51
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Thomsen RP, Malle MG, Okholm AH, Krishnan S, Bohr SSR, Sørensen RS, Ries O, Vogel S, Simmel FC, Hatzakis NS, Kjems J. A large size-selective DNA nanopore with sensing applications. Nat Commun 2019; 10:5655. [PMID: 31827087 PMCID: PMC6906287 DOI: 10.1038/s41467-019-13284-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/29/2019] [Indexed: 01/17/2023] Open
Abstract
Transmembrane nanostructures like ion channels and transporters perform key biological functions by controlling flow of molecules across lipid bilayers. Much work has gone into engineering artificial nanopores and applications in selective gating of molecules, label-free detection/sensing of biomolecules and DNA sequencing have shown promise. Here, we use DNA origami to create a synthetic 9 nm wide DNA nanopore, controlled by programmable, lipidated flaps and equipped with a size-selective gating system for the translocation of macromolecules. Successful assembly and insertion of the nanopore into lipid bilayers are validated by transmission electron microscopy (TEM), while selective translocation of cargo and the pore mechanosensitivity are studied using optical methods, including single-molecule, total internal reflection fluorescence (TIRF) microscopy. Size-specific cargo translocation and oligonucleotide-triggered opening of the pore are demonstrated showing that the DNA nanopore can function as a real-time detection system for external signals, offering potential for a variety of highly parallelized sensing applications.
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Affiliation(s)
- Rasmus P Thomsen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, 8000, Denmark
| | - Mette Galsgaard Malle
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Universitetsparken 5, Copenhagen, 2100, Denmark.,Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Anders Hauge Okholm
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, 8000, Denmark.,Arla Innovation Centre, Agro Food Park 19, 8200, Aarhus N, Denmark
| | - Swati Krishnan
- Physics Department and ZNN/WSI, Technische Universität München, 85748, Garching, Germany
| | - Søren S-R Bohr
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Universitetsparken 5, Copenhagen, 2100, Denmark.,Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | | | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Friedrich C Simmel
- Physics Department and ZNN/WSI, Technische Universität München, 85748, Garching, Germany
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Center, University of Copenhagen, Universitetsparken 5, Copenhagen, 2100, Denmark. .,Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus C, 8000, Denmark. .,Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark.
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52
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SU YY, LI CY, LI D. Progress in Membrane Fusion and Its Application in Drug Delivery. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61202-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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53
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Jia H, Schwille P. Bottom-up synthetic biology: reconstitution in space and time. Curr Opin Biotechnol 2019; 60:179-187. [DOI: 10.1016/j.copbio.2019.05.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 05/07/2019] [Indexed: 01/30/2023]
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54
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Löffler PMG, Ries O, Vogel S. DNA-Mediated Liposome Fusion Observed by Fluorescence Spectrometry. Methods Mol Biol 2019; 2063:101-118. [PMID: 31667766 DOI: 10.1007/978-1-0716-0138-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
DNA-programmed and controlled fusion of lipid membranes have recently been optimized to reliably mix the contents between two populations of liposomes, each functionalized with complementary lipidated DNA (LiNA) oligomer. In this chapter we describe a procedure for DNA-controlled fusion of liposomes mediated by LiNAs that are designed to force bilayers into close proximity. Using a self-quenching fluorescent dye (Sulforhodamine B) to monitor both the mixing of the internal volumes and leakage of the dye into the outer volume we measure the efficiency of content mixing in the bulk population, allowing for direct comparison between different LiNA designs. By generating samples for calibration corresponding to different amounts of content mixing, the average number of fusion events per labeled liposome can be estimated.
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Affiliation(s)
- Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark.
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55
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Peruzzi JA, Jacobs ML, Vu TQ, Wang KS, Kamat NP. Barcoding Biological Reactions with DNA‐Functionalized Vesicles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911544] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering Northwestern University USA
| | - Miranda L. Jacobs
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Timothy Q. Vu
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Kenneth S. Wang
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Neha P. Kamat
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
- Center for Synthetic Biology Northwestern University USA
- Chemistry of Life Processes Institute Northwestern University USA
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56
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Löffler PMG, Hansen AH, Ries O, Jakobsen U, Rabe A, Sørensen KT, Glud K, Vogel S. Lipidated Polyaza Crown Ethers as Membrane Anchors for DNA-Controlled Content Mixing between Liposomes. Sci Rep 2019; 9:13856. [PMID: 31554826 PMCID: PMC6761097 DOI: 10.1038/s41598-019-49862-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/23/2019] [Indexed: 01/21/2023] Open
Abstract
The ability to manipulate and fuse nano-compartmentalized volumes addresses a demand for spatiotemporal control in the field of synthetic biology, for example in the bottom-up construction of (bio)chemical nanoreactors and for the interrogation of enzymatic reactions in confined space. Herein, we mix entrapped sub-attoliter volumes of liposomes (~135 nm diameter) via lipid bilayer fusion, facilitated by the hybridization of membrane-anchored lipidated oligonucleotides. We report on an improved synthesis of the membrane-anchor phosphoramidites that allows for a flexible choice of lipophilic moiety. Lipid-nucleic acid conjugates (LiNAs) with and without triethylene glycol spacers between anchor and the 17 nt binding sequence were synthesized and their fusogenic potential evaluated. A fluorescence-based content mixing assay was employed for kinetic monitoring of fusion of the bulk liposome populations at different temperatures. Data obtained at 50 °C indicated a quantitative conversion of the limiting liposome population into fused liposomes and an unprecedently high initial fusion rate was observed. For most conditions and designs only low leakage during fusion was observed. These results consolidate LiNA-mediated membrane fusion as a robust platform for programming compartmentalized chemical and enzymatic reactions.
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Affiliation(s)
- Philipp M G Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Anders Højgaard Hansen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Oliver Ries
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Ulla Jakobsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark.,PET & Cyclotron Unit, Department of Nuclear Medicine, Odense University Hospital, Sdr. Boulevard 29, 5000, Odense C, Denmark
| | - Alexander Rabe
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Kristian T Sørensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Kasper Glud
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark University of Southern Denmark, Odense M, Denmark.
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57
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Stuhr-Hansen N, Vagianou CD, Blixt O. Clustering of Giant Unilamellar Vesicles Promoted by Covalent and Noncovalent Bonding of Functional Groups at Membrane-Embedded Peptides. Bioconjug Chem 2019; 30:2156-2164. [DOI: 10.1021/acs.bioconjchem.9b00394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Nicolai Stuhr-Hansen
- Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Charikleia-Despoina Vagianou
- Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Ola Blixt
- Department of Chemistry, Chemical Biology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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58
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Hu Y, Niemeyer CM. From DNA Nanotechnology to Material Systems Engineering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1806294. [PMID: 30767279 DOI: 10.1002/adma.201806294] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/29/2018] [Indexed: 05/25/2023]
Abstract
In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.
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Affiliation(s)
- Yong Hu
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 1), Hermann-von-Helmholtz-Platz 1, D-76344, Eggenstein-Leopoldshafen, Germany
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59
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Interaction of SNARE Mimetic Peptides with Lipid bilayers: Effects of Secondary Structure, Bilayer Composition and Lipid Anchoring. Sci Rep 2019; 9:7708. [PMID: 31118479 PMCID: PMC6531448 DOI: 10.1038/s41598-019-43418-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/18/2019] [Indexed: 12/24/2022] Open
Abstract
The coiled-coil forming peptides 'K' enriched in lysine and 'E' enriched in glutamic acid have been used as a minimal SNARE mimetic system for membrane fusion. Here we describe atomistic molecular dynamics simulations to characterize the interactions of these peptides with lipid bilayers for two different compositions. For neutral phosphatidylcholine (PC)/phosphatidylethanolamine (PE) bilayers the peptides experience a strong repulsive barrier against adsorption, also observed in potential of mean force (PMF) profiles calculated with umbrella sampling. For peptide K, a minimum of -12 kBT in the PMF provides an upper bound for the binding free energy whereas no stable membrane bound state could be observed for peptide E. In contrast, the electrostatic interactions with negatively charged phosphatidylglycerol (PG) lipids lead to fast adsorption of both peptides at the head-water interface. Experimental data using fluorescently labeled peptides confirm the stronger binding to PG containing bilayers. Lipid anchors have little effect on the peptide-bilayer interactions or peptide structure, when the peptide also binds to the bilayer in the absence of a lipid anchor. For peptide E, which does not bind to the PC bilayer without a lipid anchor, the presence of such an anchor strengthens the electrostatic interactions between the charged side chains and the zwitterionic head-groups and leads to a stabilization of the peptide's helical fold by the membrane.
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60
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Daudey G, Schwieger C, Rabe M, Kros A. Influence of Membrane-Fusogen Distance on the Secondary Structure of Fusogenic Coiled Coil Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5501-5508. [PMID: 30908063 PMCID: PMC6484379 DOI: 10.1021/acs.langmuir.8b04195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Liposomal membrane fusion is an important tool to study complex biological fusion mechanisms. We use lipidated derivatives of the specific heterodimeric coiled coil pair E: (EIAALEK)3 and K: (KIAALKE)3 to study and control the fusion of liposomes. In this model system, peptides are tethered to their liposomes via a poly(ethylene glycol) (PEG) spacer and a lipid anchor. The efficiency of the fusion mechanism and function of the peptides is highly affected by the PEG-spacer length and the lipid anchor type. Here, the influence of membrane-fusogen distance on the peptide-membrane interactions and the peptide secondary structures is studied with Langmuir film balance and infrared reflection absorption spectroscopy. We found that the introduction of a spacer to monolayer-tethered peptide E changes its conformation from solvated random coils to homo-oligomers. In contrast, the described peptide-monolayer interaction of peptide K is not affected by the PEG-spacer length. Furthermore, the coexistence of different conformations when both lipopeptides E and K are present at the membrane surface is demonstrated empirically, which has many implications for the design of effective fusogenic recognition units and the field of artificial membrane fusion.
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Affiliation(s)
| | | | - Martin Rabe
- Department
of Interface Chemistry and Surface Engineering, Max-Planck-Institut für Eisenforschung GmbH, 40237 Düsseldorf, Germany
| | - Alexander Kros
- Supramolecular
and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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61
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Whitehouse WL, Noble JE, Ryadnov MG, Howorka S. Cholesterol Anchors Enable Efficient Binding and Intracellular Uptake of DNA Nanostructures. Bioconjug Chem 2019; 30:1836-1844. [PMID: 30821443 DOI: 10.1021/acs.bioconjchem.9b00036] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA nanostructures constitute a rapidly advancing tool-set for exploring cell-membrane functions and intracellular sensing or advancing delivery of biomolecular cargo into cells. Chemical conjugation with lipid anchors can mediate binding of DNA nanostructures to synthetic lipid bilayers, yet how such structures interact with biological membranes and internalize cells has not been shown. Here, an archetypal 6-duplex nanobundle is used to investigate how lipid conjugation influences DNA cell binding and internalization kinetics. Cellular interactions of DNA nanobundles modified with one and three cholesterol anchors were assessed using flow cytometry and confocal microscopy. Nuclease digestion was used to distinguish surface-bound DNA, which is nuclease accessible, from internalized DNA. Three cholesterol anchors were found to enhance cellular association by up to 10-fold when compared with unmodified DNA. The bundles were endocytosed efficiently within 24 h. The results can help design controlled DNA binding and trafficking into cells.
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Affiliation(s)
- William L Whitehouse
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - James E Noble
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Stefan Howorka
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
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62
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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63
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Vybornyi M, Vyborna Y, Häner R. DNA-inspired oligomers: from oligophosphates to functional materials. Chem Soc Rev 2019; 48:4347-4360. [DOI: 10.1039/c8cs00662h] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Replacement of the natural nucleotides in DNA by non-nucleosidic building blocks leads to phosphodiester-linked oligomers with a high functional diversity.
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Affiliation(s)
- Mykhailo Vybornyi
- Laboratoire de Biochimie (LBC)
- ESPCI Paris
- PSL Research University
- CNRS UMR8231 Chimie Biologie Innovation
- 75005 Paris
| | - Yuliia Vyborna
- Sorbonne Université
- Laboratoire Jean Perrin
- 75005 Paris
- France
| | - Robert Häner
- Department of Chemistry and Biochemistry
- University of Bern
- Freiestrasse 3
- Switzerland
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64
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Arnott PM, Joshi H, Aksimentiev A, Howorka S. Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15084-15092. [PMID: 30350681 PMCID: PMC6458106 DOI: 10.1021/acs.langmuir.8b02271] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Lipid-anchored DNA can attach functional cargo to bilayer membranes in DNA nanotechnology, synthetic biology, and cell biology research. To optimize DNA anchoring, an understanding of DNA-membrane interactions in terms of binding strength, extent, and structural dynamics is required. Here we use experiments and molecular dynamics (MD) simulations to determine how the membrane binding of cholesterol-modified DNA depends on electrostatic and steric factors involving the lipid headgroup charge, duplexed or single-stranded DNA, and the buffer composition. The experiments distinguish between free and membrane vesicle-bound DNA and thereby reveal the surface density of anchored DNA and its binding affinity, something which had previously not been known. The Kd values range from 8.5 ± 4.9 to 466 ± 134 μM whereby negatively charged headgroups led to weak binding due to the electrostatic repulsion with respect to the negatively charged DNA. Atomistic MD simulations explain the findings and elucidate the dynamic nature of anchored DNA such as the mushroom-like conformation of single-stranded DNA hovering over the bilayer surface in contrast to a straight-up conformation of double-stranded DNA. The biophysical insight into the binding strength to membranes as well as the molecular accessibility of DNA for hybridization to molecular cargo is expected to facilitate the creation of biomimetic DNA versions of natural membrane nanopores and cytoskeletons for research and nanobiotechnology.
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Affiliation(s)
- Patrick M Arnott
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - Himanshu Joshi
- Department of Physics, and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Aleksei Aksimentiev
- Department of Physics, and Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
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65
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Lopez A, Liu J. DNA Oligonucleotide-Functionalized Liposomes: Bioconjugate Chemistry, Biointerfaces, and Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15000-15013. [PMID: 29936848 DOI: 10.1021/acs.langmuir.8b01368] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Interfacing DNA with liposomes has produced a diverse range of programmable soft materials, devices, and drug delivery vehicles. By simply controlling liposomal composition, bilayer fluidity, lipid domain formation, and surface charge can be systematically varied. Recent development in DNA research has produced not only sophisticated nanostructures but also new functions including ligand binding and catalysis. For noncationic liposomes, a DNA is typically covalently linked to a hydrophobic or lipid moiety that can be inserted into lipid membranes. In this article, we discuss fundamental biointerfaces formed between DNA and noncationic liposomes. The methods to prepare such conjugates and the interactions at the membrane interfaces are also discussed. The effect of DNA lateral diffusion on fluid bilayer membranes and the effect of membrane on DNA assembly are emphasized. DNA hybridization can be programmed to promote fusion of lipid membranes. Representative applications of this conjugate for drug delivery, biosensor development, and directed assembly of materials are briefly described toward the end. Some future research directions are also proposed to further understand this biointerface.
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Affiliation(s)
- Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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66
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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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67
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Pick H, Alves AC, Vogel H. Single-Vesicle Assays Using Liposomes and Cell-Derived Vesicles: From Modeling Complex Membrane Processes to Synthetic Biology and Biomedical Applications. Chem Rev 2018; 118:8598-8654. [PMID: 30153012 DOI: 10.1021/acs.chemrev.7b00777] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The plasma membrane is of central importance for defining the closed volume of cells in contradistinction to the extracellular environment. The plasma membrane not only serves as a boundary, but it also mediates the exchange of physical and chemical information between the cell and its environment in order to maintain intra- and intercellular functions. Artificial lipid- and cell-derived membrane vesicles have been used as closed-volume containers, representing the simplest cell model systems to study transmembrane processes and intracellular biochemistry. Classical examples are studies of membrane translocation processes in plasma membrane vesicles and proteoliposomes mediated by transport proteins and ion channels. Liposomes and native membrane vesicles are widely used as model membranes for investigating the binding and bilayer insertion of proteins, the structure and function of membrane proteins, the intramembrane composition and distribution of lipids and proteins, and the intermembrane interactions during exo- and endocytosis. In addition, natural cell-released microvesicles have gained importance for early detection of diseases and for their use as nanoreactors and minimal protocells. Yet, in most studies, ensembles of vesicles have been employed. More recently, new micro- and nanotechnological tools as well as novel developments in both optical and electron microscopy have allowed the isolation and investigation of individual (sub)micrometer-sized vesicles. Such single-vesicle experiments have revealed large heterogeneities in the structure and function of membrane components of single vesicles, which were hidden in ensemble studies. These results have opened enormous possibilities for bioanalysis and biotechnological applications involving unprecedented miniaturization at the nanometer and attoliter range. This review will cover important developments toward single-vesicle analysis and the central discoveries made in this exciting field of research.
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Affiliation(s)
- Horst Pick
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Horst Vogel
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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Sun L, Gao Y, Wang Y, Wei Q, Shi J, Chen N, Li D, Fan C. Guiding protein delivery into live cells using DNA-programmed membrane fusion. Chem Sci 2018; 9:5967-5975. [PMID: 30079211 PMCID: PMC6050539 DOI: 10.1039/c8sc00367j] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/14/2018] [Indexed: 11/21/2022] Open
Abstract
Intracellular delivery of proteins provides a direct means to manipulate cell function and probe the intracellular environment. However, direct cytoplasmic delivery of proteins suffers from limited availability of efficient toolsets, and thus remains challenging in research and therapeutic applications. Natural biological cargo delivery processes, like SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex mediated membrane fusion and other vesicle fusion in live cells, enable targeted delivery with high efficiency. A surrogate of SNARE machinery represents a new direction in intracellular protein delivery. Here, we report a DNA-programmed membrane fusion strategy for guiding the efficient intracellular delivery of proteins into live cells. The inherent programmability of DNA hybridization provides spatiotemporal control of the fusion between protein-encapsulated liposomes and cell membranes, enabling rapid release of proteins directly into the cytoplasm, while still remaining functional due to the bypassing of the endosomal trap. We further demonstrate that delivered exogenous Cytochrome c effectively regulates the cell fate. Hence, this DNA-mediated fusion strategy holds great potential for protein drug delivery, regenerative medicine and gene editing.
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Affiliation(s)
- Lele Sun
- Division of Physical Biology & Bioimaging Centre , Shanghai Synchrotron Radiation Facility , Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China .
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yanjing Gao
- Division of Physical Biology & Bioimaging Centre , Shanghai Synchrotron Radiation Facility , Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China .
- University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Yaoguang Wang
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong , School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , China
| | - Qin Wei
- Key Laboratory of Chemical Sensing & Analysis in Universities of Shandong , School of Chemistry and Chemical Engineering , University of Jinan , Jinan 250022 , China
| | - Jiye Shi
- Division of Physical Biology & Bioimaging Centre , Shanghai Synchrotron Radiation Facility , Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China .
| | - Nan Chen
- Division of Physical Biology & Bioimaging Centre , Shanghai Synchrotron Radiation Facility , Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China .
| | - Di Li
- Division of Physical Biology & Bioimaging Centre , Shanghai Synchrotron Radiation Facility , Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China .
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200241 , China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Centre , Shanghai Synchrotron Radiation Facility , Key Laboratory of Interfacial Physics and Technology , Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China .
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Göpfrich K, Platzman I, Spatz JP. Mastering Complexity: Towards Bottom-up Construction of Multifunctional Eukaryotic Synthetic Cells. Trends Biotechnol 2018; 36:938-951. [PMID: 29685820 PMCID: PMC6100601 DOI: 10.1016/j.tibtech.2018.03.008] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
With the ultimate aim to construct a living cell, bottom-up synthetic biology strives to reconstitute cellular phenomena in vitro - disentangled from the complex environment of a cell. Recent work towards this ambitious goal has provided new insights into the mechanisms governing life. With the fast-growing library of functional modules for synthetic cells, their classification and integration become increasingly important. We discuss strategies to reverse-engineer and recombine functional parts for synthetic eukaryotes, mimicking the characteristics of nature's own prototype. Particularly, we focus on large outer compartments, complex endomembrane systems with organelles, and versatile cytoskeletons as hallmarks of eukaryotic life. Moreover, we identify microfluidics and DNA nanotechnology as two technologies that can integrate these functional modules into sophisticated multifunctional synthetic cells.
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Affiliation(s)
- Kerstin Göpfrich
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany; Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany.
| | - Ilia Platzman
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany; Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany.
| | - Joachim P Spatz
- Max Planck Institute for Medical Research, Department of Cellular Biophysics, Jahnstraße 29, D 69120, Heidelberg, Germany; Department of Biophysical Chemistry, University of Heidelberg, Im Neuenheimer Feld 253, D 69120 Heidelberg, Germany.
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Rabe A, Löffler PMG, Ries O, Vogel S. Programmable fusion of liposomes mediated by lipidated PNA. Chem Commun (Camb) 2018; 53:11921-11924. [PMID: 29044250 DOI: 10.1039/c7cc06058k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We recently reported a DNA-programmed fusion cascade enabling the use of liposomes as nanoreactors for compartmentalized chemical reactions. This communication reports an alternative and robust strategy based on lipidated peptide nucleic acids (LiPs). LiPs enabled fusion of liposomes with remarkable 31% efficiency at 50 °C with low leakage (5%).
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Affiliation(s)
- A Rabe
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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Peptide-Mediated Liposome Fusion: The Effect of Anchor Positioning. Int J Mol Sci 2018; 19:ijms19010211. [PMID: 29320427 PMCID: PMC5796160 DOI: 10.3390/ijms19010211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/02/2018] [Accepted: 01/08/2018] [Indexed: 11/17/2022] Open
Abstract
A minimal model system for membrane fusion, comprising two complementary peptides dubbed "E" and "K" joined to a cholesterol anchor via a polyethyleneglycol spacer, has previously been developed in our group. This system promotes the fusion of large unilamellar vesicles and facilitates liposome-cell fusion both in vitro and in vivo. Whilst several aspects of the system have previously been investigated to provide an insight as to how fusion is facilitated, anchor positioning has not yet been considered. In this study, the effects of placing the anchor at either the N-terminus or in the center of the peptide are investigated using a combination of circular dichroism spectroscopy, dynamic light scattering, and fluorescence assays. It was discovered that anchoring the "K" peptide in the center of the sequence had no effect on its structure, its ability to interact with membranes, or its ability to promote fusion, whereas anchoring the 'E' peptide in the middle of the sequence dramatically decreases fusion efficiency. We postulate that anchoring the 'E' peptide in the middle of the sequence disrupts its ability to form homodimers with peptides on the same membrane, leading to aggregation and content leakage.
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Ries O, Löffler PMG, Rabe A, Malavan JJ, Vogel S. Efficient liposome fusion mediated by lipid–nucleic acid conjugates. Org Biomol Chem 2017; 15:8936-8945. [DOI: 10.1039/c7ob01939d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Highly efficient fusion and content mixing of liposomes encoded by lipidated oligonucleotides (LiNAs). “Hot fusion of biomembranes” – a low leakage process at elevated temperature.
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Affiliation(s)
- O. Ries
- Biomolecular Nanoscale Engineering Center
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense
| | - P. M. G. Löffler
- Biomolecular Nanoscale Engineering Center
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense
| | - A. Rabe
- Biomolecular Nanoscale Engineering Center
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense
| | - J. J. Malavan
- Biomolecular Nanoscale Engineering Center
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense
| | - Stefan Vogel
- Biomolecular Nanoscale Engineering Center
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense
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