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Wong SH, Kopf SN, Caroprese V, Zosso Y, Morzy D, Bastings MMC. Modulating the DNA/Lipid Interface through Multivalent Hydrophobicity. NANO LETTERS 2024; 24:11210-11216. [PMID: 39054892 PMCID: PMC11403765 DOI: 10.1021/acs.nanolett.4c02564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Lipids and nucleic acids are two of the most abundant components of our cells, and both molecules are widely used as engineering materials for nanoparticles. Here, we present a systematic study of how hydrophobic modifications can be employed to modulate the DNA/lipid interface. Using a series of DNA anchors with increasing hydrophobicity, we quantified the capacity to immobilize double-stranded (ds) DNA to lipid membranes in the liquid phase. Contrary to electrostatic effects, hydrophobic anchors are shown to be phase-independent if sufficiently hydrophobic. For weak anchors, the overall hydrophobicity can be enhanced following the concept of multivalency. Finally, we demonstrate that structural flexibility and anchor orientation overrule the effect of multivalency, emphasizing the need for careful scaffold design if strong interfaces are desired. Together, our findings guide the design of tailored DNA/membrane interfaces, laying the groundwork for advancements in biomaterials, drug delivery vehicles, and synthetic membrane mimics for biomedical research and nanomedicine.
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Affiliation(s)
- Siu Ho Wong
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Sarina Nicole Kopf
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Vincenzo Caroprese
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Yann Zosso
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Diana Morzy
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
| | - Maartje M C Bastings
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
- Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne 1015, Switzerland
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2
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Gubu A, Zhang X, Lu A, Zhang B, Ma Y, Zhang G. Nucleic acid amphiphiles: Synthesis, properties, and applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:144-163. [PMID: 37456777 PMCID: PMC10345231 DOI: 10.1016/j.omtn.2023.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Nucleic acid amphiphiles, referring to nucleic acids modified with large hydrophobic groups, have been widely used in programmable bioengineering. Since nucleic acids are intrinsically hydrophilic, the hydrophobic groups endow nucleic acid amphiphiles with unique properties, such as self-assembling, interactions with artificial or biological membranes, and transmembrane transport. Importantly, the hybridization or target binding capability of oligonucleotide itself supplies nucleic acid amphiphiles with excellent programmability. As a result, this type of molecule has attracted considerable attention in academic studies and has enormous potential for further applications. For a comprehensive understanding of nucleic acid amphiphiles, we review the reported research on nucleic acid amphiphiles from their molecular design to final applications, in which we summarize the synthetic strategies for nucleic acid amphiphiles and draw much attention to their unique properties in different contexts. Finally, a summary of the applications of nucleic acid amphiphiles in drug development, bioengineering, and bioanalysis are critically discussed.
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Affiliation(s)
- Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Xueli Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38 Xueyuan Road, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
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3
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Kodr D, Kužmová E, Pohl R, Kraus T, Hocek M. Lipid-linked nucleoside triphosphates for enzymatic synthesis of hydrophobic oligonucleotides with enhanced membrane anchoring efficiency. Chem Sci 2023; 14:4059-4069. [PMID: 37063801 PMCID: PMC10094435 DOI: 10.1039/d2sc06718h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/19/2023] [Indexed: 03/22/2023] Open
Abstract
We designed and synthesized a series of 2'-deoxyribonucleoside triphosphates (dNTPs) bearing various lipid moieties. Fatty acid- and cholesterol-modified dNTPs proved to be substrates for KOD XL DNA polymerase in primer extension reactions. They were also mutually compatible for simultaneous multiple incorporations into the DNA strand. The methodology of enzymatic synthesis opened a pathway to diverse structurally unique lipid-ON probes containing one or more lipid units. We studied interactions of such probes with the plasma membranes of live cells. Employing a rational design, we found a series of lipid-ONs with enhanced membrane anchoring efficiency. The in-membrane stability of multiply modified ONs was superior to that of commonly studied ON analogues, in which a single cholesterol molecule is typically tethered to the thread end. Notably, some of the probes were detected at the cell surface even after 24 h upon removal of the probe solution. Such an effect was general to several studied cell lines.
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Affiliation(s)
- David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Erika Kužmová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences Flemingovo namesti 2 CZ-16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague Hlavova 8 Prague-2 12843 Czech Republic
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4
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Oka Y. Exclusion of Anchor-Matched Peptide Nucleic Acid from Liquid-Ordered Domains by Hybridization with Complementary Flavin-Labeled DNA. ACS OMEGA 2023; 8:1109-1113. [PMID: 36643542 PMCID: PMC9835180 DOI: 10.1021/acsomega.2c06463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Membrane-anchored proteins and their mimics, such as peptide nucleic acids (PNAs), are known to partition preferentially into either lipid raft/liquid-ordered (lo) domains or into non-raft/liquid-disordered (ld) domains, depending on their lipophilic anchors. Here, anchor-matched PNA was demonstrated to be excluded from the lo microdomains of giant unilamellar vesicles by hybridization with the complementary flavin-labeled DNA. As shown in control experiments using Alexa Fluor 488-labeled DNA, which showed that the preferential partitioning was the lo domain, the domain distribution of PNA was not only dependent on the lipophilic anchor but also on the structure of the hybridized DNA or PNA pair. In such systems, the main factors that influence changes in the domain selectivity of the probes are most likely to also be interactivity (i.e., steric bulkiness), hydrophilicity, and self-assembling ability. These findings may have the potential to contribute to the elucidation of membrane-active peptides, the method of their activation, and their applications in medicine such as antimicrobial use, especially with regard to their actions at the interface between the lo and ld domains in cells.
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5
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Jakobsen U, Rosholm KR, Vogel S. Design, synthesis and membrane anchoring strength of lipidated polyaza crown ether DNA-conjugates (LiNAs) studied by DNA-controlled assembly of liposomes. Org Biomol Chem 2022; 20:9460-9468. [PMID: 36408737 DOI: 10.1039/d2ob01517j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hybridization-controlled assays for assembly or fusion of liposomes are versatile for detection of both DNA and RNA targets and useful for the evaluation of membrane anchoring strength of LiNAs with applications in the context of liposome assembly, liposome fusion and lipid nanoparticle formulation of therapeutic LiNAs. Herein, we report the synthesis of lipid phosphoramidite building blocks for automated LiNA synthesis and a study on design requirements for efficient lipid membrane anchoring and liposome assembly dependent on lipid membrane anchor length (C10-C20) and structure, the effect of internal linkers and locked nucleic acids (LNA) building blocks on the lipid membrane anchoring strength of LiNAs.
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Affiliation(s)
- Ulla Jakobsen
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
| | - Kadla Røskva Rosholm
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
| | - Stefan Vogel
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark.
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6
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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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7
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Rubio-Sánchez R, Barker SE, Walczak M, Cicuta P, Michele LD. A Modular, Dynamic, DNA-Based Platform for Regulating Cargo Distribution and Transport between Lipid Domains. NANO LETTERS 2021; 21:2800-2808. [PMID: 33733783 PMCID: PMC8050828 DOI: 10.1021/acs.nanolett.0c04867] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/03/2021] [Indexed: 05/04/2023]
Abstract
Cell membranes regulate the distribution of biological machinery between phase-separated lipid domains to facilitate key processes including signaling and transport, which are among the life-like functionalities that bottom-up synthetic biology aims to replicate in artificial-cellular systems. Here, we introduce a modular approach to program partitioning of amphiphilic DNA nanostructures in coexisting lipid domains. Exploiting the tendency of different hydrophobic "anchors" to enrich different phases, we modulate the lateral distribution of our devices by rationally combining hydrophobes and by changing nanostructure size and topology. We demonstrate the functionality of our strategy with a bioinspired DNA architecture, which dynamically undergoes ligand-induced reconfiguration to mediate cargo transport between domains via lateral redistribution. Our findings pave the way to next-generation biomimetic platforms for sensing, transduction, and communication in synthetic cellular systems.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Simone Eizagirre Barker
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Michal Walczak
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Pietro Cicuta
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Biological
and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- Molecular
Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
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8
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Liu Y, Wijesekara P, Kumar S, Wang W, Ren X, Taylor RE. The effects of overhang placement and multivalency on cell labeling by DNA origami. NANOSCALE 2021; 13:6819-6828. [PMID: 33885483 PMCID: PMC8161690 DOI: 10.1039/d0nr09212f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Through targeted binding to the cell membrane, structural DNA nanotechnology has the potential to guide and affix biomolecules such as drugs, growth factors and nanobiosensors to the surfaces of cells. In this study, we investigated the targeted binding efficiency of three distinct DNA origami shapes to cultured endothelial cells via cholesterol anchors. Our results showed that the labeling efficiency is highly dependent on the shape of the origami as well as the number and the location of the binding overhangs. With a uniform surface spacing of binding overhangs, 3D isotropic nanospheres and 1D anisotropic nanorods labeled cells effectively, and the isotropic nanosphere labeling fit well with an independent binding model. Face-decoration and edge-decoration of the anisotropic nanotile were performed to investigate the effects of binding overhang location on cell labeling, and only the edge-decorated nanotiles were successful at labeling cells. Edge proximity studies demonstrated that the labeling efficiency can be modulated in both nanotiles and nanorods by moving the binding overhangs towards the edges and vertices, respectively. Furthermore, we demonstrated that while double-stranded DNA (dsDNA) bridge tethers can rescue the labeling efficiency of the face-decorated rectangular plate, this effect is also dependent on the proximity of bridge tethers to the edges or vertices of the nanostructures. A final comparison of all three nanoshapes revealed that the end-labeled nanorod and the nanosphere achieved the highest absolute labeling intensities, but the highest signal-to-noise ratio, calculated as the ratio of overall labeling to initiator-free background labeling, was achieved by the end-labeled nanorod, with the edge-labeled nanotile coming in second place slightly ahead of the nanosphere. The findings from this study can help us further understand the factors that affect membrane attachment using cholesterol anchors, thus providing guidelines for the rational design of future functional DNA nanostructures.
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Affiliation(s)
- Ying Liu
- Department of Mechanical Engineering, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, USA.
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9
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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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10
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Wang W, Arias DS, Deserno M, Ren X, Taylor RE. Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics. APL Bioeng 2020; 4:041507. [PMID: 33344875 PMCID: PMC7725538 DOI: 10.1063/5.0027022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
DNA nanotechnology has proven exceptionally apt at probing and manipulating biological environments as it can create nanostructures of almost arbitrary shape that permit countless types of modifications, all while being inherently biocompatible. Emergent areas of particular interest are applications involving cellular membranes, but to fully explore the range of possibilities requires interdisciplinary knowledge of DNA nanotechnology, cell and membrane biology, and biophysics. In this review, we aim for a concise introduction to the intersection of these three fields. After briefly revisiting DNA nanotechnology, as well as the biological and mechanical properties of lipid bilayers and cellular membranes, we summarize strategies to mediate interactions between membranes and DNA nanostructures, with a focus on programmed delivery onto, into, and through lipid membranes. We also highlight emerging applications, including membrane sculpting, multicell self-assembly, spatial arrangement and organization of ligands and proteins, biomechanical sensing, synthetic DNA nanopores, biological imaging, and biomelecular sensing. Many critical but exciting challenges lie ahead, and we outline what strikes us as promising directions when translating DNA nanostructures for future in vitro and in vivo membrane applications.
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Affiliation(s)
- Weitao Wang
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - D. Sebastian Arias
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xi Ren
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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11
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12
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Sun L, Su Y, Wang JG, Xia F, Xu Y, Li D. DNA nanotweezers for stabilizing and dynamically lighting up a lipid raft on living cell membranes and the activation of T cells. Chem Sci 2020; 11:1581-1586. [PMID: 34084389 PMCID: PMC8148038 DOI: 10.1039/c9sc06203c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Lipid rafts are generally considered as nanodomains on cell membranes and play important roles in signaling, viral infection, and membrane trafficking. However, the raft hypothesis is still debated with many inconsistencies because the nanoscale and transient heterogeneous raft structure creates difficulties in its location and functional analysis. In the present study, we report a DNA nanotweezer composed of a cholesterol-functionalized DNA duplex that stabilizes transient lipid rafts, which facilitate the further analysis of the raft component and its functions via other spectroscopy tools. The proposed DNA nanotweezer can induce clustering of raft-associated components (saturated lipids, membrane protein and possibly endogenous cholesterol), leading to the T cell proliferation through clustering of a T-cell antigen receptor (TCR). The flexibility of random sequence noncoding DNA provides versatile possibilities of manipulating lipid rafts and activating T cells, and thus opens new ways in a future T cell therapy. We report a DNA nanotweezer that recruits raft-associated lipids, proteins and possibly endogenous cholesterol on living cell membrane. The DNA nanotweezers could activate T cell proliferation in a nonspecific activation manner.![]()
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Affiliation(s)
- Lele Sun
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
- Institute of Functional Nano & Soft Materials (FUNSOM)
| | - Yingying Su
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Jun-Gang Wang
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Fei Xia
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
| | - Ying Xu
- Department of Pathophysiology
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education
- Shanghai Jiao-Tong University School of Medicine
- Shanghai
- China
| | - Di Li
- School of Chemistry and Molecular Engineering
- East China Normal University
- Shanghai
- China
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13
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Mognetti BM, Cicuta P, Di Michele L. Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:116601. [PMID: 31370052 DOI: 10.1088/1361-6633/ab37ca] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes where, among other functions, they control cell adhesion, motility and tissue formation. Besides being central to several biological processes, multivalent interactions mediated by reactive linkers confined to deformable substrates underpin the design of synthetic-biological platforms and advanced biomimetic materials. Here we review recent advances on the experimental study and theoretical modelling of a heterogeneous class of biomimetic systems in which synthetic linkers mediate multivalent interactions between fluid and deformable colloidal units, including lipid vesicles and emulsion droplets. Linkers are often prepared from synthetic DNA nanostructures, enabling full programmability of the thermodynamic and kinetic properties of their mutual interactions. The coupling of the statistical effects of multivalent interactions with substrate fluidity and deformability gives rise to a rich emerging phenomenology that, in the context of self-assembled soft materials, has been shown to produce exotic phase behaviour, stimuli-responsiveness, and kinetic programmability of the self-assembly process. Applications to (synthetic) biology will also be reviewed.
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Affiliation(s)
- Bortolo Matteo Mognetti
- Université libre de Bruxelles (ULB), Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Campus Plaine, CP 231, Blvd. du Triomphe, B-1050 Brussels, Belgium
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14
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Huo S, Li H, Boersma AJ, Herrmann A. DNA Nanotechnology Enters Cell Membranes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900043. [PMID: 31131200 PMCID: PMC6523375 DOI: 10.1002/advs.201900043] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/16/2019] [Indexed: 05/19/2023]
Abstract
DNA is more than a carrier of genetic information: It is a highly versatile structural motif for the assembly of nanostructures, giving rise to a wide range of functionalities. In this regard, the structure programmability is the main advantage of DNA over peptides, proteins, and small molecules. DNA amphiphiles, in which DNA is covalently bound to synthetic hydrophobic moieties, allow interactions of DNA nanostructures with artificial lipid bilayers and cell membranes. These structures have seen rapid growth with great potential for medical applications. In this Review, the current state of the art of the synthesis of DNA amphiphiles and their assembly into nanostructures are first summarized. Next, an overview on the interaction of these DNA amphiphiles with membranes is provided, detailing on the driving forces and the stability of the interaction. Moreover, the interaction with cell surfaces in respect to therapeutics, biological sensing, and cell membrane engineering is highlighted. Finally, the challenges and an outlook on this promising class of DNA hybrid materials are discussed.
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Affiliation(s)
- Shuaidong Huo
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AG GroningenThe Netherlands
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
| | - Hongyan Li
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AG GroningenThe Netherlands
| | - Arnold J. Boersma
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
| | - Andreas Herrmann
- DWI‐Leibniz Institute for Interactive MaterialsForckenbeckstr. 5052056AachenGermany
- Zernike Institute for Advanced MaterialsUniversity of GroningenNijenborgh 49747AG GroningenThe Netherlands
- Institute of Technical and Macromolecular ChemistryRWTH Aachen UniversityWorringerweg 252074AachenGermany
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15
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Yang J, Meng Z, Liu Q, Shimada Y, Olsthoorn RCL, Spaink HP, Herrmann A, Kros A. Performing DNA nanotechnology operations on a zebrafish. Chem Sci 2018; 9:7271-7276. [PMID: 30288248 PMCID: PMC6148687 DOI: 10.1039/c8sc01771a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/16/2018] [Indexed: 12/18/2022] Open
Abstract
Nanoscale engineering of surfaces is becoming an indispensable technique to modify membranes and, thus cellular behaviour. Here, such membrane engineering related was explored on the surface of a living animal using DNA nanotechnology. We demonstrate the immobilization of oligonucleotides functionalized with a membrane anchor on 2 day old zebrafish. The protruding single-stranded DNA on the skin of zebrafish served as a handle for complementary DNAs, which allowed the attachment of small molecule cargo, liposomes and dynamic relabeling by DNA hybridization protocols. Robust anchoring of the oligonucleotides was proven as DNA-based amplification processes were successfully performed on the outer membrane of the zebrafish enabling the multiplication of surface functionalities from a single DNA-anchoring unit and the dramatic improvement of fluorescent labeling of these animals. As zebrafish are becoming an alternative to animal models in drug development, toxicology and nanoparticles characterization, we believe the platform presented here allows amalgamation of DNA nanotechnology tools with live animals and this opens up yet unexplored avenues like efficient bio-barcoding as well as in vivo tracking.
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Affiliation(s)
- Jian Yang
- Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P.O. Box 9502 , 2300 RA Leiden , The Netherlands .
| | - Zhuojun Meng
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
| | - Qing Liu
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
| | - Yasuhito Shimada
- Institute of Biology , Leiden University , Leiden , The Netherlands
- Department of Integrative Pharmacology , Mie University Graduate School of Medicine , Mie , Japan .
| | - René C L Olsthoorn
- Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P.O. Box 9502 , 2300 RA Leiden , The Netherlands .
| | - Herman P Spaink
- Institute of Biology , Leiden University , Leiden , The Netherlands
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstr. 50 , 52056 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Worringerweg 2 , 52074 , Aachen , Germany
| | - Alexander Kros
- Supramolecular & Biomaterials Chemistry , Leiden Institute of Chemistry , Leiden University , P.O. Box 9502 , 2300 RA Leiden , The Netherlands .
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16
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Das RN, Kumar YP, Kumar SA, Schütte OM, Steinem C, Dash J. Self-Assembly of a Guanosine Derivative To Form Nanostructures and Transmembrane Channels. Chemistry 2018; 24:4002-4005. [DOI: 10.1002/chem.201800205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Rabindra Nath Das
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Y. Pavan Kumar
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - S. Arun Kumar
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
| | - Ole Mathis Schütte
- Institute for Organic and Biomolecular Chemistry; Georg August University Göttingen; Tammannstr. 2 37077 Göttingen Germany
| | - Claudia Steinem
- Institute for Organic and Biomolecular Chemistry; Georg August University Göttingen; Tammannstr. 2 37077 Göttingen Germany
| | - Jyotirmayee Dash
- Department of Organic Chemistry; Indian Association for the Cultivation of Science; Jadavpur Kolkata 700032 India
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17
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Oka Y, Shishino H. Fluorescence Quenching of Alexa Fluor 488-labeled DNA by Complementary Trp-containing PNA Partitioned in Liquid-ordered Domains. CHEM LETT 2017. [DOI: 10.1246/cl.170755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yoshimi Oka
- Frontier Research Core for Life Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194
| | - Hisae Shishino
- Frontier Research Core for Life Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194
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18
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Oka Y, Shishino H. Fluorescence Imaging of Disrupted Interfaces between Liquid-Ordered and Liquid-Disordered Domains by a Flavin-Labeled PNA Duplex. ACS OMEGA 2017; 2:2912-2915. [PMID: 31457626 PMCID: PMC6641140 DOI: 10.1021/acsomega.7b00581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/12/2017] [Indexed: 06/10/2023]
Abstract
Lipid rafts and membrane-active peptides are attracting attention because they help understand basic membrane functions. In addition, we focus on flavoproteins playing some physiological roles and explore the model compounds. In this study, we demonstrate that a new flavin probe, composed of palmitoylated peptide nucleic acid (PNA) and its complementary PNA labeled with flavin, targets the liquid-ordered (lo) microdomains and disrupts its interfaces to liquid-disordered (ld) microdomains of giant unilamellar vesicles and can be visualized by using confocal laser scanning microscopy. Surprisingly, as shown in time-lapse images, vesiculation and probe aggregations appear in the lo-ld interfaces, which leads to local disruption of the membrane. We discuss a possible interpretation of the data based on a comparison with control experiments.
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19
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Czogalla A, Franquelim HG, Schwille P. DNA Nanostructures on Membranes as Tools for Synthetic Biology. Biophys J 2017; 110:1698-1707. [PMID: 27119630 PMCID: PMC4850321 DOI: 10.1016/j.bpj.2016.03.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/26/2015] [Accepted: 03/07/2016] [Indexed: 11/12/2022] Open
Abstract
Over the last decade, functionally designed DNA nanostructures applied to lipid membranes prompted important achievements in the fields of biophysics and synthetic biology. Taking advantage of the universal rules for self-assembly of complementary oligonucleotides, DNA has proven to be an extremely versatile biocompatible building material on the nanoscale. The possibility to chemically integrate functional groups into oligonucleotides, most notably with lipophilic anchors, enabled a widespread usage of DNA as a viable alternative to proteins with respect to functional activity on membranes. As described throughout this review, hybrid DNA-lipid nanostructures can mediate events such as vesicle docking and fusion, or selective partitioning of molecules into phase-separated membranes. Moreover, the major benefit of DNA structural constructs, such as DNA tiles and DNA origami, is the reproducibility and simplicity of their design. DNA nanotechnology can produce functional structures with subnanometer precision and allow for a tight control over their biochemical functionality, e.g., interaction partners. DNA-based membrane nanopores and origami structures able to assemble into two-dimensional networks on top of lipid bilayers are recent examples of the manifold of complex devices that can be achieved. In this review, we will shortly present some of the potentially most relevant avenues and accomplishments of membrane-anchored DNA nanostructures for investigating, engineering, and mimicking lipid membrane-related biophysical processes.
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Affiliation(s)
- Aleksander Czogalla
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
| | - Henri G Franquelim
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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20
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Nakajima M, Kasuya T, Yokota S, Onishi R, Ikehara T, Kugimiya A, Watanabe A. Gene Silencing Activity and Hepatic Accumulation of Antisense Oligonucleotides Bearing Cholesterol-Conjugated Thiono Triester at the Gap Region. Nucleic Acid Ther 2017; 27:232-237. [PMID: 28418770 DOI: 10.1089/nat.2017.0669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cholesterol (Chol) conjugation to the 5' or 3' end of antisense oligonucleotide (ASO) enables delivery to the liver, and Chol conjugation at the gap region can also be expected to improve delivery to the liver. In this study, we synthesized ASOs bearing the Chol-conjugated thiono triester and evaluated their activity and hepatic accumulation. We found that Chol conjugations at the gap region improved in vitro activity and hepatic accumulation when compared to unconjugated ASOs. However, Chol conjugation with phosphorothioate linkage did not improve in vivo activity in the liver, suggesting the importance of cleaving the phosphodiester between ASO and Chol. These results offer useful information for tuning the oligonucleotide structure to improve pharmaceutical properties and designing ASOs for multiple ligand conjugations and combinations with end modification.
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Affiliation(s)
- Mado Nakajima
- 1 Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd. , Toyonaka, Japan
| | - Takeshi Kasuya
- 1 Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd. , Toyonaka, Japan
| | - Shinnichi Yokota
- 1 Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd. , Toyonaka, Japan
| | - Reina Onishi
- 2 Physicochemical & Preformulation, Research Laboratory for Development, Shionogi & Co., Ltd. , Toyonaka, Japan
| | - Tatsuya Ikehara
- 3 Biomarker R&D Department, Shionogi & Co., Ltd. , Toyonaka, Japan
| | - Akira Kugimiya
- 1 Discovery Research Laboratory for Innovative Frontier Medicines, Shionogi & Co., Ltd. , Toyonaka, Japan
| | - Ayahisa Watanabe
- 2 Physicochemical & Preformulation, Research Laboratory for Development, Shionogi & Co., Ltd. , Toyonaka, Japan
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21
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Krishnan S, Ziegler D, Arnaut V, Martin TG, Kapsner K, Henneberg K, Bausch AR, Dietz H, Simmel FC. Molecular transport through large-diameter DNA nanopores. Nat Commun 2016; 7:12787. [PMID: 27658960 PMCID: PMC5036142 DOI: 10.1038/ncomms12787] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/02/2016] [Indexed: 01/10/2023] Open
Abstract
DNA-based nanopores are synthetic biomolecular membrane pores, whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, making them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Here we introduce a large DNA membrane channel with an ≈4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ≈3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, we demonstrate the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration. Artificial DNA membrane channels are promising molecular devices for biotechnology but suffer from low affinity for lipid bilayers. Here, the authors report a large DNA nanopore that spontaneously inserts into a flat lipid membrane, driven by engineered hydrophobic or streptavidin-biotin interactions.
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Affiliation(s)
- Swati Krishnan
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Daniela Ziegler
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Vera Arnaut
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Thomas G Martin
- Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Physik-Department E69, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Korbinian Kapsner
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Katharina Henneberg
- Physik-Department E27, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Andreas R Bausch
- Physik-Department E27, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany
| | - Hendrik Dietz
- Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Physik-Department E69, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Friedrich C Simmel
- Physik-Department E14, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.,Zentrum für Nanotechnologie und Nanomaterialien/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
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22
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Kumar YP, Das RN, Schütte OM, Steinem C, Dash J. Bis-triazolyl diguanosine derivatives as synthetic transmembrane ion channels. Nat Protoc 2016; 11:1039-56. [DOI: 10.1038/nprot.2016.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Montis C, Gerelli Y, Fragneto G, Nylander T, Baglioni P, Berti D. Nucleolipid bilayers: A quartz crystal microbalance and neutron reflectometry study. Colloids Surf B Biointerfaces 2016; 137:203-13. [DOI: 10.1016/j.colsurfb.2015.07.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 11/29/2022]
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24
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Le Chevalier Isaad A, Carrara P, Stano P, Krishnakumar KS, Lafont D, Zamboulis A, Buchet R, Bouchu D, Albrieux F, Strazewski P. A hydrophobic disordered peptide spontaneously anchors a covalently bound RNA hairpin to giant lipidic vesicles. Org Biomol Chem 2015; 12:6363-73. [PMID: 24915577 DOI: 10.1039/c4ob00721b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The attraction of nucleic acids to lipidic compartments is the first step for carriers of potentially inheritable information to self-organise in functionalised synthetic cells. Confocal fluorescence imaging shows that a synthetic amphiphilic peptidyl RNA molecule spontaneously accumulates at the outer bilayer membranes of phospho- and glycolipidic giant vesicles. Cooperatively attractive interactions of -3.4 to -4.0 kcal mol(-1) between a random coil hydrophobic peptide and lipid membranes can thus pilot lipophobic RNA to its compartmentation. The separation of mixed lipid phases in the membranes further enhances the local concentration of anchored RNA.
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Affiliation(s)
- Alexandra Le Chevalier Isaad
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (Unité Mixte de Recherche 5246), Université de Lyon, Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, Lyon, France.
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25
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Werz E, Rosemeyer H. Terminal lipophilization of a unique DNA dodecamer by various nucleolipid headgroups: Their incorporation into artificial lipid bilayers and hydrodynamic properties. Beilstein J Org Chem 2015; 11:913-29. [PMID: 26124894 PMCID: PMC4464448 DOI: 10.3762/bjoc.11.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/08/2015] [Indexed: 01/01/2023] Open
Abstract
A series of six cyanine-5-labeled oligonucleotides (LONs 10-15), each terminally lipophilized with different nucleolipid head groups, were synthesized using the recently prepared phosphoramidites 4b-9b. The insertion of the LONs within an artificial lipid bilayer, composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), was studied by single molecule fluorescence spectroscopy and microscopy with the help of an optically transparent microfluidic sample carrier with perfusion capabilities. The incorporation of the lipo-oligonucleotides into the bilayer was studied with respect to efficiency (maximal bilayer brightness) as well as stability against perfusion (final stable bilayer brightness). Attempts to correlate these parameters with the log P values of the corresponding nucleolipid head groups failed, a result which clearly demonstrates that not only the lipophilicity but mainly the chemical structure and topology of the head group is of decisive importance for the optimal interaction of a lipo-oligonucleotide with an artificial lipid bilayer. Moreover, fluorescence half-live and diffusion time values were measured to determine the diffusion coefficients of the lipo-oligonucleotides.
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Affiliation(s)
- Emma Werz
- Organic Chemistry I - Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastr. 7, 49069 Osnabrück, Germany ; Ionovation GmbH, Westerbreite 7, 49078 Osnabrück, Germany
| | - Helmut Rosemeyer
- Organic Chemistry I - Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastr. 7, 49069 Osnabrück, Germany
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26
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Dohno C, Matsuzaki K, Yamaguchi H, Shibata T, Nakatani K. A hybridisation-dependent membrane-insertable amphiphilic DNA. Org Biomol Chem 2015; 13:10117-21. [DOI: 10.1039/c5ob01761k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We synthesized a new class of membrane-binding amphiphilic DNA consisting of hydrophilic phosphodiester-linked DNA and hydrophobic octyl phosphotriester-linked DNA. The amphiphilic DNA binds to the lipid membrane by inserting the hydrophobic region, which is facilitated by the presence of the complementary DNA strand.
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Affiliation(s)
- C. Dohno
- Regulatory Bioorganic Chemistry
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
| | - K. Matsuzaki
- Regulatory Bioorganic Chemistry
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
| | - H. Yamaguchi
- Regulatory Bioorganic Chemistry
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
| | - T. Shibata
- Regulatory Bioorganic Chemistry
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
| | - K. Nakatani
- Regulatory Bioorganic Chemistry
- The Institute of Scientific and Industrial Research
- Osaka University
- Ibaraki 567-0047
- Japan
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27
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Das RN, Kumar YP, Schütte OM, Steinem C, Dash J. A DNA-Inspired Synthetic Ion Channel Based on G–C Base Pairing. J Am Chem Soc 2014; 137:34-7. [PMID: 25514016 DOI: 10.1021/ja510470b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rabindra Nath Das
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, West Bengal 700032, India
- Department
of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Y. Pavan Kumar
- Department
of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Ole Mathis Schütte
- Institute
of Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstr. 2, Göttingen, Lower Saxony 37077, Germany
| | - Claudia Steinem
- Institute
of Organic and Biomolecular Chemistry, Georg-August University Göttingen, Tammannstr. 2, Göttingen, Lower Saxony 37077, Germany
| | - Jyotirmayee Dash
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, West Bengal 700032, India
- Department
of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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28
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Pramanik S, Tateishi-Karimata H, Sugimoto N. Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription. Nucleic Acids Res 2014; 42:12949-59. [PMID: 25336617 PMCID: PMC4227800 DOI: 10.1093/nar/gku998] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Important biological reactions involving nucleic acids occur near the surface of membranes such as the nuclear membrane (NM) and rough endoplasmic reticulum (ER); however, the interactions between biomembranes and nucleic acids are poorly understood. We report here that transcription was facilitated in solution with liposomes, which mimic a biomembrane surface, relative to the reaction in a homogeneous aqueous solution when the template was able to form a G-quadruplex. The G-quadruplex is known to be an inhibitor of transcription, but the stability of the G-quadruplex was decreased at the liposome surface because of unfavourable enthalpy. The destabilization of the G-quadruplex was greater at the surface of NM- and ER-mimicking liposomes than at the surfaces of liposomes designed to mimic other organelles. Thermodynamic analyses revealed that the G-rich oligonucleotides adopted an extended structure at the liposome surface, whereas in solution the compact G-quadruplex was formed. Our data suggest that changes in structure and stability of nucleic acids regulate biological reactions at membrane surfaces.
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Affiliation(s)
- Smritimoy Pramanik
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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29
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Werz E, Rosemeyer H. Specific DNA duplex formation at an artificial lipid bilayer: fluorescence microscopy after Sybr Green I staining. Beilstein J Org Chem 2014; 10:2307-21. [PMID: 25298798 PMCID: PMC4187062 DOI: 10.3762/bjoc.10.240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/16/2014] [Indexed: 12/23/2022] Open
Abstract
The article describes the immobilization of different probe oligonucleotides (4, 7, 10) carrying each a racemic mixture of 2,3-bis(hexadecyloxy)propan-1-ol (1a) at the 5'-terminus on a stable artificial lipid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). The bilayer separates two compartments (cis/trans channel) of an optical transparent microfluidic sample carrier with perfusion capabilities. Injection of unlabeled target DNA sequences (6, 8, or 9), differing in sequence and length, leads in the case of complementarity to the formation of stable DNA duplexes at the bilayer surface. This could be verified by Sybr Green I double strand staining, followed by incubation periods and thorough perfusions, and was visualized by single molecule fluorescence spectroscopy and microscopy. The different bilayer-immobilized complexes consisting of various DNA duplexes and the fluorescent dye were studied with respect to the kinetics of their formation as well as to their stability against perfusion.
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Affiliation(s)
- Emma Werz
- Organic Materials Chemistry and Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany ; Ionovation GmbH, Westerbreite 7 (CUT), D-49084 Osnabrück, Germany
| | - Helmut Rosemeyer
- Organic Materials Chemistry and Bioorganic Chemistry, Institute of Chemistry of New Materials, University of Osnabrück, Barbarastr. 7, D-49069 Osnabrück, Germany
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30
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Kumar YP, Das RN, Kumar S, Schütte OM, Steinem C, Dash J. Triazole-tailored guanosine dinucleosides as biomimetic ion channels to modulate transmembrane potential. Chemistry 2014; 20:3023-8. [PMID: 24677317 DOI: 10.1002/chem.201304530] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/17/2014] [Indexed: 11/09/2022]
Abstract
A “click” ion channel platform has been established by employing a clickable guanosine azide or alkyne with covalent spacers. The resulting guanosine derivatives modulated the traffic of ions across the phospholipid bilayer, exhibiting a variation in conductance spanning three orders of magnitude (pS to nS). Förster resonance energy transfer studies of the dansyl fluorophore with the membrane binding fluorophore Nile red revealed that the dansyl fluorophore is deeply embedded in the phospholipid bilayer. Complementary cytosine can inhibit the conductance of the supramolecular guanosine channels in the phospholipid bilayers.
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31
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Makishi S, Shibata T, Okazaki M, Dohno C, Nakatani K. Modulation of binding properties of amphiphilic DNA containing multiple dodecyl phosphotriester linkages to lipid bilayer membrane. Bioorg Med Chem Lett 2014; 24:3578-81. [DOI: 10.1016/j.bmcl.2014.05.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/10/2014] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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32
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Langecker M, Arnaut V, List J, Simmel FC. DNA nanostructures interacting with lipid bilayer membranes. Acc Chem Res 2014; 47:1807-15. [PMID: 24828105 DOI: 10.1021/ar500051r] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: DNA has been previously shown to be useful as a material for the fabrication of static nanoscale objects, and also for the realization of dynamic molecular devices and machines. In many cases, nucleic acid assemblies directly mimic biological structures, for example, cytoskeletal filaments, enzyme scaffolds, or molecular motors, and many of the applications envisioned for such structures involve the study or imitation of biological processes, and even the interaction with living cells and organisms. An essential feature of biological systems is their elaborate structural organization and compartmentalization, and this most often involves membranous structures that are formed by dynamic assemblies of lipid molecules. Imitation of or interaction with biological systems using the tools of DNA nanotechnology thus ultimately and necessarily also involves interactions with lipid membrane structures, and thus the creation of DNA-lipid hybrid assemblies. Due to their differing chemical nature, however, highly charged nucleic acids and amphiphilic lipids do not seem the best match for the construction of such systems, and in fact they are rarely found in nature. In recent years, however, a large variety of lipid-interacting DNA conjugates were developed, which are now increasingly being applied also for the realization of DNA nanostructures interacting with lipid bilayer membranes. In this Account, we will present the current state of this emerging class of nanosystems. After a brief overview of the basic biophysical and biochemical properties of lipids and lipid bilayer membranes, we will discuss how DNA molecules can interact with lipid membranes through electrostatic interactions or via covalent modification with hydrophobic moieties. We will then show how such DNA-lipid interactions have been utilized for the realization of DNA nanostructures attached to or embedded within lipid bilayer membranes. Under certain conditions, DNA nanostructures remain mobile on membranes and can dynamically associate into higher order complexes. Hydrophobic modification of DNA nanostructures can further result in intra- or intermolecular aggregation, which can also be utilized as a structural switching mechanism. Appropriate design and chemical modification even allows insertion of DNA nanostructures into lipid bilayer membranes, resulting in artificial ion channel mimics made from DNA. Interactions of DNA nanodevices with living cells also involve interactions with membrane structures. DNA-based nanostructures can be directed to cell surfaces via antibody-antigen interactions, and their cellular uptake can be stimulated by modification with appropriate receptor ligands. In the future, membrane-embedded DNA nanostructures are expected to find application in diverse areas ranging from basic biological research over nanotechnology to synthetic biology.
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Affiliation(s)
- Martin Langecker
- Physics
Department − E14 and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Vera Arnaut
- Physics
Department − E14 and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Jonathan List
- Physics
Department − E14 and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Friedrich C. Simmel
- Physics
Department − E14 and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- Nanosystems Initiative
Munich, Schellingstr. 4, 80539 Munich, Germany
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33
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Schade M, Berti D, Huster D, Herrmann A, Arbuzova A. Lipophilic nucleic acids--a flexible construction kit for organization and functionalization of surfaces. Adv Colloid Interface Sci 2014; 208:235-51. [PMID: 24650567 DOI: 10.1016/j.cis.2014.02.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/26/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022]
Abstract
Lipophilic nucleic acids have become a versatile tool for structuring and functionalization of lipid bilayers and biological membranes as well as cargo vehicles to transport and deliver bioactive compounds, like interference RNA, into cells by taking advantage of reversible hybridization with complementary strands. This contribution reviews the different types of conjugates of lipophilic nucleic acids, and their physicochemical and self-assembly properties. Strategies for choosing a nucleic acid, lipophilic modification, and linker are discussed. Interaction with lipid membranes and its stability, dynamic structure and assembly of lipophilic nucleic acids upon embedding into biological membranes are specific points of the review. A large diversity of conjugates including lipophilic peptide nucleic acid and siRNA provides tailored solutions for specific applications in bio- and nanotechnology as well as in cell biology and medicine, as illustrated through some selected examples.
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Affiliation(s)
- Matthias Schade
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany
| | - Debora Berti
- Dipartimento di Chimica, Universita' di Firenze & CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Daniel Huster
- Universität Leipzig, Institut für Medizinische Physik und Biophysik, Härtelstr. 16-18, 04107 Leipzig, Germany
| | - Andreas Herrmann
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany
| | - Anna Arbuzova
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstr. 42, 10115 Berlin, Germany.
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34
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Application of nucleic acid-lipid conjugates for the programmable organisation of liposomal modules. Adv Colloid Interface Sci 2014; 207:290-305. [PMID: 24461711 DOI: 10.1016/j.cis.2013.12.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 11/29/2013] [Accepted: 12/19/2013] [Indexed: 01/06/2023]
Abstract
We present a critical review of recent work related to the assembly of multicompartment liposome clusters using nucleic acids as a specific recognition unit to link liposomal modules. The asymmetry in nucleic acid binding to its non-self complementary strand allows the controlled association of different compartmental modules into composite systems. These biomimetic multicompartment architectures could have future applications in chemical process control, drug delivery and synthetic biology. We assess the different methods of anchoring DNA to lipid membrane surfaces and discuss how lipid and DNA properties can be tuned to control the morphology and properties of liposome superstructures. We consider different methods for chemical communication between the contents of liposomal compartments within these clusters and assess the progress towards making this chemical mixing efficient, switchable and chemically specific. Finally, given the current state of the art, we assess the outlook for future developments towards functional modular networks of liposomes.
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35
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Serien D, Grimm C, Liebscher J, Herrmann A, Arbuzova A. DNA-controlled aggregation of virus like particles – mimicking a tetherin-like mechanism. NEW J CHEM 2014. [DOI: 10.1039/c4nj00724g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lipophilic DNA with two α-tocopherol anchors, mimicking tetherin, a cell protein reducing spreading of viruses, induces aggregation of virus-like particles.
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Affiliation(s)
- Daniela Serien
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
- The University of Tokyo
- Institute of Industrial Science
| | - Christiane Grimm
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
| | - Jürgen Liebscher
- Humboldt-Universität zu Berlin
- Institut für Chemie
- 12489 Berlin, Germany
- National Institute of Research and Development for Isotopic and Molecular Technologies
- Cluj-Napoca, Romania
| | - Andreas Herrmann
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
| | - Anna Arbuzova
- Humboldt-Universität zu Berlin
- Institut für Biologie
- 10115 Berlin, Germany
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36
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Huster D. Solid-state NMR spectroscopy to study protein-lipid interactions. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:1146-60. [PMID: 24333800 DOI: 10.1016/j.bbalip.2013.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 12/22/2022]
Abstract
The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K(+) channel KcsA are discussed. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.
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37
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Edwardson TGW, Carneiro KMM, McLaughlin CK, Serpell CJ, Sleiman HF. Site-specific positioning of dendritic alkyl chains on DNA cages enables their geometry-dependent self-assembly. Nat Chem 2013; 5:868-75. [DOI: 10.1038/nchem.1745] [Citation(s) in RCA: 172] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 07/29/2013] [Indexed: 12/22/2022]
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38
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Köstler K, Werz E, Malecki E, Montilla-Martinez M, Rosemeyer H. Nucleoterpenes of thymidine and 2'-deoxyinosine: synthons for a biomimetic lipophilization of oligonucleotides. Chem Biodivers 2013; 10:39-61. [PMID: 23341207 DOI: 10.1002/cbdv.201100338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Indexed: 01/01/2023]
Abstract
2'-Deoxyinosine (1) and thymidine (7) were N-alkylated with geranyl and farnesyl moieties. These hydrophobic derivatives, 3a and 3b, and 9a and 9b, respectively, represent the first synthetic biomimetic nucleoterpenes and were subsequently 5'-protected and converted into the corresponding 3'-O-phosphoramidites, 5a and 5b and 11a and 11b, respectively. The latter were used to prepare a series of lipophilized oligonucleotide dodecamers, a part of which were additionally labelled with indocarbocyanine fluorescent dyes (Cy3 or Cy5), 18-23. The insertion of the lipooligonucleotides into, as well as duplex formation at artificial lipid bilayers was studied by single-molecule fluorescence spectroscopy and fluorescence microscopy.
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Affiliation(s)
- Karl Köstler
- Organic Chemistry I - Bioorganic Chemistry, Institute of Chemistry of New Materials, Fachbereich Biologie/Chemie, University of Osnabrück, Barbarastrasse 7, D-49076 Osnabrück, Germany
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39
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Keller R, Kwak M, de Vries JW, Sawaryn C, Wang J, Anaya M, Müllen K, Butt HJ, Herrmann A, Berger R. Properties of amphiphilic oligonucleotide films at the air/water interface and after film transfer. Colloids Surf B Biointerfaces 2013; 111:439-45. [PMID: 23859875 DOI: 10.1016/j.colsurfb.2013.06.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/11/2013] [Accepted: 06/12/2013] [Indexed: 10/26/2022]
Abstract
The self-assembly of amphiphilic hybrid materials containing an oligonucleotide sequence at the air/water interface was investigated by means of pressure-molecular area (Π-A) isotherms. In addition, films were transferred onto solid substrates and imaged using scanning force microscopy. We used oligonucleotide molecules with lipid tails, which consisted of a single stranded oligonucleotide 11 mer containing two hydrophobically modified 5-(dodec-1-ynyl)uracil nucleobases (dU11) at the 5'-end of the oligonucleotide sequence. The air/water interface was used as confinement for the self-assembling process of dU11. Scanning force microscopy of films transferred via Langmuir-Blodgett technique revealed mono-, bi- (Π ≥ 2 mN/m) and multilayer formation (Π ≥ 30 mN/m). The first layer was 1.6 ± 0.1 nm thick. It was oriented with the hydrophilic oligonucleotide moiety facing the hydrophilic substrate while the hydrophobic alkyl chains faced air. In the second layer the oligonucleotide moiety was found to face the air. The second layer was found to cover up to 95% of the sample area. Our measurements indicated that the rearrangement of the molecules into bi- and multiple bilayers happened already at the air/water interface. Similar results were obtained with a second type of oligonucleotide amphiphile, an oligonucleotide block copolymer, which was composed of an oligonucleotide 11 mer covalently attached at the terminus to polypropyleneoxide (PPO).
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Affiliation(s)
- R Keller
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - M Kwak
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - J W de Vries
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - C Sawaryn
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - J Wang
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - M Anaya
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - K Müllen
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - H-J Butt
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - A Herrmann
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - R Berger
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany.
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40
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Suga K, Umakoshi H. Detection of nanosized ordered domains in DOPC/DPPC and DOPC/Ch binary lipid mixture systems of large unilamellar vesicles using a TEMPO quenching method. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4830-8. [PMID: 23506052 DOI: 10.1021/la304768f] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nanosized ordered domains formed in 1,2-dioleoyl-sn-glycero-3-phosphocholine/1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DOPC/DPPC) and DOPC/cholesterol (Ch) liposomes were characterized using a newly developed (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) quenching method. The membrane fluidity of the DOPC/DPPC liposomes, evaluated by the use of 1,6-diphenyl-1,3,5-hexatriene (DPH), increased significantly above their phase-transition temperature. The fluorescence spectra of 6-lauroyl-2-dimethylamino naphthalene (Laurdan) indicated the formation of an immiscible ordered phase in the DOPC/DPPC (50/50) liposomal membrane at 30 °C. The analysis of the membrane polarity indicated that the surface of the liquid-disordered phase was hydrated whereas that of the ordered phase was dehydrated. DOPC/DPPC and DOPC/Ch (70/30) liposomes exhibited heterogeneous membranes, indicating that nanosized ordered domains formed on the surface of the DOPC/DPPC liposomes. The size of these nanosized ordered domains was estimated using the TEMPO quenching method. Because TEMPO can quench DPH distributed in the disordered phases, the remaining fluorescence from DPH is proportional to the size of the ordered domain. The domain sizes calculated for DOPC/DPPC (50/50), DOPC/DPPC (25/75), DOPC/Ch (70/30), and DOPC/DPPC/Ch (40/40/20) were 13.9, 36.2, 13.2, and 35.5 Å, respectively.
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Affiliation(s)
- Keishi Suga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
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41
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Schade M, Knoll A, Vogel A, Seitz O, Liebscher J, Huster D, Herrmann A, Arbuzova A. Remote control of lipophilic nucleic acids domain partitioning by DNA hybridization and enzymatic cleavage. J Am Chem Soc 2012; 134:20490-7. [PMID: 23163619 DOI: 10.1021/ja309256t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Lateral partitioning of lipid-modified molecules between liquid-disordered (ld) and liquid-ordered (lo) domains depends on the type of lipid modification, presence of a spacer, membrane composition, and temperature. Here, we show that the lo domain partitioning of the palmitoylated peptide nucleic acid (PNA) can be influenced by formation of a four-component complex with the ld domain partitioning tocopherol-modified DNA: the PNA-DNA complex partitioned into the ld domains. Enzymatic cleavage of the DNA linker led to the disruption of the complex and restored the initial distribution of the lipophilic nucleic acids into the respective domains. This modular system offers strategies for dynamic functionalization of biomimetic surfaces, for example, in nanostructuring and regulation of enzyme catalysis, and it provides a tool to study the molecular basis of controlled reorganization of lipid-modified proteins in membranes, for example, during signal transduction.
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Affiliation(s)
- Matthias Schade
- Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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42
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Montis C, Milani S, Berti D, Baglioni P. Complexes of nucleolipid liposomes with single-stranded and double-stranded nucleic acids. J Colloid Interface Sci 2012; 373:57-68. [DOI: 10.1016/j.jcis.2011.10.058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/18/2011] [Accepted: 10/22/2011] [Indexed: 01/10/2023]
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43
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Raouane M, Desmaële D, Urbinati G, Massaad-Massade L, Couvreur P. Lipid conjugated oligonucleotides: a useful strategy for delivery. Bioconjug Chem 2012; 23:1091-104. [PMID: 22372953 DOI: 10.1021/bc200422w] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Oligonucleotides, including antisense oligonucleotides and siRNA, are promising therapeutic agents against a variety of diseases. Effective delivery of these molecules is critical in view of their clinical application. Therefore, cation-based nanoplexes have been developed to improve the stability as well as the intracellular penetration of these short fragments of nucleic acids. However, this approach is clearly limited by the strong interaction with proteins after administration and by the inherent toxicity of these positively charged transfection materials. Neutral lipid-oligonucleotide conjugates have become a subject of considerable interest to improve the safe delivery of oligonucleotides. These molecules have been chemically conjugated to hydrophobic moieties such as cholesterol, squalene, or fatty acids to enhance their pharmacokinetic behavior and trans-membrane delivery. The present review gives an account of the main synthetic methods available to conjugate lipids to oligonucleotides and will discuss the pharmacological efficacy of this approach.
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Affiliation(s)
- Mouna Raouane
- Laboratoire de physicochimie, Pharmacotechnie et biopharmacie, UMR CNRS 8612, Université Paris Sud 11 , Faculté de pharmacie, 5 rue J. B. Clément, 92296 Châtenay-Malabry, France
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44
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Amado E, Kressler J. Interactions of amphiphilic block copolymers with lipid model membranes. Curr Opin Colloid Interface Sci 2011. [DOI: 10.1016/j.cocis.2011.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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45
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Brodersen N, Arbuzova A, Herrmann A, Egger H, Liebscher J. Synthesis of novel amphiphilic conjugates with a biological recognition function for developing targeted triggered liposomal delivery systems. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.07.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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46
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Goldenbogen B, Brodersen N, Gramatica A, Loew M, Liebscher J, Herrmann A, Egger H, Budde B, Arbuzova A. Reduction-sensitive liposomes from a multifunctional lipid conjugate and natural phospholipids: reduction and release kinetics and cellular uptake. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:10820-10829. [PMID: 21819046 DOI: 10.1021/la201160y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The development of targeted and triggerable delivery systems is of high relevance for anticancer therapies. We report here on reduction-sensitive liposomes composed of a novel multifunctional lipidlike conjugate, containing a disulfide bond and a biotin moiety, and natural phospholipids. The incorporation of the disulfide conjugate into vesicles and the kinetics of their reduction were studied using dansyl-labeled conjugate 1 in using the dansyl fluorescence environmental sensitivity and the Förster resonance energy transfer from dansyl to rhodamine-labeled phospholipids. Cleavage of the disulfide bridge (e.g., by tris(2-carboxyethyl)phosphine (TCEP), dithiothreitol (DTT), l-cysteine, or glutathione (GSH)) removed the hydrophilic headgroup of the conjugate and thus changed the membrane organization leading to the release of entrapped molecules. Upon nonspecific uptake of vesicles by macrophages, calcein release from reduction-sensitive liposomes consisting of the disulfide conjugate and phospholipids was more efficient than from reduction-insensitive liposomes composed only of phospholipids. The binding of streptavidin to the conjugates did not interfere with either the subsequent reduction of the disulfide bond of the conjugate or the release of entrapped molecules. Breast cancer cell line BT-474, overexpressing the HER2 receptor, showed a high uptake of the reduction-sensitive doxorubicin-loaded liposomes functionalized with the biotin-tagged anti-HER2 antibody. The release of the entrapped cargo inside the cells was observed, implying the potential of using our system for active targeting and delivery.
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Affiliation(s)
- Björn Goldenbogen
- Institute of Biology/Molecular Biophysics, Humboldt-University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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47
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Patwa A, Gissot A, Bestel I, Barthélémy P. Hybrid lipid oligonucleotide conjugates: synthesis, self-assemblies and biomedical applications. Chem Soc Rev 2011; 40:5844-54. [PMID: 21611637 DOI: 10.1039/c1cs15038c] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hybrid lipid oligonucleotide conjugates are finding more and more biotechnological applications. This short critical review highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology (111 references).
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Affiliation(s)
- Amit Patwa
- Université Bordeaux Segalen, Bordeaux, F-33076, France
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48
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Comparative study of liponucleosides in Langmuir monolayers as cell membrane models. Biophys Chem 2011; 153:154-8. [DOI: 10.1016/j.bpc.2010.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 10/20/2010] [Accepted: 10/22/2010] [Indexed: 11/19/2022]
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49
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Loew M, Springer R, Scolari S, Altenbrunn F, Seitz O, Liebscher J, Huster D, Herrmann A, Arbuzova A. Lipid domain specific recruitment of lipophilic nucleic acids: a key for switchable functionalization of membranes. J Am Chem Soc 2010; 132:16066-72. [PMID: 20964327 DOI: 10.1021/ja105714r] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lipid domains in mammalian plasma membranes serve as platforms for specific recruitment or separation of proteins involved in various functions. Here, we have applied this natural strategy of lateral separation to functionalize lipid membranes at micrometer scale in a switchable and reversible manner. Membrane-anchored peptide nucleic acid and DNA, differing in their lipophilic moieties, partition into different lipid domains in model and biological membranes. Separation was visualized by hybridization with the respective complementary fluorescently labeled DNA strands. Upon heating, domains vanished, and both lipophilic nucleic acid structures intermixed with each other. Reformation of the lipid domains by cooling led again to separation of membrane-anchored nucleic acids. By linking appropriate structures/functions to complementary strands, this approach offers a reversible tool for triggering interactions among the structures and for the arrangement of reactions and signaling cascades on biomimetic surfaces.
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Affiliation(s)
- Martin Loew
- Institute of Biology/Biophysics, Humboldt-University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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50
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Gambinossi F, Banchelli M, Durand A, Berti D, Brown T, Caminati G, Baglioni P. Modulation of density and orientation of amphiphilic DNA anchored to phospholipid membranes. I. Supported lipid bilayers. J Phys Chem B 2010; 114:7338-47. [PMID: 20446700 DOI: 10.1021/jp100730x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the present series of papers, we describe the results of a systematic study on the anchoring of cholesterol-tagged oligonucleotides to phospholipids bilayers followed by membrane-assisted hybridization of the complementary strand in solution. This paper describes the anchoring of novel cholesterol-modified DNA-18mers in supported lipid bilayers (SLB) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine: we compared the behavior of two anchoring functionalities differing in the number of cholesterol units and in the length of a spacer group. Quartz Crystal Microbalance with impedance monitoring (QCM-Z) measurements showed that both oligonucleotides insert into the bilayer membrane through cholesterol anchoring; however, dramatic differences, in terms of surface organization and thickness, are found as the number of anchoring units increases. In the case of multiple cholesterol units, a peculiar three-regimes concentration dependence was revealed and correlated to the effective size of the adsorbing units. Interestingly, for high oligonucleotide concentration, the adsorption process was rationalized in terms of a compaction model of amphiphilic DNA molecules. QCM-Z temperature cycles of the SLB-anchored double strands provided clear evidence for reversible hybridization at the bilayer interface.
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Affiliation(s)
- Filippo Gambinossi
- Department of Chemistry and CSGI, University of Florence, via della Lastruccia 3-Sesto Fiorentino, 50019 Florence, Italy
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