51
|
|
52
|
Journot CA, Ramakrishna V, Wallace MI, Turberfield AJ. Modifying Membrane Morphology and Interactions with DNA Origami Clathrin-Mimic Networks. ACS NANO 2019; 13:9973-9979. [PMID: 31418553 PMCID: PMC6764109 DOI: 10.1021/acsnano.8b07734] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
We describe the triggered assembly of a bioinspired DNA origami meshwork on a lipid membrane. DNA triskelia, three-armed DNA origami nanostructures inspired by the membrane-modifying protein clathrin, are bound to lipid mono- and bilayers using cholesterol anchors. Polymerization of triskelia, triggered by the addition of DNA staples, links triskelion arms to form a mesh. Using transmission electron microscopy, we observe nanoscale local deformation of a lipid monolayer induced by triskelion polymerization that is reminiscent of the formation of clathrin-coated pits. We also show that the polymerization of triskelia bound to lipid bilayers modifies interactions between them, inhibiting the formation of a synapse between giant unilamellar vesicles and a supported lipid bilayer.
Collapse
Affiliation(s)
- Céline
M. A. Journot
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Vivek Ramakrishna
- Department
of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
- London
Centre for Nanotechnology, Strand, London WC2R 2LS, United
Kingdom
| | - Mark I. Wallace
- Department
of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, United Kingdom
- London
Centre for Nanotechnology, Strand, London WC2R 2LS, United
Kingdom
| | - Andrew J. Turberfield
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
- E-mail:
| |
Collapse
|
53
|
Bahrami A, Bahrami AH. Vesicle constriction by rings of Janus nanoparticles and aggregates of curved proteins. NANOTECHNOLOGY 2019; 30:345101. [PMID: 31048566 DOI: 10.1088/1361-6528/ab1ed5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Membrane constriction and associated scission by proteins and nano structures are crucial to many processes in cellular and synthetic biology. We report mechanical constriction of vesicles by rings of adsorbed Janus nanoparticles that represent synthetic nano structures and mimic contractile proteins, and by aggregates of curved crescents that mimic scaffold proteins. Membrane energetics from Monte Carlo simulations and simulated annealing of the elastic membrane model confirms spontaneous vesicle constriction by aggregates of sufficiently-curved crescents of various lengths and by rings of Janus nanoparticles with a variety of ring lengths, particle sizes, and particle area fractions. We show that shorter rings of smaller particles with higher area fractions reinforce the constriction by increasing the energetic drive towards the constricted vesicle with smaller constriction radius. We demonstrate that vesicle constriction by crescent aggregates strongly depends on the crescent curvature. In contrast to aggregates of sufficiently-curved crescents that are capable of inducing full vesicle constriction, those of near flat crescents with negligible curvature leave the vesicle unconstricted. Our results offer promising perspectives for designing membrane-constricting nano structures such as nanoparticle aggregates and clusters of synthetic curved proteins such as DNA origami scaffolds with applications in synthetic biology. Our findings reveal the significant contribution of highly-curved F-BAR domains to cell division and explain how contractile protein rings such as dynamin GTPase, actomyosin rings, and endosomal sorting complexes required for transport constrict the membrane.
Collapse
Affiliation(s)
- Arash Bahrami
- School of Mechanical Engineering, College of Engineering, University of Tehran, North Kargar St., 14399-57131 Tehran, Iran
| | | |
Collapse
|
54
|
Grome M, Zhang Z, Lin C. Stiffness and Membrane Anchor Density Modulate DNA-Nanospring-Induced Vesicle Tubulation. ACS APPLIED MATERIALS & INTERFACES 2019; 11:22987-22992. [PMID: 31252462 PMCID: PMC6613048 DOI: 10.1021/acsami.9b05401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
DNA nanotechnology provides an avenue for the construction of rationally designed artificial assemblages with well-defined and tunable architectures. Shaped to mimic natural membrane-deforming proteins and equipped with membrane anchoring molecules, curved DNA nanostructures can reproduce subcellular membrane remodeling events such as vesicle tubulation in vitro. To systematically analyze how structural stiffness and membrane affinity of DNA nanostructures affect the membrane remodeling outcome, here we build DNA-origami curls with varying thickness and amphipathic peptide density, and have them polymerize into nanosprings on the surface of liposomes. We find that modestly reducing rigidity and maximizing the number of membrane anchors not only promote membrane binding and remodeling but also lead to the formation of lipid tubules with better defined diameters, highlighting the ability of programmable DNA-based constructs to controllably deform the membrane.
Collapse
|
55
|
Kretschmer S, Ganzinger KA, Franquelim HG, Schwille P. Synthetic cell division via membrane-transforming molecular assemblies. BMC Biol 2019; 17:43. [PMID: 31126285 PMCID: PMC6533746 DOI: 10.1186/s12915-019-0665-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Reproduction, i.e. the ability to produce new individuals from a parent organism, is a hallmark of living matter. Even the simplest forms of reproduction require cell division: attempts to create a designer cell therefore should include a synthetic cell division machinery. In this review, we will illustrate how nature solves this task, describing membrane remodelling processes in general and focusing on bacterial cell division in particular. We discuss recent progress made in their in vitro reconstitution, identify open challenges, and suggest how purely synthetic building blocks could provide an additional and attractive route to creating artificial cell division machineries.
Collapse
|
56
|
Shen H, Wang Y, Wang J, Li Z, Yuan Q. Emerging Biomimetic Applications of DNA Nanotechnology. ACS APPLIED MATERIALS & INTERFACES 2019; 11:13859-13873. [PMID: 29939004 DOI: 10.1021/acsami.8b06175] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Re-engineering cellular components and biological processes has received great interest and promised compelling advantages in applications ranging from basic cell biology to biomedicine. With the advent of DNA nanotechnology, the programmable self-assembly ability makes DNA an appealing candidate for rational design of artificial components with different structures and functions. This Forum Article summarizes recent developments of DNA nanotechnology in mimicking the structures and functions of existing cellular components. We highlight key successes in the achievements of DNA-based biomimetic membrane proteins and discuss the assembly behavior of these artificial proteins. Then, we focus on the construction of higher-order structures by DNA nanotechnology to recreate cell-like structures. Finally, we explore the current challenges and speculate on future directions of DNA nanotechnology in biomimetics.
Collapse
Affiliation(s)
- Haijing Shen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Yingqian Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Jie Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Zhihao Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| | - Quan Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan , 430072 , China
| |
Collapse
|
57
|
Idema T, Kraft DJ. Interactions between model inclusions on closed lipid bilayer membranes. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2019.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
58
|
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.
Collapse
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
| |
Collapse
|
59
|
Kempter S, Khmelinskaia A, Strauss MT, Schwille P, Jungmann R, Liedl T, Bae W. Single Particle Tracking and Super-Resolution Imaging of Membrane-Assisted Stop-and-Go Diffusion and Lattice Assembly of DNA Origami. ACS NANO 2019; 13:996-1002. [PMID: 30588792 DOI: 10.1021/acsnano.8b04631] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA nanostructures offer the possibility to mimic functional biological membrane components due to their nanometer-precise shape configurability and versatile biochemical functionality. Here we show that the diffusional behavior of DNA nanostructures and their assembly into higher order membrane-bound lattices can be controlled in a stop-and-go manner and that the process can be monitored with super-resolution imaging. The DNA structures are transiently immobilized on glass-supported lipid bilayers by changing the mono- and divalent cation concentrations of the surrounding buffer. Using DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy, we confirm the fixation of DNA origami structures with different shapes. On mica-supported lipid bilayers, in contrast, we observe residual movement. By increasing the concentration of NaCl and depleting MgCl2, a large fraction of DNA structures restarts to diffuse freely on both substrates. After addition of a set of oligonucleotides that enables three Y-shaped monomers to assemble into a three-legged shape (triskelion), the triskelions can be stopped and super-resolved. Exchanging buffer and adding another set of oligonucleotides triggers the triskelions to diffuse and assemble into hexagonal 2D lattices. This stop-and-go imaging technique provides a way to control and observe the diffusional behavior of DNA nanostructures on lipid membranes that could also lead to control of membrane-associated cargos.
Collapse
Affiliation(s)
- Susanne Kempter
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
| | | | - Maximilian T Strauss
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
- Max Planck Institute of Biochemistry , Martinsried 82152 , Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
| | - Wooli Bae
- Faculty of Physics and Center for NanoScience , Ludwig-Maximilians-Universität , München 80539 , Germany
| |
Collapse
|
60
|
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.
Collapse
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
| |
Collapse
|
61
|
Chidchob P, Offenbartl-Stiegert D, McCarthy D, Luo X, Li J, Howorka S, Sleiman HF. Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions. J Am Chem Soc 2018; 141:1100-1108. [DOI: 10.1021/jacs.8b11898] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Dillon McCarthy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Xin Luo
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| |
Collapse
|
62
|
Wu N, Chen F, Zhao Y, Yu X, Wei J, Zhao Y. Functional and Biomimetic DNA Nanostructures on Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14721-14730. [PMID: 30044097 DOI: 10.1021/acs.langmuir.8b01818] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sophisticated and dynamic membrane-anchored DNA nanostructures were developed to mimic a variety of membrane proteins, which play crucial roles in cellular functions. DNA biomimetic constructions bound on membranes are capable of modulating the morphologies, physical properties, and functions of lipid membranes, via mobility on membranes and/or inherent architectural features. This inspired young field of DNA-lipid-based nanobiomimetic systems is on the foundation of DNA nanotechnology. In this review, we highlight key successes in the development of structural DNA nanotechnology and demonstrate some typical static and dynamic complex DNA nanostructures first. Then, we discuss the biophysical properties of lipid membranes. Primary approaches are shown to attach hydrophilic DNA to hydrophobic lipid membranes. With appropriate designs, membrane-floating DNA nanostructures assemble and disassemble on membranes, modulated by external stimuluses. The aggregation of DNA nanostructures could influence the physical properties of lipid membranes. We also summarize artificial nanochannels made of DNA, analogous to transmembrane proteins. Transformations of DNA nanopores might be achieved under certain conditions and realize the transport of small molecules across membranes. Next, we focus on membrane-shaping functions of membrane-anchored DNA nanostructures. Curvature of the membrane is closely related to the rich diversity of cellular functions. Mimicking membrane-sculpting proteins, such as BAR family domains and SNARE proteins etc., DNA biomimetic nanostructures induce the transformations of lipid membranes and modulate membrane adhesion and membrane fusion processes. Although recent studies in DNA nanostructure-lipid membrane biomimetic nanosystems have made great progress, this field is still facing many challenges. In the future, the designs of more elaborated DNA architectures will be explored. Sophisticated dynamic DNA nanostructures inspired by natural membrane machines will be driven by the synergistic effect of multiple interactions, including hydrophobic force, electrostatic force, and ligand-receptor interactions by chemical modifications on bases, to expand their applications in vivo from model membrane to cell membrane to karyotheca.
Collapse
Affiliation(s)
- Na Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yue Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Xu Yu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Jing Wei
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| | - Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology , Xi'an Jiaotong University , Xi'an 710049 , People's Republic of China
| |
Collapse
|
63
|
Khmelinskaia A, Mücksch J, Petrov EP, Franquelim HG, Schwille P. Control of Membrane Binding and Diffusion of Cholesteryl-Modified DNA Origami Nanostructures by DNA Spacers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14921-14931. [PMID: 30253101 DOI: 10.1021/acs.langmuir.8b01850] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA origami nanotechnology is being increasingly used to mimic membrane-associated biophysical phenomena. Although a variety of DNA origami nanostructures has already been produced to target lipid membranes, the requirements for membrane binding have so far not been systematically assessed. Here, we used a set of elongated DNA origami structures with varying placement and number of cholesteryl-based membrane anchors to compare different strategies for their incorporation. Single and multiple cholesteryl anchors were attached to DNA nanostructures using single- and double-stranded DNA spacers of varying length. The produced DNA nanostructures were studied in terms of their membrane binding and diffusion. Our results show that the location and number of anchoring moieties play a crucial role for membrane binding of DNA nanostructures mainly if the cholesteryl anchors are in close proximity to the bulky DNA nanostructures. Moreover, the use of DNA spacers largely overcomes local steric hindrances and thus enhances membrane binding. Fluorescence correlation spectroscopy measurements demonstrate that the distinct physical properties of single- and double-stranded DNA spacers control the interaction of the amphipathic DNA nanostructures with lipid membranes. Thus, we provide a rational basis for the design of amphipathic DNA origami nanostructures to efficiently bind lipid membranes in various environments.
Collapse
Affiliation(s)
- Alena Khmelinskaia
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Jonas Mücksch
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Eugene P Petrov
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
- Faculty of Physics , Ludwig Maximilian University of Munich , Geschwister-Scholl-Platz 1 , 80539 Munich , Germany
| | - Henri G Franquelim
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| |
Collapse
|
64
|
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.
Collapse
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
| |
Collapse
|
65
|
Ge Z, Gu H, Li Q, Fan C. Concept and Development of Framework Nucleic Acids. J Am Chem Soc 2018; 140:17808-17819. [PMID: 30516961 DOI: 10.1021/jacs.8b10529] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhilei Ge
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongzhou Gu
- Center for Biotechnology and Biomedical Engineering, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| |
Collapse
|
66
|
Iric K, Subramanian M, Oertel J, Agarwal NP, Matthies M, Periole X, Sakmar TP, Huber T, Fahmy K, Schmidt TL. DNA-encircled lipid bilayers. NANOSCALE 2018; 10:18463-18467. [PMID: 30272763 DOI: 10.1039/c8nr06505e] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Lipid bilayers and lipid-associated proteins play crucial roles in biology. As in vivo studies and manipulation are inherently difficult, membrane-mimetic systems are useful for the investigation of lipidic phases, lipid-protein interactions, membrane protein function and membrane structure in vitro. In this work, we describe a route to leverage the programmability of DNA nanotechnology and create DNA-encircled bilayers (DEBs). DEBs are made of multiple copies of an alkylated oligonucleotide hybridized to a single-stranded minicircle, in which up to two alkyl chains per helical turn point to the inside of the toroidal DNA ring. When phospholipids are added, a bilayer is observed to self-assemble within the ring such that the alkyl chains of the oligonucleotides stabilize the hydrophobic rim of the bilayer to prevent formation of vesicles and support thermotropic lipid phase transitions. The DEBs are completely free of protein and can be synthesized from commercially available components using routine equipment. The diameter of DEBs can be varied in a predictable manner. The well-established toolbox from structural DNA nanotechnology, will ultimately enable the rational design of DEBs so that their size, shape or functionalization can be adapted to the specific needs of biophysical investigations of lipidic phases and the properties of membrane proteins embedded into DEB nanoparticle bilayers.
Collapse
Affiliation(s)
- Katarina Iric
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
67
|
|
68
|
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.
Collapse
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.
| |
Collapse
|
69
|
Birkholz O, Burns JR, Richter CP, Psathaki OE, Howorka S, Piehler J. Multi-functional DNA nanostructures that puncture and remodel lipid membranes into hybrid materials. Nat Commun 2018; 9:1521. [PMID: 29670084 PMCID: PMC5906680 DOI: 10.1038/s41467-018-02905-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023] Open
Abstract
Synthetically replicating key biological processes requires the ability to puncture lipid bilayer membranes and to remodel their shape. Recently developed artificial DNA nanopores are one possible synthetic route due to their ease of fabrication. However, an unresolved fundamental question is how DNA nanopores bind to and dynamically interact with lipid bilayers. Here we use single-molecule fluorescence microscopy to establish that DNA nanopores carrying cholesterol anchors insert via a two-step mechanism into membranes. Nanopores are furthermore shown to locally cluster and remodel membranes into nanoscale protrusions. Most strikingly, the DNA pores can function as cytoskeletal components by stabilizing autonomously formed lipid nanotubes. The combination of membrane puncturing and remodeling activity can be attributed to the DNA pores’ tunable transition between two orientations to either span or co-align with the lipid bilayer. This insight is expected to catalyze the development of future functional nanodevices relevant in synthetic biology and nanobiotechnology. DNA nanopores can span lipid bilayers but how they interact with lipids is not known. Here the authors establish at single-molecule level the insertion mechanism and show that DNA nanopores can locally cluster and remodel membranes, and stabilize autonomously formed lipid nanotubes.
Collapse
|
70
|
Grome MW, Zhang Z, Pincet F, Lin C. Vesicle Tubulation with Self-Assembling DNA Nanosprings. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Michael W. Grome
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Frédéric Pincet
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
- Laboratoire de Physique Statistique; Ecole Normale Supérieure; PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS; 24 rue Lhomond 75005 Paris France
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| |
Collapse
|
71
|
Grome MW, Zhang Z, Pincet F, Lin C. Vesicle Tubulation with Self-Assembling DNA Nanosprings. Angew Chem Int Ed Engl 2018; 57:5330-5334. [PMID: 29575478 DOI: 10.1002/anie.201800141] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/23/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Michael W. Grome
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Zhao Zhang
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| | - Frédéric Pincet
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
- Laboratoire de Physique Statistique; Ecole Normale Supérieure; PSL Research University; Université Paris Diderot Sorbonne Paris Cité; Sorbonne Universités UPMC Univ Paris 06, CNRS; 24 rue Lhomond 75005 Paris France
| | - Chenxiang Lin
- Department of Cell Biology & Nanobiology Institute; Yale University; 850 West Campus Drive West Haven CT 06516 USA
| |
Collapse
|
72
|
Bayrak T, Helmi S, Ye J, Kauert D, Kelling J, Schönherr T, Weichelt R, Erbe A, Seidel R. DNA-Mold Templated Assembly of Conductive Gold Nanowires. NANO LETTERS 2018; 18:2116-2123. [PMID: 29482327 DOI: 10.1021/acs.nanolett.8b00344] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We introduce a new concept for the solution-based fabrication of conductive gold nanowires using DNA templates. To this end, we employ DNA nanomolds, inside which electroless gold deposition is initiated by site-specific attached seeds. Using programmable interfaces, individual molds self-assemble into micrometer-long mold superstructures. During subsequent internal gold deposition, the mold walls constrain the metal growth, such that highly homogeneous nanowires with 20-30 nm diameters are obtained. Wire contacting using electron-beam lithography and electrical conductance characterization at temperatures between 4.2 K and room temperature demonstrate that metallic conducting wires were produced, although for part of the wires, the conductance is limited by boundaries between gold grains. Using different mold designs, our synthesis scheme will, in the future, allow the fabrication of complex metal structures with programmable shapes.
Collapse
Affiliation(s)
| | - Seham Helmi
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics , Universität Leipzig , 04103 Leipzig , Germany
| | - Jingjing Ye
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics , Universität Leipzig , 04103 Leipzig , Germany
| | - Dominik Kauert
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics , Universität Leipzig , 04103 Leipzig , Germany
| | | | | | | | | | - Ralf Seidel
- Molecular Biophysics Group, Peter Debye Institute for Soft Matter Physics , Universität Leipzig , 04103 Leipzig , Germany
| |
Collapse
|
73
|
Franquelim HG, Khmelinskaia A, Sobczak JP, Dietz H, Schwille P. Membrane sculpting by curved DNA origami scaffolds. Nat Commun 2018; 9:811. [PMID: 29476101 PMCID: PMC5824810 DOI: 10.1038/s41467-018-03198-9] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/24/2018] [Indexed: 11/24/2022] Open
Abstract
Membrane sculpting and transformation is essential for many cellular functions, thus being largely regulated by self-assembling and self-organizing protein coats. Their functionality is often encoded by particular spatial structures. Prominent examples are BAR domain proteins, the ‘banana-like’ shapes of which are thought to aid scaffolding and membrane tubulation. To elucidate whether 3D structure can be uncoupled from other functional features of complex scaffolding proteins, we hereby develop curved DNA origami in various shapes and stacking features, following the presumable design features of BAR proteins, and characterize their ability for membrane binding and transformation. We show that dependent on curvature, membrane affinity and surface density, DNA origami coats can indeed reproduce the activity of membrane-sculpting proteins such as BAR, suggesting exciting perspectives for using them in bottom-up approaches towards minimal biomimetic cellular machineries. BAR domain proteins feature a “banana-like” shape which is thought to aid membrane scaffolding and membrane tubulation. Here authors use DNA origami mimicking BAR domains, giant unilamellar vesicles and fluorescence imaging to study how different BAR domain shapes bind and deform membranes.
Collapse
Affiliation(s)
- Henri G Franquelim
- Max Planck Institute of Biochemistry, D-82152, Martinsried near Munich, Planegg, Germany
| | - Alena Khmelinskaia
- Max Planck Institute of Biochemistry, D-82152, Martinsried near Munich, Planegg, Germany.,Graduate School of Quantitative Biosciences, Ludwig-Maximilans-University, D-81337, Munich, Germany
| | - Jean-Philippe Sobczak
- Physics Department and Institute of Advanced Study, Technische Universität München, D-85748, Garching near Munich, Germany
| | - Hendrik Dietz
- Physics Department and Institute of Advanced Study, Technische Universität München, D-85748, Garching near Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, D-82152, Martinsried near Munich, Planegg, Germany.
| |
Collapse
|
74
|
Arora AA, de Silva C. Beyond the smiley face: applications of structural DNA nanotechnology. NANO REVIEWS & EXPERIMENTS 2018; 9:1430976. [PMID: 30410711 PMCID: PMC6171786 DOI: 10.1080/20022727.2018.1430976] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/17/2018] [Indexed: 01/27/2023]
Abstract
Since the development of DNA origami by Paul Rothemund in 2006, the field of structural DNA nanotechnology has undergone tremendous growth. Through DNA origami and related approaches, self-assembly of specified DNA sequences allows for the ‘bottom-up’ construction of diverse nanostructures. By utilizing different sets of small ‘staple’ DNA strands to direct the folding of a long scaffold strand in diverse ways, DNA origami has particularly been incorporated into a variety of prototypical applications beyond the two-dimensional (2D) smiley face. In this review, the basis of DNA nanotechnology, methods of self-assembly, and Rothemund’s DNA origami breakthrough are discussed first. Next, some of the most promising applications of structural DNA nanotechnology since 2006 are summarized. These include utilizing DNA origami as a tool for creating 3D nanostructures (including DNA bricks), as well as structural (ligand capsid binding, viral capsid binding, DNA NanoOctahedron, DNA mold, photonic devices, energy transfer units), and dynamic (DNA box-with-lid, DNA nano-robot, DNA barges, amphipathic DNA structures, DNA nanocircuits) applications of DNA origami.
Collapse
|
75
|
Sun L, Gao Y, Xu Y, Chao J, Liu H, Wang L, Li D, Fan C. Real-Time Imaging of Single-Molecule Enzyme Cascade Using a DNA Origami Raft. J Am Chem Soc 2017; 139:17525-17532. [DOI: 10.1021/jacs.7b09323] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Lele Sun
- Division of Physical Biology & Bioimaging Center, 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 Center, 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
| | - Yan Xu
- Division of Physical Biology & Bioimaging Center, 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
| | - Jie Chao
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM), School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Huajie Liu
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lianhui Wang
- Key
Laboratory for Organic Electronics and Information Displays (KLOEID),
Institute of Advanced Materials (IAM), School of Materials Science
and Engineering, Nanjing University of Posts and Telecommunications, Nanjing 210046, China
| | - Di Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| |
Collapse
|
76
|
Peng R, Wang H, Lyu Y, Xu L, Liu H, Kuai H, Liu Q, Tan W. Facile Assembly/Disassembly of DNA Nanostructures Anchored on Cell-Mimicking Giant Vesicles. J Am Chem Soc 2017; 139:12410-12413. [PMID: 28841373 PMCID: PMC5877790 DOI: 10.1021/jacs.7b07485] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanostructures assembled on living cell membranes have become powerful research tools. Synthetic lipid membranes have been used as a membrane model to study the dynamic behavior of DNA nanostructures on fluid soft lipid bilayers, but without the inherent complexity of natural membranes. Herein, we report the assembly and disassembly of DNA nanoprisms on cell-mimicking micrometer-scale giant membrane vesicles derived from living mammalian cells. Three-dimensional DNA nanoprisms with a DNA arm and a cholesterol anchor were efficiently localized on the membrane surface. The assembly and disassembly of DNA nanoprisms were dynamically manipulated by DNA strand hybridization and toehold-mediated strand displacement. Furthermore, the heterogeneity of reversible assembly/disassembly of DNA nanoprisms was monitored by Förster resonance energy transfer. This study suggests the feasibility of DNA-mediated functional biomolecular assembly on cell membranes for biomimetics studies and delivery systems.
Collapse
Affiliation(s)
- Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Huijing Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liujun Xu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hailan Kuai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| |
Collapse
|
77
|
Howorka S. Building membrane nanopores. NATURE NANOTECHNOLOGY 2017; 12:619-630. [PMID: 28681859 DOI: 10.1038/nnano.2017.99] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 04/19/2017] [Indexed: 05/28/2023]
Abstract
Membrane nanopores-hollow nanoscale barrels that puncture biological or synthetic membranes-have become powerful tools in chemical- and biosensing, and have achieved notable success in portable DNA sequencing. The pores can be self-assembled from a variety of materials, including proteins, peptides, synthetic organic compounds and, more recently, DNA. But which building material is best for which application, and what is the relationship between pore structure and function? In this Review, I critically compare the characteristics of the different building materials, and explore the influence of the building material on pore structure, dynamics and function. I also discuss the future challenges of developing nanopore technology, and consider what the next-generation of nanopore structures could be and where further practical applications might emerge.
Collapse
Affiliation(s)
- Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK
| |
Collapse
|
78
|
Udomprasert A, Kangsamaksin T. DNA origami applications in cancer therapy. Cancer Sci 2017; 108:1535-1543. [PMID: 28574639 PMCID: PMC5543475 DOI: 10.1111/cas.13290] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 12/31/2022] Open
Abstract
Due to the complexity and heterogeneity of cancer, the development of cancer diagnosis and therapy is still progressing, and a complete understanding of cancer biology remains elusive. Recently, cancer nanomedicine has gained much interest as a promising diagnostic and therapeutic strategy, as a wide range of nanomaterials possess unique physical properties that can render drug delivery systems safer and more effective. Also, targeted drug delivery and precision medicine have now become a new paradigm in cancer therapy. With nanocarriers, chemotherapeutic drugs could be directly delivered into target cancer cells, resulting in enhanced efficiency with fewer side-effects. DNA, a biomolecule with molecular self-assembly properties, has emerged as a versatile nanomaterial to construct multifunctional platforms; DNA nanostructures can be modified with functional groups to improve their utilities as biosensors or drug carriers. Such applications have become possible with the advent of the scaffolded DNA origami method. This breakthrough technique in structural DNA nanotechnology provides an easier and faster way to construct DNA nanostructures with various shapes. Several experiments proved that DNA origami nanostructures possess abilities to enhance efficacies of chemotherapy, reduce adverse side-effects, and even circumvent drug resistance. Here, we highlight the principles of the DNA origami technique and its applications in cancer therapeutics and discuss current challenges and opportunities to improve cancer detection and targeted drug delivery.
Collapse
Affiliation(s)
- Anuttara Udomprasert
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Thaned Kangsamaksin
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| |
Collapse
|
79
|
|
80
|
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.
Collapse
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.
| |
Collapse
|
81
|
Dohno C, Makishi S, Nakatani K, Contera S. Amphiphilic DNA tiles for controlled insertion and 2D assembly on fluid lipid membranes: the effect on mechanical properties. NANOSCALE 2017; 9:3051-3058. [PMID: 28186523 DOI: 10.1039/c6nr07084a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Future lipid membrane-associated DNA nanostructures are expected to find applications ranging from synthetic biology to nanomedicine. Here we have designed and synthesized DNA tiles and modified them with amphiphilic covalent moieties. dod-DEG groups, which consist of a hydrophilic diethylene glycol (DEG) and a hydrophobic dodecyl group, are introduced at the phosphate backbone to create amphiphilic DNA strands which are subsequently introduced into one face of the DNA tiles. In this way the tile becomes able to stably bind to lipid membranes by insertion of the hydrophobic groups inside the bilayer core. The functionalized tiles do not aggregate in solution. Our results show that these amphiphilic DNA tiles can bind and assemble into 2D lattices on both gel and fluid lipid bilayers. The binding of the DNA structures to membranes is dependent on the lipid phase of the membrane, the concentration of Mg2+ cations, the length of the amphiphilic modifications to the DNA as well as on the density of the modifications within the tile. Atomic force microscopy-based force spectroscopy is used to investigate the effect of the inserted DNA tiles on the mechanical properties of the lipid membranes. The results indicate that the insertion of DNA tiles produces an approx. 20% increase of the bilayer breakthrough force.
Collapse
Affiliation(s)
- Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan. and PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Shingo Makishi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan.
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, Osaka, Ibaraki 567-0047, Japan.
| | - Sonia Contera
- Clarendon Laboratory, Physics Department, University of Oxford, Oxford, OX1 3PU, UK.
| |
Collapse
|
82
|
Dong Y, Yang YR, Zhang Y, Wang D, Wei X, Banerjee S, Liu Y, Yang Z, Yan H, Liu D. Cuboid Vesicles Formed by Frame‐Guided Assembly on DNA Origami Scaffolds. Angew Chem Int Ed Engl 2017; 56:1586-1589. [DOI: 10.1002/anie.201610133] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Yuanchen Dong
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Yuhe Renee Yang
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Dianming Wang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Xixi Wei
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Saswata Banerjee
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Yan Liu
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| | - Hao Yan
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign InstituteArizona State University Tempe AZ 85287 USA
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of ChemistryTsinghua University Beijing 100084 China
| |
Collapse
|
83
|
Dong Y, Yang YR, Zhang Y, Wang D, Wei X, Banerjee S, Liu Y, Yang Z, Yan H, Liu D. Cuboid Vesicles Formed by Frame-Guided Assembly on DNA Origami Scaffolds. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610133] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuanchen Dong
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Yuhe Renee Yang
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Yiyang Zhang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Dianming Wang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Xixi Wei
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Saswata Banerjee
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Yan Liu
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Zhongqiang Yang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| | - Hao Yan
- School of Molecular Sciences and Center of Molecular Design & Biomimetics at Biodesign Institute; Arizona State University; Tempe AZ 85287 USA
| | - Dongsheng Liu
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry; Tsinghua University; Beijing 100084 China
| |
Collapse
|
84
|
Multiscale simulations of protein-facilitated membrane remodeling. J Struct Biol 2016; 196:57-63. [PMID: 27327264 DOI: 10.1016/j.jsb.2016.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.
Collapse
|
85
|
|
86
|
Hayashi M, Nishiyama M, Kazayama Y, Toyota T, Harada Y, Takiguchi K. Reversible Morphological Control of Tubulin-Encapsulating Giant Liposomes by Hydrostatic Pressure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3794-3802. [PMID: 27023063 DOI: 10.1021/acs.langmuir.6b00799] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Liposomes encapsulating cytoskeletons have drawn much recent attention to develop an artificial cell-like chemical-machinery; however, as far as we know, there has been no report showing isothermally reversible morphological changes of liposomes containing cytoskeletons because the sets of various regulatory factors, that is, their interacting proteins, are required to control the state of every reaction system of cytoskeletons. Here we focused on hydrostatic pressure to control the polymerization state of microtubules (MTs) within cell-sized giant liposomes (diameters ∼10 μm). MT is the cytoskeleton formed by the polymerization of tubulin, and cytoskeletal systems consisting of MTs are very dynamic and play many important roles in living cells, such as the morphogenesis of nerve cells and formation of the spindle apparatus during mitosis. Using real-time imaging with a high-pressure microscope, we examined the effects of hydrostatic pressure on the morphology of tubulin-encapsulating giant liposomes. At ambient pressure (0.1 MPa), many liposomes formed protrusions due to tubulin polymerization within them. When high pressure (60 MPa) was applied, the protrusions shrank within several tens of seconds. This process was repeatedly inducible (around three times), and after the pressure was released, the protrusions regenerated within several minutes. These deformation rates of the liposomes are close to the velocities of migrating or shape-changing living cells rather than the shortening and elongation rates of the single MTs, which have been previously measured. These results demonstrate that the elongation and shortening of protrusions of giant liposomes is repeatedly controllable by regulating the polymerization state of MTs within them by applying and releasing hydrostatic pressure.
Collapse
Affiliation(s)
- Masahito Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University , Nagoya 464-8602, Japan
| | | | | | | | | | - Kingo Takiguchi
- Division of Biological Science, Graduate School of Science, Nagoya University , Nagoya 464-8602, Japan
- Structural Biology Research Center, Nagoya University , Nagoya 464-8601, Japan
| |
Collapse
|
87
|
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.
Collapse
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
| |
Collapse
|