqi Liu
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Jiawei Zhang
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Ellen Adams
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | - Jingjing Gong
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Wenhui Li
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Bing Wang
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Xueqing Liu
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Renqiang Yang
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China
| | - Feng Wei
- School of Optoelectronic Materials and Technology, & Key Laboratory of Optoelectronic Chemical Materials and Devices, Ministry of Education, Jianghan University, Wuhan 430056, China.
| | - Heather C Allen
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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4
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He W, Kirmizialtin S. Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations. Biomacromolecules 2024; 25:4819-4830. [PMID: 39011747 PMCID: PMC11323003 DOI: 10.1021/acs.biomac.4c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024]
Abstract
The condensation of nucleic acids by lipids is a widespread phenomenon in biology with crucial implications for drug delivery. However, the mechanisms of DNA assembly in lipid bilayers remain insufficiently understood due to challenges in measuring and assessing each component's contribution in the lipid-DNA-cation system. This study uses all-atom molecular dynamics simulations to investigate DNA condensation in cationic lipid bilayers. Our exhaustive exploration of the thermodynamic factors reveals unique roles for phospholipid head groups and cations. We observed that bridging cations between lipid and DNA drastically reduce charges, while mobile magnesium cations "ping-ponging" between double strands create charge fluctuations. While the first factor stabilizes the DNA-lipid complex, the latter creates attractive forces to induce the spontaneous condensation of DNAs. This novel mechanism not only sheds light on the current data regarding cationic lipid-induced DNA condensation but also provides potential design strategies for creating efficient gene delivery vectors for drug delivery.
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Affiliation(s)
- Weiwei He
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Serdal Kirmizialtin
- Chemistry
Program, Science Division, New York University
Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department
of Chemistry, New York University, New York, New York 10003, United States
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5
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Samardak K, Bâcle J, Moriel-Carretero M. Behind the stoNE wall: A fervent activity for nuclear lipids. Biochimie 2024:S0300-9084(24)00179-2. [PMID: 39111564 DOI: 10.1016/j.biochi.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/27/2024]
Abstract
The four main types of biomolecules are nucleic acids, proteins, carbohydrates and lipids. The knowledge about their respective interactions is as important as the individual understanding of each of them. However, while, for example, the interaction of proteins with the other three groups is extensively studied, that of nucleic acids and lipids is, in comparison, very poorly explored. An iconic paradigm of physical (and likely functional) proximity between DNA and lipids is the case of the genomic DNA in eukaryotes: enclosed within the nucleus by two concentric lipid bilayers, the wealth of implications of this interaction, for example in genome stability, remains underassessed. Nuclear lipid-related phenotypes have been observed for 50 years, yet in most cases kept as mere anecdotical descriptions. In this review, we will bring together the evidence connecting lipids with both the nuclear envelope and the nucleoplasm, and will make critical analyses of these descriptions. Our exploration establishes a scenario in which lipids irrefutably play a role in nuclear homeostasis.
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Affiliation(s)
- Kseniya Samardak
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - Janélie Bâcle
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM) UMR5237, Université de Montpellier, Centre National de La Recherche Scientifique, 34293 Montpellier Cedex 5, France.
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6
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Skalny M, Rokowska A, Szuwarzynski M, Gajewska M, Dziewit L, Bajda T. Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates. CHEMOSPHERE 2024; 362:142602. [PMID: 38871190 DOI: 10.1016/j.chemosphere.2024.142602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/15/2024]
Abstract
In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7-161.6 m2/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: <11 Kb, <6 Kb, and <3 Kb) and assessed the impact of Ca2+ and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca2+, and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca2+ led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.
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Affiliation(s)
- Mateusz Skalny
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland.
| | - Anna Rokowska
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Michal Szuwarzynski
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Marta Gajewska
- Academic Centre for Materials and Nanotechnology, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Bajda
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Krakow, Mickiewicza 30, 30-059, Krakow, Poland
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7
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Sun C, Li M, Wang F. Programming and monitoring surface-confined DNA computing. Bioorg Chem 2024; 143:107080. [PMID: 38183684 DOI: 10.1016/j.bioorg.2023.107080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
DNA-based molecular computing has evolved to encompass a diverse range of functions, demonstrating substantial promise for both highly parallel computing and various biomedical applications. Recent advances in DNA computing systems based on surface reactions have demonstrated improved levels of specificity and computational speed compared to their solution-based counterparts that depend on three-dimensional molecular collisions. Herein, computational biomolecular interactions confined by various surfaces such as DNA origamis, nanoparticles, lipid membranes and chips are systematically reviewed, along with their manipulation methodologies. Monitoring techniques and applications for these surface-based computing systems are also described. The advantages and challenges of surface-confined DNA computing are discussed.
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Affiliation(s)
- Chenyun Sun
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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8
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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9
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Saikia BJ, Bhardwaj J, Paul S, Sharma S, Neog A, Paul SR, Binukumar BK. Understanding the Roles and Regulation of Mitochondrial microRNAs (MitomiRs) in Neurodegenerative Diseases: Current Status and Advances. Mech Ageing Dev 2023:111838. [PMID: 37329989 DOI: 10.1016/j.mad.2023.111838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
MicroRNAs (miRNA) are a class of small non-coding RNA, roughly 21 - 22 nucleotides in length, which are master gene regulators. These miRNAs bind to the mRNA's 3' - untranslated region and regulate post-transcriptional gene regulation, thereby influencing various physiological and cellular processes. Another class of miRNAs known as mitochondrial miRNA (MitomiRs) has been found to either originate from the mitochondrial genome or be translocated directly into the mitochondria. Although the role of nuclear DNA encoded miRNA in the progression of various neurological diseases such as Parkinson's disease, Alzheimer's disease, Huntington's disease, etc. is well known, accumulating evidence suggests the possible role of deregulated mitomiRs in the progression of various neurodegenerative diseases with unknown mechanism. We have attempted to outline the current state of mitomiRs role in controlling mitochondrial gene expression and function through this review, paying particular attention to their contribution to neurological processes, their etiology, and their potential therapeutic use.
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Affiliation(s)
- Bhaskar Jyoti Saikia
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Juhi Bhardwaj
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Sangita Paul
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Srishti Sharma
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Anindita Neog
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007
| | - Swaraj Ranjan Paul
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007
| | - B K Binukumar
- CSIR Institute of Genomics and Integrative Biology, Mall Road, New Delhi - 110007; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
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10
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Flores-Sánchez R, Bigorra-Mir M, Gámez F, Lopes-Costa T, Argudo P, Martín-Romero M, Camacho L, Pedrosa J. Interaction between acetylsalicylic acid and a cationic amphiphile model: An experimental approach using surface techniques. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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11
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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12
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Xavier P, Bhat SA, Yelamaggad CV, Viswanath P. Phase behaviour and adsorption of deoxyribonucleic acid onto an azobenzene liquid crystalline ligand at the interfaces. Biophys Chem 2023; 296:106980. [PMID: 36889134 DOI: 10.1016/j.bpc.2023.106980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
Azobenzene liquid crystalline (ALC) ligand contains a cholesteryl group linked to an azobenzene moiety through a carbonyl dioxy spacer (C7) and terminated with an amine group as a polar head. The phase behaviour of the C7 ALC ligand at the air-water (A-W) interface is investigated employing surface manometry. The surface pressure-area per molecule isotherm shows that C7 ALC ligand exhibit two different phases following the phase sequence viz., liquid expanded (LE1 and LE2) and then collapse to three-dimensional crystallites. Further, our investigations under different pH conditions and in the presence of DNA reveal the following. Compared to the bulk, the acid dissociation constant (pKa) of an individual amine reduces to 5 at the interfaces. For pH (3.5) < pKa, the protonation of amine groups of C7 ALC ligand facilitates the condensation of the film and enhances the stability. For pH values > pKa, the phase behaviour of the ligand remains the same due to the partial dissociation of the amine groups. The presence of DNA in the sub-phase result in the expansion of isotherm to the higher area per molecule and the compressional modulus extracted reveals the phase sequence; liquid expanded, liquid condensed, followed by a collapse. Further, the kinetics of adsorption of DNA to the amine groups of the ligand is investigated, suggesting the interactions are influenced by surface pressure corresponding to different phases and pH of the sub-phase. Brewster angle microscope studies are carried out at different surface densities of the ligand as well as in the presence of DNA also supports this inference. Atomic force microscope is employed to acquire the surface topography and height profile of C7 ALC ligand (1 layer) after transferring on onto a silicon substrate using Langmuir Blodgett deposition. The difference in the surface topography and thickness of the film indicates the adsorption of DNA onto the amine groups of the ligand. The characteristic UV-visible absorption bands of the ligand films (10 layers) at the air-solid interface are tracked and the hypsochromic shift of these bands is also attributed to these DNA interactions.
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Affiliation(s)
- Pinchu Xavier
- Centre for Nano and Soft Matter Sciences, Bengaluru 562 162, India; Manipal Academy of Higher Education, Manipal 576 104, India
| | - Sachin A Bhat
- Centre for Nano and Soft Matter Sciences, Bengaluru 562 162, India
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13
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Elbahnasawy MA, Nasr ML. DNA-nanostructure-templated assembly of planar and curved lipid-bilayer membranes. Front Chem 2023; 10:1047874. [PMID: 36844038 PMCID: PMC9944057 DOI: 10.3389/fchem.2022.1047874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 02/10/2023] Open
Abstract
Lipid-bilayer nanodiscs and liposomes have been developed to stabilize membrane proteins in order to study their structures and functions. Nanodiscs are detergent-free, water-soluble, and size-controlled planar phospholipid-bilayer platforms. On the other hand, liposomes are curved phospholipid-bilayer spheres with an aqueous core used as drug delivery systems and model membrane platforms for studying cellular activities. A long-standing challenge is the generation of a homogenous and monodispersed lipid-bilayer system with a very wide range of dimensions and curvatures (elongation, bending, and twisting). A DNA-origami template provides a way to control the shapes, sizes, and arrangements of lipid bilayers via enforcing the assembly of lipid bilayers within the cavities created by DNA nanostructures. Here, we provide a concise overview and discuss how to design planar and curved lipid-bilayer membranes by using DNA-origami nanostructures as templates. Finally, we will discuss the potential applications of DNA-origami nanostructures in the structural and functional studies of large membrane proteins and their complexes.
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Affiliation(s)
- Mostafa A. Elbahnasawy
- Immunology Laboratory, Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mahmoud L. Nasr
- Renal Division and Engineering in Medicine Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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14
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Investigation of the ionic conditions in SiRNA-mediated delivery through its carriers in the cell membrane: a molecular dynamic simulation. Sci Rep 2022; 12:17520. [PMID: 36266467 PMCID: PMC9582388 DOI: 10.1038/s41598-022-22509-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/17/2022] [Indexed: 01/12/2023] Open
Abstract
SiRNA is a new generation of drug molecules and a new approach for treating a variety of diseases such as cancer and viral infections. SiRNA delivery to cells and translocation into cytoplasm are the main challenges in the clinical application of siRNA. Lipid carriers are one of the most successful carriers for siRNA delivery. In this study, we investigated the interaction of siRNA with a zwitterionic bilayer and how ion concentration and lipid conjugation can affect it. The divalent cation such as Mg2+ ions could promote the siRNA adsorption on the bilayer surface. The cation ions can bind to the head groups of lipids and the grooves of siRNA molecules and form bridges between the siRNA and bilayer surface. Our findings demonstrated the bridges formed by divalent ions could facilitate the attachment of siRNA to the membrane surface. We showed that the divalent cations can regulate the bridging-driven membrane attachment and it seems the result of this modulation can be used for designing biomimetic devices. In the following, we examined the effect of cations on the interaction between siRNA modified by cholesterol and the membrane surface. Our MD simulations showed that in the presence of Mg2+, the electrostatic and vdW energy between the membrane and siRNA were higher compared to those in the presence of NA+. We showed that the electrostatic interaction between membrane and siRNA cannot be facilitated only by cholesterol conjugated. Indeed, cations are essential to create coulomb repulsion and enable membrane attachment. This study provides important insight into liposome carriers for siRNA delivery and could help us in the development of siRNA-based therapeutics. Due to the coronavirus pandemic outbreak, these results may shed light on the new approach for treating these diseases and their molecular details.
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15
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Hao P, Niu L, Luo Y, Wu N, Zhao Y. Surface Engineering of Lipid Vesicles Based on DNA Nanotechnology. Chempluschem 2022; 87:e202200074. [PMID: 35604011 DOI: 10.1002/cplu.202200074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Pengyan Hao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Liqiong Niu
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Yuanyuan Luo
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Na Wu
- Xi'an Jiaotong University School of Life Science and Technology No.28, West Xianning Road 710049 Xi'an CHINA
| | - Yongxi Zhao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
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16
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Elucidation of physico-chemical principles of high-density lipoprotein-small RNA binding interactions. J Biol Chem 2022; 298:101952. [PMID: 35447119 PMCID: PMC9133651 DOI: 10.1016/j.jbc.2022.101952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 11/03/2022] Open
Abstract
Extracellular small RNAs (sRNAs) are abundant in many biofluids, but little is known about their mechanisms of transport and stability in RNase-rich environments. We previously reported that high-density lipoproteins (HDLs) in mice were enriched with multiple classes of sRNAs derived from the endogenous transcriptome, but also from exogenous organisms. Here, we show that human HDL transports tRNA-derived sRNAs (tDRs) from host and nonhost species, the profiles of which were found to be altered in human atherosclerosis. We hypothesized that HDL binds to tDRs through apolipoprotein A-I (apoA-I) and that these interactions are conferred by RNA-specific features. We tested this using microscale thermophoresis and electrophoretic mobility shift assays and found that HDL binds to tDRs and other single-stranded sRNAs with strong affinity but did not bind to double-stranded RNA or DNA. Furthermore, we show that natural and synthetic RNA modifications influenced tDR binding to HDL. We demonstrate that reconstituted HDL bound to tDRs only in the presence of apoA-I, and purified apoA-I alone were able to bind sRNA. Conversely, phosphatidylcholine vesicles did not bind tDRs. In summary, we conclude that HDL binds to single-stranded sRNAs likely through nonionic interactions with apoA-I. These results highlight binding properties that likely enable extracellular RNA communication and provide a foundation for future studies to manipulate HDL-sRNA interactions for therapeutic approaches to prevent or treat disease.
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17
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DNA penetration into a monolayer of amphiphilic polyelectrolyte. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Czerniak T, Saenz JP. Lipid membranes modulate the activity of RNA through sequence-dependent interactions. Proc Natl Acad Sci U S A 2022; 119:e2119235119. [PMID: 35042820 PMCID: PMC8794826 DOI: 10.1073/pnas.2119235119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022] Open
Abstract
RNA is a ubiquitous biomolecule that can serve as both catalyst and information carrier. Understanding how RNA bioactivity is controlled is crucial for elucidating its physiological roles and potential applications in synthetic biology. Here, we show that lipid membranes can act as RNA organization platforms, introducing a mechanism for riboregulation. The activity of R3C ribozyme can be modified by the presence of lipid membranes, with direct RNA-lipid interactions dependent on RNA nucleotide content, base pairing, and length. In particular, the presence of guanine in short RNAs is crucial for RNA-lipid interactions, and G-quadruplex formation further promotes lipid binding. Lastly, by artificially modifying the R3C substrate sequence to enhance membrane binding, we generated a lipid-sensitive ribozyme reaction with riboswitch-like behavior. These findings introduce RNA-lipid interactions as a tool for developing synthetic riboswitches and RNA-based lipid biosensors and bear significant implications for RNA world scenarios for the origin of life.
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Affiliation(s)
- Tomasz Czerniak
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - James P Saenz
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
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19
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Singh PC, Ahmed M, Nihonyanagi S, Yamaguchi S, Tahara T. DNA-Induced Reorganization of Water at Model Membrane Interfaces Investigated by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy. J Phys Chem B 2022; 126:840-846. [DOI: 10.1021/acs.jpcb.1c08581] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Prashant Chandra Singh
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Mohammed Ahmed
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Satoshi Nihonyanagi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shoichi Yamaguchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Applied Chemistry, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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20
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Chirkov NS, Campbell RA, Michailov AV, Vlasov PS, Noskov BA. DNA Interaction with a Polyelectrolyte Monolayer at Solution-Air Interface. Polymers (Basel) 2021; 13:2820. [PMID: 34451359 PMCID: PMC8400178 DOI: 10.3390/polym13162820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 01/17/2023] Open
Abstract
The formation of ordered 2D nanostructures of double stranded DNA molecules at various interfaces attracts more and more focus in medical and engineering research, but the underlying intermolecular interactions still require elucidation. Recently, it has been revealed that mixtures of DNA with a series of hydrophobic cationic polyelectrolytes including poly(N,N-diallyl-N-hexyl-N-methylammonium) chloride (PDAHMAC) form a network of ribbonlike or threadlike aggregates at the solution-air interface. In the present work, we adopt a novel approach to confine the same polyelectrolyte at the solution-air interface by spreading it on a subphase with elevated ionic strength. A suite of techniques-rheology, microscopy, ellipsometry, and spectroscopy-are applied to gain insight into main steps of the adsorption layer formation, which results in non-monotonic kinetic dependencies of various surface properties. A long induction period of the kinetic dependencies after DNA is exposed to the surface film results only if the initial surface pressure corresponds to a quasiplateau region of the compression isotherm of a PDAHMAC monolayer. Despite the different aggregation mechanisms, the micromorphology of the mixed PDAHMAC/DNA does not depend noticeably on the initial surface pressure. The results provide new perspective on nanostructure formation involving nucleic acids building blocks.
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Affiliation(s)
- Nikolay S. Chirkov
- Institute of Chemistry, Saint Petersburg State University, 198504 St. Petersburg, Russia; (N.S.C.); (A.V.M.); (P.S.V.)
| | - Richard A. Campbell
- Division of Pharmacy and Optometry, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK;
| | - Alexander V. Michailov
- Institute of Chemistry, Saint Petersburg State University, 198504 St. Petersburg, Russia; (N.S.C.); (A.V.M.); (P.S.V.)
| | - Petr S. Vlasov
- Institute of Chemistry, Saint Petersburg State University, 198504 St. Petersburg, Russia; (N.S.C.); (A.V.M.); (P.S.V.)
| | - Boris A. Noskov
- Institute of Chemistry, Saint Petersburg State University, 198504 St. Petersburg, Russia; (N.S.C.); (A.V.M.); (P.S.V.)
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21
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Jones S, Joshi H, Terry SJ, Burns JR, Aksimentiev A, Eggert US, Howorka S. Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes. J Am Chem Soc 2021; 143:8305-8313. [PMID: 34015219 PMCID: PMC8193631 DOI: 10.1021/jacs.0c13235] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 12/18/2022]
Abstract
Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA-membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA-bilayer interactions will guide the rational design of membrane-targeting nanostructures.
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Affiliation(s)
- Sioned
F. Jones
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
| | - Himanshu Joshi
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stephen J. Terry
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
- UCL
Ear Institute, London WC1X 8EE, United Kingdom
| | - Jonathan R. Burns
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Aleksei Aksimentiev
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Ulrike S. Eggert
- Randall
Centre for Cell and Molecular Biophysics, School of Basic and Medical
Biosciences, and Department of Chemistry, King’s College London, London SE1 1UL, United Kingdom
| | - Stefan Howorka
- Department
of Chemistry, Institute of Structural and Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
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22
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Morzy D, Rubio-Sánchez R, Joshi H, Aksimentiev A, Di Michele L, Keyser UF. Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures. J Am Chem Soc 2021; 143:7358-7367. [PMID: 33961742 PMCID: PMC8154537 DOI: 10.1021/jacs.1c00166] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The interplay between nucleic acids
and lipids underpins several
key processes in molecular biology, synthetic biotechnology, vaccine
technology, and nanomedicine. These interactions are often electrostatic
in nature, and much of their rich phenomenology remains unexplored
in view of the chemical diversity of lipids, the heterogeneity of
their phases, and the broad range of relevant solvent conditions.
Here we unravel the electrostatic interactions between zwitterionic
lipid membranes and DNA nanostructures in the presence of physiologically
relevant cations, with the purpose of identifying new routes to program
DNA–lipid complexation and membrane-active nanodevices. We
demonstrate that this interplay is influenced by both the phase of
the lipid membranes and the valency of the ions and observe divalent
cation bridging between nucleic acids and gel-phase bilayers. Furthermore,
even in the presence of hydrophobic modifications on the DNA, we find
that cations are still required to enable DNA adhesion to liquid-phase
membranes. We show that the latter mechanism can be exploited to control
the degree of attachment of cholesterol-modified DNA nanostructures
by modifying their overall hydrophobicity and charge. Besides their
biological relevance, the interaction mechanisms we explored hold
great practical potential in the design of biomimetic nanodevices,
as we show by constructing an ion-regulated DNA-based synthetic enzyme.
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Affiliation(s)
- Diana Morzy
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Roger Rubio-Sánchez
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Lorenzo Di Michele
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom.,Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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23
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Piao J, Yuan W, Dong Y. Recent Progress of DNA Nanostructures on Amphiphilic Membranes. Macromol Biosci 2021; 21:e2000440. [PMID: 33759366 DOI: 10.1002/mabi.202000440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/24/2021] [Indexed: 11/11/2022]
Abstract
Employing DNA nanostructures mimicking membrane proteins on artificial amphiphilic membranes have been widely developed to understand the structures and functions of the natural membrane systems. In this review, the recent developments in artificial systems constructed by amphiphilic membranes and DNA nanostructures are summarized. First, the preparations and properties of the amphipathic bilayer models are introduced. Second, the interactions are discussed between the membrane and the DNA nanostructures, as well as their coassembly behaviors. Next, the alternative systems related to membrane protein-mediated signal transmission, selective distribution, transmembrane channels, and membrane fusion are also introduced. Moreover, the constructions of membrane skeleton protein-mimicking DNA nanostructures are also highlighted.
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Affiliation(s)
- Jiafang Piao
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Wei Yuan
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
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24
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Waku T, Kasai A, Kobori A, Tanaka N. Investigation on the Interactions between Self-Assembled β-Sheet Peptide Nanofibers and Model Cell Membranes. Int J Mol Sci 2020; 21:ijms21249518. [PMID: 33327660 PMCID: PMC7765088 DOI: 10.3390/ijms21249518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/16/2022] Open
Abstract
Self-assembled peptide nanofibers (NFs) obtained from β-sheet peptides conjugated with drugs, including antigenic peptides, have recently attracted significant attention. However, extensive studies on the interactions of β-sheet peptide NFs with model cell membranes have not been reported. In this study, we investigated the interactions between three types of NFs, composed of PEG-peptide conjugates with different ethylene glycol (EG) lengths (6-, 12- and 24-mer), and dipalmitoylphosphatidylcholine (DPPC) Langmuir membranes. When increasing the EG chain length, those interactions significantly decreased considering measurements in the presence of the NFs of: (i) changes in surface pressure of the DPPC Langmuir monolayers and (ii) surface pressure-area (π-A) compression isotherms of DPPC. Because the observed trend was similar to the EG length dependency with regard to cellular association and cytotoxicity of the NFs that was reported previously, the interaction of NFs with phospholipid membranes represented a crucial factor to determine the cellular association and toxicity of the NFs. In contrast to NFs, no changes were observed with varying EG chain length on the interaction of the building block peptide with the DPPC membrane. The results obtained herein can provide a design guideline on the formulation of β-sheet peptide NFs, which may broaden its potential.
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25
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Shen Q, Grome MW, Yang Y, Lin C. Engineering Lipid Membranes with Programmable DNA Nanostructures. ADVANCED BIOSYSTEMS 2020; 4:1900215. [PMID: 31934608 PMCID: PMC6957268 DOI: 10.1002/adbi.201900215] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Indexed: 12/18/2022]
Abstract
Lipid and DNA are abundant biomolecules with critical functions in cells. The water-insoluble, amphipathic lipid molecules are best known for their roles in energy storage (e.g. as triglyceride), signaling (e.g. as sphingolipid), and compartmentalization (e.g. by forming membrane-enclosed bodies). The soluble, highly negatively charged DNA, which stores cells' genetic information, has proven to be an excellent material for constructing programmable nanostructures in vitro thanks to its self-assembling capabilities. These two seemingly distant molecules make contact within cell nuclei, often via lipidated proteins, with proposed functions of modulating chromatin structures. Carefully formulated lipid/DNA complexes are promising reagents for gene therapy. The past few years saw an emerging research field of interfacing DNA nanostructures with lipid membranes, with an overarching goal of generating DNA/lipid hybrid materials that possess novel and controllable structure, dynamics, and function. An arsenal of DNA-based tools has been created to coat, mold, deform, and penetrate lipid bilayers, affording us the ability to manipulate membranes with nanoscopic precision. These membrane engineering methods not only enable quantitative biophysical studies, but also open new opportunities in synthetic biology (e.g. artificial cells) and therapeutics (e.g. drug delivery).
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Affiliation(s)
- Qi Shen
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Michael W Grome
- Department of Cell Biology and Nanobiology Institute, Yale University
| | - Yang Yang
- Department of Cell Biology and Nanobiology Institute, Yale University
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chenxiang Lin
- Department of Cell Biology and Nanobiology Institute, Yale University
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26
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Pannwitt S, Slama K, Depoix F, Helm M, Schneider D. Against Expectations: Unassisted RNA Adsorption onto Negatively Charged Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14704-14711. [PMID: 31626734 DOI: 10.1021/acs.langmuir.9b02830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The composition and physicochemical properties of biological membranes can be altered by diverse membrane integral and peripheral proteins as well as by small molecules, natural and synthetic. Diverse oligonucleotides have been shown to electrostatically interact with cationic and bivalent ion loaded zwitterionic liposomes, leading to the formation of oligonucleotide-liposome aggregates. However, interaction of RNAs with other membrane surfaces remains ill understood. We used the nonnatural RNA10 to investigate RNA binding to anionic and net-uncharged membrane surfaces. RNA10 had initially been selected in a screen for nonnatural RNA motives that bind to phosphatidylcholine liposomes in the presence of Mg2+. Here we show that interaction of defined RNA molecules with membrane surfaces crucially depends on electrostatic surface properties. Furthermore, RNA10 electrostatically binds to anionic lipid bilayers in the absence of Mg2+ or other bivalent cations, and this interaction leads to measurably changed physicochemical properties of the bilayer and the oligonucleotide. Thus, the structure of polyanionic RNA can be modulated via contact with negatively charged membrane surfaces and vice versa.
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Affiliation(s)
- Stefanie Pannwitt
- Institute of Pharmacy and Biochemistry , Johannes Gutenberg University , Johann-Joachim-Becherweg 30 , 55128 Mainz , Germany
| | - Kaouthar Slama
- Institute of Pharmacy and Biochemistry , Johannes Gutenberg University , Staudinger Weg 5 , 55128 Mainz , Germany
| | - Frank Depoix
- Institute of Molecular Physiology , Johannes Gutenberg University , Johann-Joachim-Becherweg 9-11 , 55128 Mainz , Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry , Johannes Gutenberg University , Staudinger Weg 5 , 55128 Mainz , Germany
| | - Dirk Schneider
- Institute of Pharmacy and Biochemistry , Johannes Gutenberg University , Johann-Joachim-Becherweg 30 , 55128 Mainz , Germany
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27
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Brezesinski G, Schneck E. Investigating Ions at Amphiphilic Monolayers with X-ray Fluorescence. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8531-8542. [PMID: 30835476 PMCID: PMC6727669 DOI: 10.1021/acs.langmuir.9b00191] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/04/2019] [Indexed: 06/09/2023]
Abstract
Amphiphilic monolayers formed at the soft air/liquid interface are easy-to-handle and versatile model systems for material and life sciences. Helmuth Möhwald was one of the pioneers in this field. Over the last few decades, total-reflection X-ray fluorescence (TRXF) has become an important analytical tool for the investigation of monolayer interactions with ions. Here, the theoretical background of TRXF is described, and practical aspects are discussed. The experimentally determined fluorescence intensity from the adsorbed ions can be interpreted quantitatively either by a calibration procedure utilizing monolayers with known charge density or by calibration with respect to the bare aqueous surface. Both calibration approaches yield quantitatively consistent results within <10% accuracy. Some examples demonstrating the power of TRXF for the study of ion adsorption to charged and noncharged monolayers as well as for the characterization of the physicochemical properties of novel cationic lipids used for improved gene delivery are given.
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Affiliation(s)
- Gerald Brezesinski
- Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Emanuel Schneck
- Max Planck Institute of
Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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28
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Luque-Caballero G, Maldonado-Valderrama J, Quesada-Pérez M, Martín-Molina A. Interaction of DNA with likely-charged lipid monolayers: An experimental study. Colloids Surf B Biointerfaces 2019; 178:170-176. [PMID: 30856586 DOI: 10.1016/j.colsurfb.2019.02.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/31/2022]
Abstract
Anionic lipids are increasingly being used in lipoplexes for synthetic gene vectors as an alternative to cationic lipids. This is primarily due to their lower toxicity, which makes them biocompatible and adaptable to be tissue specific. However, anionic lipoplexes require the presence of multivalent cations to promote the electrostatic attraction between DNA and anionic lipid mono- and bilayers. In this work we provide for the first time experimental results of the adsorption of linear DNA onto anionic/zwitterionic lipid monolayers without any addition of cations. This is demonstrated experimentally by means of Langmuir monolayers of DOPE/DOPG (1:1) lipids spread on a water subphase that contains calf thymus DNA. The adsorption of DNA onto anionic/zwitterionic lipid monolayers is discussed in terms of the surface pressure-molecular area isotherms recorded in the absence and in the presence of different electrolytes. Measurements of the surface potential provide additional evidence of the different interaction of DNA anionic/zwitterionic lipid monolayers depending on the presence and nature of electrolyte. These experimental results are further analysed in terms of the overall dipole moment normal to the monolayers providing new insight into the behaviour of anionic lipoplexes and the role of zwitterionic lipids.
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Affiliation(s)
- German Luque-Caballero
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, 18071, Granada, Spain
| | - Julia Maldonado-Valderrama
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, 18071, Granada, Spain; Unidad de excelencia "Modelling Nature" (MNat), Universidad de Granada, Spain
| | - Manuel Quesada-Pérez
- Departamento de Física, Escuela Politécnica Superior de Linares, Universidad de Jaén, 23700, Linares, Jaén, Spain
| | - Alberto Martín-Molina
- Departamento de Física Aplicada, Universidad de Granada, Campus de Fuentenueva sn, 18071, Granada, Spain; Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, Spain.
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29
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Kempter S, Khmelinskaia A, Strauss MT, Schwille P, Jungmann R, Liedl T, Bae W. Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami. ACS NANO 2019; 13:996-1002. [PMID: 30588792 DOI: 10.1021/acsnano.8b04631] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA nanostructures offer the possibility to mimic functional biological membrane components due to their nanometer-precise shape configurability and versatile biochemical functionality. Here we show that the diffusional behavior of DNA nanostructures and their assembly into higher order membrane-bound lattices can be controlled in a stop-and-go manner and that the process can be monitored with super-resolution imaging. The DNA structures are transiently immobilized on glass-supported lipid bilayers by changing the mono- and divalent cation concentrations of the surrounding buffer. Using DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy, we confirm the fixation of DNA origami structures with different shapes. On mica-supported lipid bilayers, in contrast, we observe residual movement. By increasing the concentration of NaCl and depleting MgCl2, a large fraction of DNA structures restarts to diffuse freely on both substrates. After addition of a set of oligonucleotides that enables three Y-shaped monomers to assemble into a three-legged shape (triskelion), the triskelions can be stopped and super-resolved. Exchanging buffer and adding another set of oligonucleotides triggers the triskelions to diffuse and assemble into hexagonal 2D lattices. This stop-and-go imaging technique provides a way to control and observe the diffusional behavior of DNA nanostructures on lipid membranes that could also lead to control of membrane-associated cargos.
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Affiliation(s)
- Susanne Kempter
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
| | | | - Maximilian T Strauss
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
| | - Wooli Bae
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
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30
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Tassler S, Pawlowska D, Janich C, Dobner B, Wölk C, Brezesinski G. Lysine-based amino-functionalized lipids for gene transfection: the influence of the chain composition on 2D properties. Phys Chem Chem Phys 2018; 20:6936-6944. [PMID: 29464262 DOI: 10.1039/c8cp00047f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The influence of the chain composition on the physical-chemical properties will be discussed for five transfection lipids containing the same lysine-based head group. For this purpose, the chain composition will be gradually varied from saturated tetradecyl (C14:0) and hexadecyl (C16:0) chains to longer but unsaturated oleyl (C18:1) chains with double bonds in the cis configuration. In this work, we investigated the lipids as Langmuir monolayers at the air-water-interface in the absence and presence of calf thymus DNA applying different techniques such as infrared reflection absorption spectroscopy (IRRAS) and grazing incidence X-ray diffraction (GIXD). The replacement of saturated tetradecyl (C14:0) and hexadecyl (C16:0) chains by unsaturated oleyl (C18:1) chains increases the fluidity of the lipid monolayer: TH10 < TT10 < OH10 < OT10 < OO10 resulting in a smaller packing density. TH10 forms the stiffest and OO10 the most fluid monolayer in this structure-property study. OO10 has a higher protonation degree compared to the saturated lipids TT10 and TH10 as well as to the hybrids OT10 and OH10 because of a better accessibility of the amine groups. Depending on the bulk pH, different scenarios of DNA coupling to the lipid monolayers have been proposed.
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Affiliation(s)
- Stephanie Tassler
- Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, Am Mühlenberg 1, 14476 Potsdam, Germany.
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31
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Wu N, Chen F, Zhao Y, Yu X, Wei J, Zhao Y. Functional and Biomimetic DNA Nanostructures on Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14721-14730. [PMID: 30044097 DOI: 10.1021/acs.langmuir.8b01818] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sophisticated and dynamic membrane-anchored DNA nanostructures were developed to mimic a variety of membrane proteins, which play crucial roles in cellular functions. DNA biomimetic constructions bound on membranes are capable of modulating the morphologies, physical properties, and functions of lipid membranes, via mobility on membranes and/or inherent architectural features. This inspired young field of DNA-lipid-based nanobiomimetic systems is on the foundation of DNA nanotechnology. In this review, we highlight key successes in the development of structural DNA nanotechnology and demonstrate some typical static and dynamic complex DNA nanostructures first. Then, we discuss the biophysical properties of lipid membranes. Primary approaches are shown to attach hydrophilic DNA to hydrophobic lipid membranes. With appropriate designs, membrane-floating DNA nanostructures assemble and disassemble on membranes, modulated by external stimuluses. The aggregation of DNA nanostructures could influence the physical properties of lipid membranes. We also summarize artificial nanochannels made of DNA, analogous to transmembrane proteins. Transformations of DNA nanopores might be achieved under certain conditions and realize the transport of small molecules across membranes. Next, we focus on membrane-shaping functions of membrane-anchored DNA nanostructures. Curvature of the membrane is closely related to the rich diversity of cellular functions. Mimicking membrane-sculpting proteins, such as BAR family domains and SNARE proteins etc., DNA biomimetic nanostructures induce the transformations of lipid membranes and modulate membrane adhesion and membrane fusion processes. Although recent studies in DNA nanostructure-lipid membrane biomimetic nanosystems have made great progress, this field is still facing many challenges. In the future, the designs of more elaborated DNA architectures will be explored. Sophisticated dynamic DNA nanostructures inspired by natural membrane machines will be driven by the synergistic effect of multiple interactions, including hydrophobic force, electrostatic force, and ligand-receptor interactions by chemical modifications on bases, to expand their applications in vivo from model membrane to cell membrane to karyotheca.
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Affiliation(s)
- Na Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Xu Yu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
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32
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Khmelinskaia A, Mücksch J, Petrov EP, Franquelim HG, Schwille P. Control of Membrane Binding and Diffusion of Cholesteryl-Modified DNA Origami Nanostructures by DNA Spacers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14921-14931. [PMID: 30253101 DOI: 10.1021/acs.langmuir.8b01850] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA origami nanotechnology is being increasingly used to mimic membrane-associated biophysical phenomena. Although a variety of DNA origami nanostructures has already been produced to target lipid membranes, the requirements for membrane binding have so far not been systematically assessed. Here, we used a set of elongated DNA origami structures with varying placement and number of cholesteryl-based membrane anchors to compare different strategies for their incorporation. Single and multiple cholesteryl anchors were attached to DNA nanostructures using single- and double-stranded DNA spacers of varying length. The produced DNA nanostructures were studied in terms of their membrane binding and diffusion. Our results show that the location and number of anchoring moieties play a crucial role for membrane binding of DNA nanostructures mainly if the cholesteryl anchors are in close proximity to the bulky DNA nanostructures. Moreover, the use of DNA spacers largely overcomes local steric hindrances and thus enhances membrane binding. Fluorescence correlation spectroscopy measurements demonstrate that the distinct physical properties of single- and double-stranded DNA spacers control the interaction of the amphipathic DNA nanostructures with lipid membranes. Thus, we provide a rational basis for the design of amphipathic DNA origami nanostructures to efficiently bind lipid membranes in various environments.
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Affiliation(s)
- Alena Khmelinskaia
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Eugene P Petrov
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
- Faculty of Physics , Ludwig Maximilian University of Munich , Geschwister-Scholl-Platz 1 , 80539 Munich , Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
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33
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Lopez A, Liu J. DNA Oligonucleotide-Functionalized Liposomes: Bioconjugate Chemistry, Biointerfaces, and Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15000-15013. [PMID: 29936848 DOI: 10.1021/acs.langmuir.8b01368] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Interfacing DNA with liposomes has produced a diverse range of programmable soft materials, devices, and drug delivery vehicles. By simply controlling liposomal composition, bilayer fluidity, lipid domain formation, and surface charge can be systematically varied. Recent development in DNA research has produced not only sophisticated nanostructures but also new functions including ligand binding and catalysis. For noncationic liposomes, a DNA is typically covalently linked to a hydrophobic or lipid moiety that can be inserted into lipid membranes. In this article, we discuss fundamental biointerfaces formed between DNA and noncationic liposomes. The methods to prepare such conjugates and the interactions at the membrane interfaces are also discussed. The effect of DNA lateral diffusion on fluid bilayer membranes and the effect of membrane on DNA assembly are emphasized. DNA hybridization can be programmed to promote fusion of lipid membranes. Representative applications of this conjugate for drug delivery, biosensor development, and directed assembly of materials are briefly described toward the end. Some future research directions are also proposed to further understand this biointerface.
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Affiliation(s)
- Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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34
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Antipina AY, Gurtovenko AA. Toward Understanding Liposome-Based siRNA Delivery Vectors: Atomic-Scale Insight into siRNA-Lipid Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8685-8693. [PMID: 29932659 DOI: 10.1021/acs.langmuir.8b01211] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Liposome carriers for delivering small interfering RNA (siRNA) into target cells are of tremendous importance because the siRNA-based therapy offers a completely new approach for treating a wide range of diseases, including cancer and viral infections. In this paper, we employ the state-of-the-art computer simulations to get an atomic-scale insight into the interactions of siRNA with zwitterionic (neutral) lipids. Our computational findings clearly demonstrate that siRNA does adsorb on the surface of a neutral lipid bilayer. The siRNA adsorption, being rather weak and unstable, is driven by attractive interactions of overhanging unpaired nucleotides with choline moieties of lipid molecules. It is the presence of the unpaired terminal nucleotides that underlies a drastic difference between siRNA and DNA; the latter is not able to bind to the zwitterionic lipid bilayer. We also show that adding divalent Ca ions leads to the formation of stable siRNA-lipid system complexes; these complexes are stabilized by Ca-mediated aggregates of siRNA and lipid molecules rather than by the overhanging siRNA nucleotides. Furthermore, the molecular mechanism of interactions between siRNA and the lipid bilayer in the presence of divalent cations seems to involve exchange of Ca ions between the outer mouth of the major groove of siRNA and the lipid/water interface. Overall, our findings contribute significantly to a deeper understanding of the structure and function of liposome carriers used for siRNA delivery and can be used as a theoretical basis for further development of siRNA-based therapeutics.
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Affiliation(s)
- Alexandra Yu Antipina
- Department of Photonics and Optical Information Technology , ITMO University , 49 Kronverksky Pr. , St. Petersburg 197101 , Russia
| | - Andrey A Gurtovenko
- Institute of Macromolecular Compounds , Russian Academy of Sciences , Bolshoi Prospect V.O. 31 , St. Petersburg 199004 , Russia
- Faculty of Physics , St. Petersburg State University , Ulyanovskaya Street 3, Petrodvorets , St. Petersburg 198504 , Russia
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35
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Bhowal AC, Kundu S. A comparative study on intrinsic fluorescence of BSA and lysozyme proteins in presence of different divalent ions from their solution and thin film conformations. LUMINESCENCE 2017; 33:267-276. [PMID: 29052335 DOI: 10.1002/bio.3409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/21/2017] [Accepted: 08/24/2017] [Indexed: 01/04/2023]
Abstract
Optical emission behaviours of lysozyme and bovine serum albumin, from bulk and thin film geometry, were studied in the presence of three different divalent ions (Mg2+ , Ca2+ or Ba2+ ) using different spectroscopic [steady-state fluorescence, UV-Vis and Fourier transform infra-red (FTIR)] techniques. Additionally, protein thin films on silicon surfaces were prepared and morphological studies were carried out using atomic force microscopy. Dynamic quenching was mainly identified for both proteins in the presence of Mg2+ , Ca2+ and Ba2+ ions. The molecular conformation of the proteins was modified in thin films compared with that in solution, consequently quenching efficiencies also varied. ATR-FTIR studies confirmed the conformational changes of proteins in the presence of all divalent ions. All metal ions used were divalent in nature and belonged to the same group of the periodic table but, depending on their individual characteristics such as electron affinity, ionic radius, etc., the magnitude of the protein and hydrated ion interaction varied and accordingly the quenching efficiency was modified. Quenching was maximum for Ca2+ ions, followed by the other two ions. Our study clearly illustrates the geometry-dependent physical and biological functions of proteins.
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Affiliation(s)
- Ashim Chandra Bhowal
- Soft Nano Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam, India
| | - Sarathi Kundu
- Soft Nano Laboratory, Physical Sciences Division, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam, India
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36
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Wölk C, Janich C, Bakowsky U, Langner A, Brezesinski G. Malonic acid based cationic lipids - The way to highly efficient DNA-carriers. Adv Colloid Interface Sci 2017; 248:20-34. [PMID: 28842122 DOI: 10.1016/j.cis.2017.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 01/21/2023]
Abstract
Cationic lipids play an important role as non-viral nucleic acid carriers in gene therapy since 3 decades. This review will introduce malonic acid derived cationic lipids as nucleic acid carriers which appeared in the literature dealing with lipofection 10years ago. The family of amino-functionalized branched fatty acid amides will be presented as well as different generations of malonic acid diamides. Both groups of cationic lipids yield lipid mixtures with highly efficient nucleic acid transfer activities in in-vitro cell culture models. The DNA transfer screening of lipid libraries with directed structural variations in the lipophilic as well as in the hydrophilic part of the amphiphiles yields structure/activity relationships. Furthermore, the detailed characterizations of selected lipid composites at the air/water interface and in bulk systems are summarized with regard to transfection determining physical-chemical properties. The findings are also discussed in comparison to results obtained with other families of cationic lipids.
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Affiliation(s)
- Christian Wölk
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Saale, Germany.
| | - Christopher Janich
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Saale, Germany
| | - Udo Bakowsky
- Department of Pharmaceutics and Biopharmaceutics, University Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Andreas Langner
- Martin Luther University Halle-Wittenberg, Institute of Pharmacy, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Saale, Germany
| | - Gerald Brezesinski
- Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, Am Mühlenberg 1, 14476 Potsdam, Germany.
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37
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Fabry-Wood A, Fetrow ME, Brown CW, Baker NA, Oropeza NF, Shreve AP, Montaño GA, Stefanovic D, Lakin MR, Graves SW. A Microsphere-Supported Lipid Bilayer Platform for DNA Reactions on a Fluid Surface. ACS APPLIED MATERIALS & INTERFACES 2017; 9:30185-30195. [PMID: 28809101 PMCID: PMC6119471 DOI: 10.1021/acsami.7b11046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report a versatile microsphere-supported lipid bilayer system that can serve as a general-purpose platform for implementing DNA nanotechnologies on a fluid surface. To demonstrate our platform, we implemented both toehold-mediated strand displacement (TMSD) and DNAzyme reactions, which are typically performed in solution and which are the cornerstone of DNA-based molecular logic and dynamic DNA nanotechnology, on the surface. We functionalized microspheres bearing supported lipid bilayers (μSLBs) with membrane-bound nucleic acid components. Using functionalized μSLBs, we developed TMSD and DNAzyme reactions by optimizing reaction conditions to reduce nonspecific interactions between DNA and phospholipids and to enhance bilayer stability. Additionally, the physical and optical properties of the bilayer were tuned via lipid composition and addition of fluorescently tagged lipids to create stable and multiplexable μSLBs that are easily read out by flow cytometry. Multiplexed TMSD reactions on μSLBs enabled the successful operation of a Dengue serotyping assay that correctly identified all 16 patterns of target sequences to demonstrate detection of DNA strands derived from the sequences of all four Dengue serotypes. The limit of detection for this assay was 3 nM. Furthermore, we demonstrated DNAzyme reactions on a fluid lipid surface, which benefit from free diffusion on the surface. This work provides the basis for expansion of both TMSD and DNAzyme based molecular reactions on supported lipid bilayers for use in molecular logic and DNA nanotechnology. As our system is multiplexable and results in fluid surfaces, it may be of use in compartmentalization and improved kinetics of molecular logic reactions and as a useful building block in a variety of DNA nanotechnology systems.
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Affiliation(s)
| | | | - Carl W. Brown
- Center for Biomedical Engineering, University of New Mexico
| | - Nicholas A. Baker
- Center for Biomedical Engineering, University of New Mexico
- Department of Chemical and Biological Engineering, University of New Mexico
| | | | - Andrew P. Shreve
- Center for Biomedical Engineering, University of New Mexico
- Department of Chemical and Biological Engineering, University of New Mexico
| | | | - Darko Stefanovic
- Center for Biomedical Engineering, University of New Mexico
- Department of Computer Science, University of New Mexico
| | - Matthew R. Lakin
- Center for Biomedical Engineering, University of New Mexico
- Department of Chemical and Biological Engineering, University of New Mexico
- Department of Computer Science, University of New Mexico
| | - Steven W. Graves
- Center for Biomedical Engineering, University of New Mexico
- Department of Chemical and Biological Engineering, University of New Mexico
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38
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Applications of Brewster angle microscopy from biological materials to biological systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1749-1766. [PMID: 28655618 DOI: 10.1016/j.bbamem.2017.06.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 12/22/2022]
Abstract
Brewster angle microscopy (BAM) is a powerful technique that allows for real-time visualization of Langmuir monolayers. The lateral organization of these films can be investigated, including phase separation and the formation of domains, which may be of different sizes and shapes depending on the properties of the monolayer. Different molecules or small changes within a molecule such as the molecule's length or presence of a double bond can alter the monolayer's lateral organization that is usually undetected using surface pressure-area isotherms. The effect of such changes can be clearly observed using BAM in real-time, under full hydration, which is an experimental advantage in many cases. While previous BAM reviews focused more on selected compounds or compared the impact of structural variations on the lateral domain formation, this review provided a broader overview of BAM application using biological materials and systems including the visualization of amphiphilic molecules, proteins, drugs, extracts, DNA, and nanoparticles at the air-water interface.
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39
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Dohno C, Makishi S, Nakatani K, Contera S. Amphiphilic DNA tiles for controlled insertion and 2D assembly on fluid lipid membranes: the effect on mechanical properties. NANOSCALE 2017; 9:3051-3058. [PMID: 28186523 DOI: 10.1039/c6nr07084a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Future lipid membrane-associated DNA nanostructures are expected to find applications ranging from synthetic biology to nanomedicine. Here we have designed and synthesized DNA tiles and modified them with amphiphilic covalent moieties. dod-DEG groups, which consist of a hydrophilic diethylene glycol (DEG) and a hydrophobic dodecyl group, are introduced at the phosphate backbone to create amphiphilic DNA strands which are subsequently introduced into one face of the DNA tiles. In this way the tile becomes able to stably bind to lipid membranes by insertion of the hydrophobic groups inside the bilayer core. The functionalized tiles do not aggregate in solution. Our results show that these amphiphilic DNA tiles can bind and assemble into 2D lattices on both gel and fluid lipid bilayers. The binding of the DNA structures to membranes is dependent on the lipid phase of the membrane, the concentration of Mg2+ cations, the length of the amphiphilic modifications to the DNA as well as on the density of the modifications within the tile. Atomic force microscopy-based force spectroscopy is used to investigate the effect of the inserted DNA tiles on the mechanical properties of the lipid membranes. The results indicate that the insertion of DNA tiles produces an approx. 20% increase of the bilayer breakthrough force.
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Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan. and PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Shingo Makishi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan.
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan.
| | - Sonia Contera
- Clarendon Laboratory, Physics Department, University of Oxford, Oxford, OX1 3PU, UK.
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40
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Das A, Adhikari C, Chakraborty A. Interaction of Different Divalent Metal Ions with Lipid Bilayer: Impact on the Encapsulation of Doxorubicin by Lipid Bilayer and Lipoplex Mediated Deintercalation. J Phys Chem B 2017; 121:1854-1865. [DOI: 10.1021/acs.jpcb.6b11443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Anupam Das
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh 452020, India
| | - Chandan Adhikari
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh 452020, India
| | - Anjan Chakraborty
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh 452020, India
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41
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Mora-Boza A, Lopes-Costa T, Gámez F, Pedrosa JM. Unveiling the interaction of DNA–octadecylamine at the air–water interface by ultraviolet-visible reflection spectroscopy. RSC Adv 2017. [DOI: 10.1039/c6ra27903a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, ultraviolet-visible reflection spectroscopy is proposed as a technique that, in combination with classical surface pressure–area isotherms, allows to study in situ the adsorption of DNA to octadecylamine monolayers.
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Affiliation(s)
- A. Mora-Boza
- Department of Physical, Chemical and Natural Systems
- Universidad Pablo de Olavide
- 41013 Seville
- Spain
| | - T. Lopes-Costa
- Department of Physical, Chemical and Natural Systems
- Universidad Pablo de Olavide
- 41013 Seville
- Spain
| | - F. Gámez
- Department of Physical, Chemical and Natural Systems
- Universidad Pablo de Olavide
- 41013 Seville
- Spain
| | - J. M. Pedrosa
- Department of Physical, Chemical and Natural Systems
- Universidad Pablo de Olavide
- 41013 Seville
- Spain
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42
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Lyadinskaya VV, Lin SY, Michailov AV, Povolotskiy AV, Noskov BA. Phase Transitions in DNA/Surfactant Adsorption Layers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:13435-13445. [PMID: 27993018 DOI: 10.1021/acs.langmuir.6b03396] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The adsorption layers of complexes between DNA and oppositely charged surfactants dodecyltrimethylammonium bromide (DTAB) and cetyltrimethylammonium bromide (CTAB) at the solution/air interface were studied with surface tensiometry, dilational surface rheology, atomic force microscopy, Brewster angle microscopy, infrared absorption-reflection spectroscopy, and ellipsometry. Measurements of the kinetic dependencies of the surface properties gave a possibility to discover the time intervals corresponding to the coexistence of two-dimensional phases. One can assume that the observed phase transition is of the first order, unlike the formation of microaggregates in the adsorption layers of mixed solutions of synthetic polyelectrolytes and surfactants. The multitechniques approach together with the calculations of the adsorption kinetics allowed the elucidation of the structure of coexisting surface phases and the distinguishing of four main steps of adsorption layer formation at the surface of DNA/surfactant solutions.
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Affiliation(s)
- Vanda V Lyadinskaya
- National Taiwan University of Science and Technology , Chemical Engineering Department, 43 Keelung Road, Section 4, 106 Taipei, Taiwan
| | - Shi-Yow Lin
- National Taiwan University of Science and Technology , Chemical Engineering Department, 43 Keelung Road, Section 4, 106 Taipei, Taiwan
| | - Alexander V Michailov
- Institute of Chemistry, St. Petersburg State University , Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - Alexey V Povolotskiy
- Institute of Chemistry, St. Petersburg State University , Universitetsky pr. 26, 198504 St. Petersburg, Russia
| | - Boris A Noskov
- Institute of Chemistry, St. Petersburg State University , Universitetsky pr. 26, 198504 St. Petersburg, Russia
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43
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Abstract
Lipids and nucleic acids (NAs) can hierarchically self-organize into a variety of nanostructures of increasingly complex geometries such as the 1D lamellar, 2D hexagonal, and 3D bicontinuous cubic phases. The diversity and complexity of those lipid-NA assemblies are interesting from a fundamental perspective as well as being relevant to the performance in gene delivery and gene silencing applications. The finding that not only the chemical make of the lipid-NA constructs, but their actual supramolecular organization, affects their gene transfection and silencing efficiencies has inspired physicists, chemists, and engineers to this field of research. At the moment it remains an open question how exactly the different lipid-NA structures interact with cells and organelles in order to output an optimal response. This article reviews our current understanding of the structures of different lipid-NA complexes and the corresponding cellular interaction mechanisms. The recent advances in designing optimal lipid-based NA carriers will be introduced with an emphasis on the structure-function relations.
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Affiliation(s)
- Minjee Kang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Hojun Kim
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Cecilia Leal
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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44
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Moehwald H, Brezesinski G. From Langmuir Monolayers to Multilayer Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10445-10458. [PMID: 27540629 DOI: 10.1021/acs.langmuir.6b02518] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This feature article is intended to describe a route from Langmuir monolayers as the most suitable and well-defined models to polyelectrolyte multilayers. The latter are structurally controlled not with angstrom but with nanometer precision; however, they are very modular with regard to building blocks and function and are robust, therefore promising many diverse applications. There have been many methods developed to structurally characterize Langmuir monolayers; therefore, they serve as models in membrane biophysics and materials science as well as in general physics as two-dimensional model systems. Many of these methods as well as ideas to control interfaces could be taken over to study polyelectrolyte multilayers with their extended internal interfaces. Finally, as an outlook we try to sketch various aspects to transit toward systems with higher structural hierarchy, enabling the coupling of different functions and arriving at responsive three-dimensional systems.
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Affiliation(s)
- Helmuth Moehwald
- Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Gerald Brezesinski
- Max-Planck-Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany
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45
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Das A, Adhikari C, Chakraborty A. Lipoplex-Mediated Deintercalation of Doxorubicin from Calf Thymus DNA-Doxorubicin Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:8889-8899. [PMID: 27465781 DOI: 10.1021/acs.langmuir.6b01860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this paper, we report the lipoplex-mediated deintercalation of anticancer drug doxorubicin (DOX) from the DOX-DNA complex under controlled experimental conditions. We used three zwitterionic liposomes, namely, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC), which are widely different in their phase transition temperatures to form a lipoplex with calf thymus DNA in the presence of Ca(2+) ions. The study revealed that DPPC being in sol-gel phase was more effective in releasing the drug from the DOX-DNA complex compared with liposomes that remain in liquid crystalline phase (DMPC and POPC). The higher extent of drug release in the case of DPPC liposomes was attributed to the stronger lipoplex formation with DNA as compared with that of other liposomes. Owing to the relatively smaller head group area, the DPPC liposomes in their sol-gel phase can absorb a larger number of Ca(2+) ions and hence offer a strong electrostatic interaction with DNA. This interaction was confirmed by time-resolved anisotropy and circular dichroism spectroscopy. Apart from the electrostatic interaction, the possible hydrophobic interaction between the liposomes and DNA was also taken into account for the observed deintercalation. The successful uptake of drug molecules by liposomes from the drug-DNA complex in the post-release period was also confirmed using confocal laser scanning microscopy (CLSM).
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Affiliation(s)
- Anupam Das
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh, India
| | - Chandan Adhikari
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh, India
| | - Anjan Chakraborty
- Discipline of Chemistry, Indian Institute of Technology Indore , Indore 453552, Madhya Pradesh, India
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46
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Hernández-Ainsa S, Ricci M, Hilton L, Aviñó A, Eritja R, Keyser UF. Controlling the Reversible Assembly of Liposomes through a Multistimuli Responsive Anchored DNA. NANO LETTERS 2016; 16:4462-6. [PMID: 27367802 PMCID: PMC4956241 DOI: 10.1021/acs.nanolett.6b01618] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/23/2016] [Indexed: 05/21/2023]
Abstract
We present a novel approach to reversibly control the assembly of liposomes through an anchored multistimuli responsive DNA oligonucleotide decorated with an azobenzene moiety (AZO-ON1). We show that liposomes assembly can be simultaneously controlled by three external stimuli: light, Mg(2+), and temperature. (i) Light alters the interaction of AZO-ON1 with liposomes, which influences DNA coating and consequently liposomes assembly. (ii) Mg(2+) induces the assembly, hence variation in its concentration enables for reversibility. (iii) Double-stranded AZO-ON1 is more efficient than single-stranded AZO-ON1 in triggering the assembly of liposomes and temperature has been used for controllable assembly through DNA thermal denaturation. Our multiresponsive AZO-ON1 represents a unique example in which multiple stimuli can be simultaneously applied to regulate the reversible assembly of liposomes.
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Affiliation(s)
- Silvia Hernández-Ainsa
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Maria Ricci
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Lloyd Hilton
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
| | - Anna Aviñó
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramon Eritja
- IQAC−CSIC, CIBER-BBN Networking Centre on Bioengineering,
Biomaterials and Nanomedicine, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ulrich F. Keyser
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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47
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Yang PW, Lin TL, Liu IT, Hu Y, Jeng US, Gilbert EP. Small-Angle Neutron Scattering Studies on the Multilamellae Formed by Mixing Lamella-Forming Cationic Diblock Copolymers with Lipids and Their Interaction with DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1828-1835. [PMID: 26818185 DOI: 10.1021/acs.langmuir.5b04672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We demonstrate that the lamella-forming polystyrene-block-poly(N-methyl-4-vinylpyridinium iodine) (PS-b-P4VPQ), with similar sizes of the PS and P4VPQ blocks, can be dispersed in the aqueous solutions by forming lipid/PS-b-P4VPQ multilamellae. Using small-angle neutron scattering (SANS) and 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine (d62-DPPC) in D2O, a broad correlation peak is found in the scattering profile that signifies the formation of the loosely ordered d62-DPPC/PS-b-P4VPQ multilamellae. The thicknesses of the hydrophobic and hydrophilic layers of the d62-DPPC/PS-b-P4VPQ multilamellae are close to the PS layer and the condensed brush layer thicknesses as determined from previous neutron reflectometry studies on the PS-b-P4VPQ monolayer at the air-water interface. Such well-dispersed d62-DPPC/PS-b-P4VPQ multilamellae are capable of forming multilamellae with DNA in aqueous solution. It is found that the encapsulation of DNA in the hydrophilic layer of the d62-DPPC/PS-b-P4VPQ multilamellae slightly increases the thickness of the hydrophilic layer. Adding CaCl2 can enhance the DNA adsorption in the hydrophilic brush layer, and it is similar to that observed in the neutron reflectometry study of the DNA adsorption by the PS-b-P4VPQ monolayer.
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Affiliation(s)
- Po-Wei Yang
- Department of Engineering and System Science, National Tsing Hua University , Hsinchu 300, Taiwan, Republic of China
| | - Tsang-Lang Lin
- Department of Engineering and System Science, National Tsing Hua University , Hsinchu 300, Taiwan, Republic of China
| | - I-Ting Liu
- Department of Engineering and System Science, National Tsing Hua University , Hsinchu 300, Taiwan, Republic of China
| | - Yuan Hu
- Department of Engineering and System Science, National Tsing Hua University , Hsinchu 300, Taiwan, Republic of China
| | - U-Ser Jeng
- National Synchrotron Radiation Research Center (NSRRC) , Hsinchu, 300, Taiwan, Republic of China
| | - Elliot Paul Gilbert
- Bragg Institute, Australian Nuclear Science and Technology Organisation (ANSTO) , Locked Bag 2001, Kirrawee DC, New South Wales 2232, Australia
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48
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Ahmed T, Kamel AO, Wettig SD. Interactions between DNA and gemini surfactant: impact on gene therapy: part II. Nanomedicine (Lond) 2016; 11:403-20. [PMID: 26784450 DOI: 10.2217/nnm.15.204] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Nonviral gene delivery, provides distinct treatment modalities for the inherited and acquired diseases, relies upon the encapsulation of a gene of interest, which is then ideally delivered to the target cells. Variations in the chemical structure of gemini surfactants and subsequent physicochemical characteristics of the gemini-based lipoplexes and their impact on efficient gene transfection were assessed in part I, which was published in first March 2016 issue of Nanomedicine (1103). In order to design an efficient vector using gemini surfactants, the interaction of the surfactant with DNA and other components of the delivery system must be characterized, and more critically, well understood. Such studies will help to understand how nonviral transfection complexes, in general, overcome various cellular barriers. The Langmuir-Blodgett monolayer studies, atomic force microscopy, differential scanning calorimetry, isothermal titration calorimetry, small-angle x-ray scattering, are extensively used to evaluate the interaction behavior of gemini surfactants with DNA and other vector components. Part II of this review focuses on the use of these unique techniques to understand their interaction with DNA.
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Affiliation(s)
- Taksim Ahmed
- School of Pharmacy, University of Waterloo, 200 University Ave. W., Waterloo, ON, N2L 3G1, Canada.,Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON, M5S 3M2, Canada
| | - Amany O Kamel
- School of Pharmacy, University of Waterloo, 200 University Ave. W., Waterloo, ON, N2L 3G1, Canada.,Department of Pharmaceutics & Industrial Pharmacy, Faculty of Pharmacy, Ain Shams University, Khalifa El-Maamon Street, Abbasiya Square, Cairo 11566, Egypt
| | - Shawn D Wettig
- School of Pharmacy, University of Waterloo, 200 University Ave. W., Waterloo, ON, N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W., Waterloo, ON, N2L 3G1, Canada
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49
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Radiation damage on Langmuir monolayers of the anionic 1.2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (sodium salt)(DPPG) phospholipid at the air–DNA solution interface. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 58:576-9. [DOI: 10.1016/j.msec.2015.09.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 08/21/2015] [Accepted: 09/03/2015] [Indexed: 11/20/2022]
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50
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Antipina AY, Gurtovenko AA. Molecular-level insight into the interactions of DNA with phospholipid bilayers: barriers and triggers. RSC Adv 2016. [DOI: 10.1039/c6ra05607e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A zwitterionic phospholipid bilayer represents a repulsive barrier for DNA binding; this barrier can be overcome through adsorption of divalent cations to the bilayer surface.
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Affiliation(s)
- A. Yu. Antipina
- Faculty of Physics
- St. Petersburg State University
- St. Petersburg 198504
- Russia
- Department of Photonics and Optical Information Technology
| | - A. A. Gurtovenko
- Faculty of Physics
- St. Petersburg State University
- St. Petersburg 198504
- Russia
- Institute of Macromolecular Compounds
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