1
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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2
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Abraham GR, Chaderjian AS, N Nguyen AB, Wilken S, Saleh OA. Nucleic acid liquids. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:066601. [PMID: 38697088 DOI: 10.1088/1361-6633/ad4662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by base-pairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.
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Affiliation(s)
- Gabrielle R Abraham
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Aria S Chaderjian
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Anna B N Nguyen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
| | - Sam Wilken
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
| | - Omar A Saleh
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
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3
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Katzmeier F, Simmel FC. Reversible Self-Assembly of Nucleic Acids in a Diffusiophoretic Trap. Angew Chem Int Ed Engl 2024; 63:e202317118. [PMID: 38349772 DOI: 10.1002/anie.202317118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
The formation and dissociation of duplexes or higher order structures from nucleic acid strands is a fundamental process with widespread applications in biochemistry and nanotechnology. Here, we introduce a simple experimental system-a diffusiophoretic trap-for the non-equilibrium self-assembly of nucleic acid structures that uses an electrolyte gradient as the driving force. DNA strands can be concentrated up to hundredfold by a diffusiophoretic trapping force that is caused by the electric field generated by the electrolyte gradient. We present a simple equation for the field to guide selection of appropriate trapping electrolytes. Experiments with carboxylated silica particles demonstrate that the diffusiophoretic force is long-ranged, extending over hundreds of micrometers. As an application, we explore the reversible self-assembly of branched DNA nanostructures in the trap into a macroscopic gel. The structures assemble in the presence of an electrolyte gradient, and disassemble upon its removal, representing a prototypical adaptive response to a macroscopic non-equilibrium state.
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Affiliation(s)
- Florian Katzmeier
- Technical University of Munich, Physics of Synthetic Biological Systems, Arcisstraße 21, 80333, München, Germany
| | - Friedrich C Simmel
- Technical University of Munich, Physics of Synthetic Biological Systems, Arcisstraße 21, 80333, München, Germany
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4
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Gao D, Wilken S, Nguyen ABN, Abraham GR, Liedl T, Saleh OA. Controlling the size and adhesion of DNA droplets using surface- enriched DNA molecules. SOFT MATTER 2024; 20:1275-1281. [PMID: 38236226 DOI: 10.1039/d3sm01264f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Liquid droplets of biomolecules serve as organizers of the cellular interior and are of interest in biosensing and biomaterials applications. Here, we investigate means to tune the interfacial properties of a model biomolecular liquid consisting of multi-armed DNA 'nanostar' particles. We find that long DNA molecules that have binding affinity for the nanostars are preferentially enriched on the interface of nanostar droplets, thus acting as surfactants. Fluorescent measurements indicate that, in certain conditions, the interfacial density of the surfactant is around 20 per square micron, indicative of a sparse brush-like structure of the long, polymeric DNA. Increasing surfactant concentration leads to decreased droplet size, down to the sub-micron scale, consistent with droplet coalesence being impeded by the disjoining pressure created by the brush-like surfactant layer. Added DNA surfactant also keeps droplets from adhering to both hydrophobic and hydrophilic solid surfaces, apparently due to this same disjoining effect of the surfactant layer. We thus demonstrate control of the size and adhesive properties of droplets of a biomolecular liquid, with implications for basic biophysical understanding of such droplets, as well as for their applied use.
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Affiliation(s)
- Daqian Gao
- Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Sam Wilken
- Physics Department, University of California, Santa Barbara, California 93106, USA
- Materials Department, University of California, Santa Barbara, California 93106, USA.
| | - Anna B N Nguyen
- Biomolecular Science & Engineering Program, University of California, Santa Barbara, California 93106, USA
| | - Gabrielle R Abraham
- Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Tim Liedl
- Department für Physik, Ludwig-Maximilians-Universität, München 80539, Germany
| | - Omar A Saleh
- Physics Department, University of California, Santa Barbara, California 93106, USA
- Biomolecular Science & Engineering Program, University of California, Santa Barbara, California 93106, USA
- Materials Department, University of California, Santa Barbara, California 93106, USA.
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5
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Zavala-Martínez AB, Grelet E. M13-Phage-Based Star-Shaped Particles with Internal Flexibility. ACS NANO 2024; 18:281-287. [PMID: 38113352 DOI: 10.1021/acsnano.3c06134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
We report on the construction and the dynamics of monodisperse star-shaped particles, mimicking, at the mesoscale, star polymers. Such multiarm star-like particles result from the self-assembly of gold nanoparticles, forming the core, with tip-linked filamentous viruses (M13 bacteriophages) acting as spines in a sea urchin-like structure. By combining fluorescence and dark-field microscopy with dynamic light scattering, we investigate the diffusion of these hybrid spiny particles. We reveal the internal dynamics of the star particles by probing their central metallic core, which exhibits a hindered motion that can be described as a Brownian particle trapped in a harmonic potential. We therefore show that the filamentous viruses and specifically their tip proteins behave as entropic springs, extending the relevance of the study of such hybrid mesoscopic analogues of star polymers to phage biotechnology.
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Affiliation(s)
- Arantza B Zavala-Martínez
- Univ. Bordeaux, CNRS, Centre de Recherche Paul-Pascal, UMR 5031,115Avenue du Dr. Schweitzer, F-33600 Pessac, France
| | - Eric Grelet
- Univ. Bordeaux, CNRS, Centre de Recherche Paul-Pascal, UMR 5031,115Avenue du Dr. Schweitzer, F-33600 Pessac, France
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6
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Lallemang M, Akintayo CO, Wenzel C, Chen W, Sielaff L, Ripp A, Jessen HJ, Balzer BN, Walther A, Hugel T. Hierarchical Mechanical Transduction of Precision-Engineered DNA Hydrogels with Sacrificial Bonds. ACS APPLIED MATERIALS & INTERFACES 2023; 15:59714-59721. [PMID: 38095074 DOI: 10.1021/acsami.3c15135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Engineering the response to external signals in mechanically switchable hydrogels is important to promote smart materials applications. However, comparably little attention has focused on embedded precision mechanisms for autonomous nonlinear response in mechanical profiles in hydrogels, and we lack understanding of how the behavior from the molecular scale transduces to the macroscale. Here, we design a nonlinear stress-strain response into hydrogels by engineering sacrificial DNA hairpin loops into model network hydrogels formed from star-shaped building blocks. We characterize the force-extension response of single DNA hairpins and are able to describe how the specific topology influences the nonlinear mechanical behavior at different length scales. For this purpose, we utilize force spectroscopy as well as microscopic and macroscopic deformation tests. This study contributes to a better understanding of designing nonlinear strain-adaptive features into hydrogel materials.
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Affiliation(s)
- Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Cecilia Oluwadunsin Akintayo
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Weixiang Chen
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
| | - Lucca Sielaff
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Alexander Ripp
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Henning J Jessen
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Institute of Organic Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Freiburg 79104, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg, Albertstrasse 21, Freiburg 79104, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg 79110, Germany
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7
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Lin Z, Beneyton T, Baret JC, Martin N. Coacervate Droplets for Synthetic Cells. SMALL METHODS 2023; 7:e2300496. [PMID: 37462244 DOI: 10.1002/smtd.202300496] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/15/2023] [Indexed: 12/24/2023]
Abstract
The design and construction of synthetic cells - human-made microcompartments that mimic features of living cells - have experienced a real boom in the past decade. While many efforts have been geared toward assembling membrane-bounded compartments, coacervate droplets produced by liquid-liquid phase separation have emerged as an alternative membrane-free compartmentalization paradigm. Here, the dual role of coacervate droplets in synthetic cell research is discussed: encapsulated within membrane-enclosed compartments, coacervates act as surrogates of membraneless organelles ubiquitously found in living cells; alternatively, they can be viewed as crowded cytosol-like chassis for constructing integrated synthetic cells. After introducing key concepts of coacervation and illustrating the chemical diversity of coacervate systems, their physicochemical properties and resulting bioinspired functions are emphasized. Moving from suspensions of free floating coacervates, the two nascent roles of these droplets in synthetic cell research are highlighted: organelle-like modules and cytosol-like templates. Building the discussion on recent studies from the literature, the potential of coacervate droplets to assemble integrated synthetic cells capable of multiple life-inspired functions is showcased. Future challenges that are still to be tackled in the field are finally discussed.
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Affiliation(s)
- Zi Lin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
| | - Thomas Beneyton
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
| | - Jean-Christophe Baret
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
| | - Nicolas Martin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
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8
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Takinoue M. DNA droplets for intelligent and dynamical artificial cells: from the viewpoint of computation and non-equilibrium systems. Interface Focus 2023; 13:20230021. [PMID: 37577000 PMCID: PMC10415743 DOI: 10.1098/rsfs.2023.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
Living systems are molecular assemblies whose dynamics are maintained by non-equilibrium chemical reactions. To date, artificial cells have been studied from such physical and chemical viewpoints. This review briefly gives a perspective on using DNA droplets in constructing artificial cells. A DNA droplet is a coacervate composed of DNA nanostructures, a novel category of synthetic DNA self-assembled systems. The DNA droplets have programmability in physical properties based on DNA base sequence design. The aspect of DNA as an information molecule allows physical and chemical control of nanostructure formation, molecular assembly and molecular reactions through the design of DNA base pairing. As a result, the construction of artificial cells equipped with non-equilibrium behaviours such as dynamical motions, phase separations, molecular sensing and computation using chemical energy is becoming possible. This review mainly focuses on such dynamical DNA droplets for artificial cell research in terms of computation and non-equilibrium chemical reactions.
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Affiliation(s)
- Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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9
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Naskar S, Bhatia D, Lin ST, Maiti PK. Mechanistic insight into the structure, thermodynamics and dynamics of equilibrium gels of multi-armed DNA nanostars. Phys Chem Chem Phys 2023; 25:7847-7858. [PMID: 36857659 DOI: 10.1039/d2cp04683k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The unique sequence specificity rule of DNA makes it an ideal molecular building block for constructing periodic arrays and devices with nanoscale accuracy and precision. Here, we present the self-assembly of DNA nanostars having three, four and five arms into a gel phase using a simplistic coarse-grained bead-spring model developed by Z. Xing, C. Ness, D. Frenkel and E. Eiser (Macromolecules, 2019, 52, 504-512). Our simulations show that the DNA nanostars form a thermodynamically stable fully bonded gel phase from an unstructured liquid phase with the lowering of temperature. We characterize the phase transition by calculating several structural features such as the radial distribution function and structure factor. The thermodynamics of gelation is quantified by the potential energy and translational pair-entropy of the system. The phase transition from an arrested gel phase to an unstructured liquid phase has been modelled using a two-state theoretical model. We find that this transition is enthalpy driven, and loss of configuration and translational entropy is counterpoised by enthalpic interaction of the DNA sticky-ends, which gives rise to a gel phase at low temperature. The absolute rotational and translational entropy of the systems, measured using a two-phase thermodynamic model, also substantiates the gel transition. The slowing down of the dynamics upon approaching the transition temperature from a high temperature demonstrates the phase transition to a gel phase. A detailed numerical simulation study of the morphology, dynamics and thermodynamics of DNA gelation can provide guidance for future experiments, is easily extensible to other polymeric systems, and is expected to help in understanding the physics of self-assembly.
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Affiliation(s)
- Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Shiang-Tai Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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10
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Udono H, Gong J, Sato Y, Takinoue M. DNA Droplets: Intelligent, Dynamic Fluid. Adv Biol (Weinh) 2023; 7:e2200180. [PMID: 36470673 DOI: 10.1002/adbi.202200180] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Jing Gong
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
| | - Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan
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11
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Conrad N, Chang G, Fygenson DK, Saleh OA. Emulsion imaging of a DNA nanostar condensate phase diagram reveals valence and electrostatic effects. J Chem Phys 2022; 157:234203. [PMID: 36550026 DOI: 10.1063/5.0130808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) in macromolecular solutions (e.g., coacervation) is relevant both to technology and to the process of mesoscale structure formation in cells. The LLPS process is characterized by a phase diagram, i.e., binodal lines in the temperature/concentration plane, which must be quantified to predict the system's behavior. Experimentally, this can be difficult due to complications in handling the dense macromolecular phase. Here, we develop a method for accurately quantifying the phase diagram without direct handling: We confine the sample within micron-scale, water-in-oil emulsion droplets and then use precision fluorescent imaging to measure the volume fraction of the condensate within the droplet. We find that this volume fraction grows linearly with macromolecule concentration; thus, by applying the lever rule, we can directly extract the dense and dilute binodal concentrations. We use this approach to study a model LLPS system of self-assembled, fixed-valence DNA particles termed nanostars (NSs). We find that temperature/concentration phase diagrams of NSs display, with certain exceptions, a larger co-existence regime upon increasing salt or valence, in line with expectations. Aspects of the measured phase behavior validate recent predictions that account for the role of valence in modulating the connectivity of the condensed phase. Generally, our results on NS phase diagrams give fundamental insight into limited-valence phase separation, while the method we have developed will likely be useful in the study of other LLPS systems.
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Affiliation(s)
- Nathaniel Conrad
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Grace Chang
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Deborah K Fygenson
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Omar A Saleh
- Department of Physics, University of California, Santa Barbara, California 93106, USA
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12
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Russo J, Leoni F, Martelli F, Sciortino F. The physics of empty liquids: from patchy particles to water. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:016601. [PMID: 34905739 DOI: 10.1088/1361-6633/ac42d9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Empty liquids represent a wide class of materials whose constituents arrange in a random network through reversible bonds. Many key insights on the physical properties of empty liquids have originated almost independently from the study of colloidal patchy particles on one side, and a large body of theoretical and experimental research on water on the other side. Patchy particles represent a family of coarse-grained potentials that allows for a precise control of both the geometric and the energetic aspects of bonding, while water has arguably the most complex phase diagram of any pure substance, and a puzzling amorphous phase behavior. It was only recently that the exchange of ideas from both fields has made it possible to solve long-standing problems and shed new light on the behavior of empty liquids. Here we highlight the connections between patchy particles and water, focusing on the modelling principles that make an empty liquid behave like water, including the factors that control the appearance of thermodynamic and dynamic anomalies, the possibility of liquid-liquid phase transitions, and the crystallization of open crystalline structures.
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Affiliation(s)
- John Russo
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fabio Leoni
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fausto Martelli
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | - Francesco Sciortino
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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13
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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14
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Lee T, Do S, Lee JG, Kim DN, Shin Y. The flexibility-based modulation of DNA nanostar phase separation. NANOSCALE 2021; 13:17638-17647. [PMID: 34664044 DOI: 10.1039/d1nr03495b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Phase separation of biomolecules plays key roles in physiological compartmentalization as well as pathological aggregation. A deeper understanding of biomolecular phase separation requires dissection of a relation between intermolecular interactions and resulting phase behaviors. DNA nanostars, multivalent DNA assemblies of which sticky ends define attractive interactions, represent an ideal system to probe this fundamental relation governing phase separation processes. Here, we use DNA nanostars to systematically study how structural flexibility exhibited by interacting species impacts their phase behaviors. We design multiple nanostars with a varying degree of flexibility using single-stranded gaps of different lengths in the arm of each nanostar unit. We find that structural flexibility drastically alters the phase diagram of DNA nanostars in such a way that the phase separation of more flexible structures is strongly inhibited. This result is not due to self-inhibition from the loss of valency but rather ascribed to a generic flexibility-driven change in the thermodynamics of the system. Our work provides not only potential regulatory mechanisms cells may exploit to dynamically control intracellular phase separation but also a route to build synthetic systems of which assembly can be controlled in a signal dependent manner.
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Affiliation(s)
- Taehyun Lee
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea.
| | - Sungho Do
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea.
| | - Jae Gyung Lee
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea.
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea.
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
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15
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Akintayo CO, Creusen G, Straub P, Walther A. Tunable and Large-Scale Model Network StarPEG-DNA Hydrogels. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Cecilia Oluwadunsin Akintayo
- A3BMS Lab, Active, Adaptive and Autonomous Bioinspired Materials, Department of Chemistry, University of Mainz, 55128 Mainz, Germany
- DFG Cluster of Excellence @ FIT “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Koehler-Allee 105, 79110 Freiburg, Germany
| | - Guido Creusen
- A3BMS Lab, Active, Adaptive and Autonomous Bioinspired Materials, Department of Chemistry, University of Mainz, 55128 Mainz, Germany
| | - Paula Straub
- DFG Cluster of Excellence @ FIT “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Koehler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- A3BMS Lab, Active, Adaptive and Autonomous Bioinspired Materials, Department of Chemistry, University of Mainz, 55128 Mainz, Germany
- DFG Cluster of Excellence @ FIT “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Koehler-Allee 105, 79110 Freiburg, Germany
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16
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Formanek M, Rovigatti L, Zaccarelli E, Sciortino F, Moreno AJ. Gel Formation in Reversibly Cross-Linking Polymers. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maud Formanek
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, CB2 1LR Cambridge, U.K
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
- CNR-ISC Uos Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
- CNR-ISC Uos Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, IT-00185 Roma, Italy
| | - Angel J. Moreno
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
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17
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Gravina NM, Gumbart JC, Kim HD. Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding. J Phys Chem B 2021; 125:4016-4024. [PMID: 33870695 DOI: 10.1021/acs.jpcb.1c00432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be utilized to program specific binding sites for DNA tile and origami assembly. This reaction is generally understood as a bimolecular reaction dictated by the local concentration of the sticky ends. Its dependence on the relative orientation between the sticky ends, however, is less understood. Here we report on the interactions between DNA sticky ends using the coarse-grained oxDNA model; specifically, we consider how the orientational alignment of the double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind, τb. We specify the orientation of the dsDNA segments with three parameters: θ, which measures the angle between the helical axes, and ϕ1 and ϕ2, which measure rotations of each strand around the helical axis. We find that the binding time depends strongly on both θ and ϕ2: ∼20-fold change with θ and 10-fold change with ϕ2. The binding time is the fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points. Our result is relevant for predicting hybridization efficiency of sticky ends that are rotationally restricted.
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Affiliation(s)
- Nicholas M Gravina
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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18
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Mechanical Properties of DNA Hydrogels: Towards Highly Programmable Biomaterials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11041885] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA hydrogels are self-assembled biomaterials that rely on Watson–Crick base pairing to form large-scale programmable three-dimensional networks of nanostructured DNA components. The unique mechanical and biochemical properties of DNA, along with its biocompatibility, make it a suitable material for the assembly of hydrogels with controllable mechanical properties and composition that could be used in several biomedical applications, including the design of novel multifunctional biomaterials. Numerous studies that have recently emerged, demonstrate the assembly of functional DNA hydrogels that are responsive to stimuli such as pH, light, temperature, biomolecules, and programmable strand-displacement reaction cascades. Recent studies have investigated the role of different factors such as linker flexibility, functionality, and chemical crosslinking on the macroscale mechanical properties of DNA hydrogels. In this review, we present the existing data and methods regarding the mechanical design of pure DNA hydrogels and hybrid DNA hydrogels, and their use as hydrogels for cell culture. The aim of this review is to facilitate further study and development of DNA hydrogels towards utilizing their full potential as multifeatured and highly programmable biomaterials with controlled mechanical properties.
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19
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Song J, Rizvi MH, Lynch BB, Ilavsky J, Mankus D, Tracy JB, McKinley GH, Holten-Andersen N. Programmable Anisotropy and Percolation in Supramolecular Patchy Particle Gels. ACS NANO 2020; 14:17018-17027. [PMID: 33289544 DOI: 10.1021/acsnano.0c06389] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Patchy particle interactions are predicted to facilitate the controlled self-assembly and arrest of particles into phase-stable and morphologically tunable "equilibrium" gels, which avoids the arrested phase separation and subsequent aging that is typically observed in traditional particle gels with isotropic interactions. Despite these promising traits of patchy particle interactions, such tunable equilibrium gels have yet to be realized in the laboratory due to experimental limitations associated with synthesizing patchy particles in high yield. Here, we introduce a supramolecular metal-coordination platform consisting of metallic nanoparticles linked by telechelic polymer chains, which validates the predictions associated with patchy particle interactions and facilitates the design of equilibrium particle hydrogels through limited valency interactions. We demonstrate that the interaction valency and self-assembly of the particles can be effectively controlled by adjusting the relative concentration of polymeric linkers to nanoparticles, which enables the gelation of patchy particle hydrogels with programmable local anisotropy, morphology, and low mechanical percolation thresholds. Moreover, by crowding the local environment around the patchy particles with competing interactions, we introduce an independent method to control the self-assembly of the nanoparticles, thereby enabling the design of highly anisotropic particle hydrogels with substantially reduced percolation thresholds. We thus establish a canonical platform that facilitates multifaceted control of the self-assembly of the patchy nanoparticles en route to the design of patchy particle gels with tunable valencies, morphologies, and percolation thresholds. These advances lay important foundations for further fundamental studies of patchy particle systems and for designing tunable gel materials that address a wide range of engineering applications.
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Affiliation(s)
| | - Mehedi H Rizvi
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Brian B Lynch
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jan Ilavsky
- X-ray Science Division at the Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | | | - Joseph B Tracy
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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20
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Ventura Rosales IE, Rovigatti L, Bianchi E, Likos CN, Locatelli E. Shape control of soft patchy nanoparticles under confinement. NANOSCALE 2020; 12:21188-21197. [PMID: 33034608 DOI: 10.1039/d0nr05058j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular building blocks undergoing a hierarchical assembly process form nano-scale objects which can further assemble into supramolecular structures. When the intermediate units have a limited valence in bonding, complex structures with tailored properties can be created. Here, we consider a composite, star-shaped particle made of f diblock copolymer chains uniformly grafted on a spherical colloid and investigate its first self-assembly stage both in the bulk and under lateral confinement. By means of numerical simulations, we show that, in the bulk, this system develops aggregates whose number and size depend on the temperature as well as on the relative ratio of solvophobic monomers. The emerging aggregates are referred to as patches and impart directionality in bonding to the complex particle. We further characterize how we can control, by changing the lateral confinement, the shape of the brush and the patch properties as a function of the distance between the confining walls. We find that the number of the patches can be determined by tuning the degree of confinement imposed on the particle. Finally, we employ a continuum mechanics model, known as the Liquid Drop Model, to gain insight into the elastic properties of the system. This theoretical approach allows to connect the patch properties to the elastic response of the composite particle.
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21
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Jeon BJ, Nguyen DT, Saleh OA. Sequence-Controlled Adhesion and Microemulsification in a Two-Phase System of DNA Liquid Droplets. J Phys Chem B 2020; 124:8888-8895. [PMID: 32960601 DOI: 10.1021/acs.jpcb.0c06911] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Membrane-less organelles, the liquid droplets formed via liquid-liquid phase separation (LLPS) of biomolecules in cells, act to organize intracellular components into multiple compartments. As a model for this process, and as a potential vehicle for in vitro exploitation of its properties, we explore here a synthetic multiphase LLPS system consisting of a mixture of self-assembled DNA particles. The particles, termed "DNA nanostars" (NSs), consist of four double-stranded DNA arms that each terminate in a single-stranded overhang. NSs condense into droplets due to overhang hybridization. Using two types of NSs with orthogonal overhangs enables the creation of two types of immiscible DNA droplets. Adhesion between the droplets can be tuned by the addition of "cross-linker NSs" that have two overhang sequences of each type. We find that increasing the amount of the cross-linker NSs decreases the droplet/droplet surface tension until a microemulsion transition occurs. Controlled droplet adhesion can also be achieved, without cross-linkers, using overhangs that can weakly hybridize. Finally, we show that solutes can be specifically targeted to the DNA phases by labeling them with appropriate sticky-ends. Overall, our findings demonstrate the ability to create a multiphase LLPS system, and to control its mesoscale configuration, via sequence design of the component molecules.
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Affiliation(s)
- Byoung-Jin Jeon
- Materials Department, University of California, Santa Barbara, California 93110, United States
| | - Dan T Nguyen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93110, United States
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, California 93110, United States.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93110, United States
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22
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Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary. Proc Natl Acad Sci U S A 2020; 117:16160-16166. [PMID: 32601183 DOI: 10.1073/pnas.2001654117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biomolecules can undergo liquid-liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA "nanostar" particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this "active dissolution" process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution ("boiling") temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation ("bubbling") events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.
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23
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Rao A, Shaw J, Neophytou A, Morphew D, Sciortino F, Johnston RL, Chakrabarti D. Leveraging Hierarchical Self-Assembly Pathways for Realizing Colloidal Photonic Crystals. ACS NANO 2020; 14:5348-5359. [PMID: 32374160 PMCID: PMC7304928 DOI: 10.1021/acsnano.9b07849] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/22/2020] [Indexed: 05/27/2023]
Abstract
Colloidal open crystals are attractive materials, especially for their photonic applications. Self-assembly appeals as a bottom-up route for structure fabrication, but self-assembly of colloidal open crystals has proven to be elusive for their mechanical instability due to being low-coordinated. For such a bottom-up route to yield a desired colloidal open crystal, the target structure is required to be thermodynamically favored for designer building blocks and also kinetically accessible via self-assembly pathways in preference to metastable structures. Additionally, the selection of a particular polymorph poses a challenge for certain much sought-after colloidal open crystals for their applications as photonic crystals. Here, we devise hierarchical self-assembly pathways, which, starting from designer triblock patchy particles, yield in a cascade of well-separated associations first tetrahedral clusters and then tetrastack crystals. The designed pathways avoid trapping into an amorphous phase. Our analysis reveals how such a two-stage self-assembly pathway via tetrahedral clusters promotes crystallization by suppressing five- and seven-membered rings that hinder the emergence of the ordered structure. We also find that slow annealing promotes a bias toward the cubic polymorph relative to the hexagonal counterpart. Finally, we calculate the photonic band structures, showing that the cubic polymorph exhibits a complete photonic band gap for the dielectric filling fraction directly realizable from the designer triblock patchy particles. Unexpectedly, we find that the hexagonal polymorph also supports a complete photonic band gap, albeit only for an increased filling fraction, which can be realized via postassembly processing.
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Affiliation(s)
- Abhishek
B. Rao
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - James Shaw
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Andreas Neophytou
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Daniel Morphew
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Francesco Sciortino
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Roy L. Johnston
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Dwaipayan Chakrabarti
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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24
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Abstract
AbstractThe self-assembly of Janus ring polymers is studied via a coarse-grained molecular dynamics employing a bead spring model including bending rigidity contributions to the Hamiltonian. We examine the formation and the morphology of amphiphilicity-driven clusters in the system using the number density ρN, the temperature T, the fraction of solvophobic monomers α, and the stiffness of the polymer rings κ as control parameters. We present a quantitative analysis of several characteristics for the formed clusters of Janus rings. Measured quantities include the distribution of the cluster size MC and the shape of the clusters in the form of the prolate/oblate factor Q and shape factors sf. We demonstrate Janus rings form polymorphic micelles that vary from a spherical shape, akin to that known for linear block copolymers, to a novel type of toroidal shape, and we highlight the role played by the key physical parameters leading to the stabilization of such structures.
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25
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Nguyen DT, Jeon BJ, Abraham GR, Saleh OA. Length-Dependence and Spatial Structure of DNA Partitioning into a DNA Liquid. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14849-14854. [PMID: 31638820 DOI: 10.1021/acs.langmuir.9b02098] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cells can spatially and temporally control biochemistry using liquid-liquid phase separation to form membrane-less organelles. Synthetic biomolecular liquids offer a means to study the mechanisms of this process, as well as offering a route to the creation of functional biomimetic materials. With these goals in mind, we here examine the partitioning of long double-stranded DNA linkers into a liquid composed of small DNA particles ("nanostars") whose phase separation is driven by base pairing. We find that linker partitioning is length-dependent because of a confinement penalty of inserting long strands within the liquid's characteristic mesh size. We quantify this entropic-confinement effect using a simple partitioning theory and show that its magnitude is consistent with classic Odijk pictures of confined worm-like chains. Linker partitioning can also lead to inhomogeneous structures: long linkers excluded from the liquid interior tend to preferentially accumulate on the surface of liquid droplets (i.e., acting as surfactants), while linkers forced at high concentrations into the liquid undergo a secondary phase separation, forming metastable droplet-in-droplet structures. Altogether, our work demonstrates the ability to rationally engineer the composition and structure of a model biomolecular liquid.
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26
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Gu M, Ma X, Zhang L, Lin J. Reversible Polymerization-like Kinetics for Programmable Self-Assembly of DNA-Encoded Nanoparticles with Limited Valence. J Am Chem Soc 2019; 141:16408-16415. [PMID: 31553167 DOI: 10.1021/jacs.9b07919] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A similarity between the polymerization reaction of molecules and the self-assembly of nanoparticles provides a unique way to reliably predict structural characteristics of nanoparticle ensembles. However, the quantitative elucidation of programmable self-assembly kinetics of DNA-encoded nanoparticles is still challenging due to the existence of hybridization and dehybridization of DNA strands. Herein, a joint theoretical-computational method is developed to explicate the mechanism and kinetics of programmable self-assembly of limited-valence nanoparticles with surface encoding of complementary DNA strands. It is revealed that the DNA-encoded nanoparticles are programmed to form a diverse range of self-assembled superstructures with complex architecture, such as linear chains, sols, and gels of nanoparticles. It is theoretically demonstrated that the programmable self-assembly of DNA-encoded nanoparticles with limited valence generally obeys the kinetics and statistics of reversible step-growth polymerization originally proposed in polymer science. Furthermore, the theoretical-computational method is applied to capture the programmable self-assembly behavior of bivalent DNA-protein conjugates. The obtained results not only provide fundamental insights into the programmable self-assembly of DNA-encoded nanoparticles but also offer design rules for the DNA-programmed superstructures with elaborate architecture.
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Affiliation(s)
- Mengxin Gu
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Xiaodong Ma
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Liangshun Zhang
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
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27
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Gârlea IC, Jaramillo-Cano D, Likos CN. Self-organization of gel networks formed by block copolymer stars. SOFT MATTER 2019; 15:3527-3540. [PMID: 30944917 DOI: 10.1039/c9sm00111e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The equilibrium properties of block copolymer star networks (BCS) are studied via computer simulations. We employ both molecular dynamics and multiparticle collisional dynamics simulations to investigate the self-organization of BCS with f = 9 functionalized arms close to their overlap concentrations under conditions of different fractions of functionalization and varying attraction strength. We find three distinct macroscopic self-organized states depending on fraction of attractive end-monomers and the strength of the attraction. At weak attractions, ergodic, diffusive liquids result, with short-lived bonds between the stars. As the attraction strength grows, the whole system forms a percolating cluster, while at the same time the individual molecules are diffusive. Finally, arrested gels emerge when the attractions become strong. The conformation of the BCS in these solutions is found to be strongly affected by the concentration, with the stars assuming typically spherical, open configurations in seeking to maximize inter-star associations as opposed to the inter-star collapse that results at infinite dilution, giving rise to strongly aspherical shapes and reduced sizes.
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Affiliation(s)
- Ioana C Gârlea
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria.
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28
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Conrad N, Kennedy T, Fygenson DK, Saleh OA. Increasing valence pushes DNA nanostar networks to the isostatic point. Proc Natl Acad Sci U S A 2019; 116:7238-7243. [PMID: 30914457 PMCID: PMC6462066 DOI: 10.1073/pnas.1819683116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The classic picture of soft material mechanics is that of rubber elasticity, in which material modulus is related to the entropic elasticity of flexible polymeric linkers. The rubber model, however, largely ignores the role of valence (i.e., the number of network chains emanating from a junction). Recent work predicts that valence, and particularly the Maxwell isostatic point, plays a key role in determining the mechanics of semiflexible polymer networks. Here, we report a series of experiments confirming the prominent role of valence in determining the mechanics of a model system. The system is based on DNA nanostars (DNAns): multiarmed, self-assembled nanostructures that form thermoreversible equilibrium gels through base pair-controlled cross-linking. We measure the linear and nonlinear elastic properties of these gels as a function of DNAns arm number, f, and concentration [DNAns]. We find that, as f increases from three to six, the gel's high-frequency plateau modulus strongly increases, and its dependence on [DNAns] transitions from nonlinear to linear. Additionally, higher-valence gels exhibit less strain hardening, indicating that they have less configurational freedom. Minimal strain hardening and linear dependence of shear modulus on concentration at high f are consistent with predictions for isostatic systems. Evident strain hardening and nonlinear concentration dependence of shear modulus suggest that the low-f networks are subisostatic and have a transient, potentially fractal percolated structure. Overall, our observations indicate that network elasticity is sensitive both to entropic elasticity of network chains and to junction valence, with an apparent isostatic point [Formula: see text] in agreement with the Maxwell prediction.
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Affiliation(s)
- Nathaniel Conrad
- Department of Physics, University of California, Santa Barbara, CA 93106;
| | - Tynan Kennedy
- Department of Physics, University of California, Santa Barbara, CA 93106
| | - Deborah K Fygenson
- Department of Physics, University of California, Santa Barbara, CA 93106;
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106
| | - Omar A Saleh
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106;
- Materials Department, University of California, Santa Barbara, CA 93106
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29
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Brady RA, Kaufhold WT, Brooks NJ, Foderà V, Di Michele L. Flexibility defines structure in crystals of amphiphilic DNA nanostars. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:074003. [PMID: 30523829 DOI: 10.1088/1361-648x/aaf4a1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and bond directionality have been recognised as key design features for DNA motifs to sustain long-range order in 3D, but the practical challenges associated with prescribing building-block geometry with sufficient accuracy have limited the variety of available designs. We have recently introduced a novel platform for the one-pot preparation of crystalline DNA frameworks supported by a combination of Watson-Crick base pairing and hydrophobic forces (Brady et al 2017 Nano Lett. 17 3276-81). Here we use small angle x-ray scattering and coarse-grained molecular simulations to demonstrate that, as opposed to available all-DNA approaches, amphiphilic motifs do not rely on structural rigidity to support long-range order. Instead, the flexibility of amphiphilic DNA building-blocks is a crucial feature for successful crystallisation.
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Affiliation(s)
- Ryan A Brady
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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30
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Xing Z, Ness C, Frenkel D, Eiser E. Structural and Linear Elastic Properties of DNA Hydrogels by Coarse-Grained Simulation. Macromolecules 2019. [DOI: 10.1021/acs.macromol.8b01948] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Zhongyang Xing
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Christopher Ness
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Erika Eiser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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31
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Brady RA, Brooks NJ, Foderà V, Cicuta P, Di Michele L. Amphiphilic-DNA Platform for the Design of Crystalline Frameworks with Programmable Structure and Functionality. J Am Chem Soc 2018; 140:15384-15392. [PMID: 30351920 DOI: 10.1021/jacs.8b09143] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The reliable preparation of functional, ordered, nanostructured frameworks would be a game changer for many emerging technologies, from energy storage to nanomedicine. Underpinned by the excellent molecular recognition of nucleic acids, along with their facile synthesis and breadth of available functionalizations, DNA nanotechnology is widely acknowledged as a prime route for the rational design of nanostructured materials. Yet, the preparation of crystalline DNA frameworks with programmable structure and functionality remains a challenge. Here we demonstrate the potential of simple amphiphilic DNA motifs, dubbed "C-stars", as a versatile platform for the design of programmable DNA crystals. In contrast to all-DNA materials, in which structure depends on the precise molecular details of individual building blocks, the self-assembly of C-stars is controlled uniquely by their topology and symmetry. Exploiting this robust self-assembly principle, we design a range of topologically identical, but structurally and chemically distinct C-stars that following a one-pot reaction self-assemble into highly porous, functional, crystalline frameworks. Simple design variations allow us to fine-tune the lattice parameter and thus control the partitioning of macromolecules within the frameworks, embed responsive motifs that can induce isothermal disassembly, and include chemical moieties to capture target proteins specifically and reversibly.
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Affiliation(s)
- Ryan A Brady
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Nicholas J Brooks
- Department of Chemistry , Imperial College London , London SW7 2AZ , United Kingdom
| | - Vito Foderà
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
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32
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Jeon BJ, Nguyen DT, Abraham GR, Conrad N, Fygenson DK, Saleh OA. Salt-dependent properties of a coacervate-like, self-assembled DNA liquid. SOFT MATTER 2018; 14:7009-7015. [PMID: 30109341 DOI: 10.1039/c8sm01085d] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Liquid-liquid phase separation of a polymer-rich phase from a polymer-dilute solution, known generally as coacervation, has been observed in a variety of biomolecular systems. Understanding of this process, and the properties of the resulting liquid, has been hampered in typical systems by the complexity of the components and of the intermolecular interactions. Here, we examine a single-component system comprised entirely of DNA, in which tetravalent DNA nanostar particles condense into liquids through attractive bonds formed from basepairing interactions. We measure the density, viscosity, particle self-diffusion, and surface tension of NS-liquid droplets. The sequence- and salt-dependent thermodynamics of basepairing accounts for most properties, particularly indicating that particle transport is an activated process whose barrier is the breaking of a single bond, and that very few bonds are broken at the surface. However, more complex effects are also seen. The relation of density to salt shows that electrostatic screening compacts the NS particles. Further, the interrelation of the transport properties indicates a breakdown of the Stokes-Einstein relation. This observation, in concert with the low surface tension and single-bond transport barrier, suggests this DNA liquid has a heterogeneous, clustered structure that is likely enabled by internal NS particle flexibility. We discuss these results in comparison to other coacervate systems.
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Affiliation(s)
- Byoung-Jin Jeon
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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33
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Palmer JC, Poole PH, Sciortino F, Debenedetti PG. Advances in Computational Studies of the Liquid–Liquid Transition in Water and Water-Like Models. Chem Rev 2018; 118:9129-9151. [DOI: 10.1021/acs.chemrev.8b00228] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy C. Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States
| | - Peter H. Poole
- Department of Physics, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada
| | - Francesco Sciortino
- Dipartimento di Fisica and CNR-ISC, Sapienza Universita’ di Roma, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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34
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Xing Z, Caciagli A, Cao T, Stoev I, Zupkauskas M, O'Neill T, Wenzel T, Lamboll R, Liu D, Eiser E. Microrheology of DNA hydrogels. Proc Natl Acad Sci U S A 2018; 115:8137-8142. [PMID: 30045862 PMCID: PMC6094134 DOI: 10.1073/pnas.1722206115] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A key objective in DNA-based material science is understanding and precisely controlling the mechanical properties of DNA hydrogels. We perform microrheology measurements using diffusing wave spectroscopy (DWS) to investigate the viscoelastic behavior of a hydrogel made of Y-shaped DNA (Y-DNA) nanostars over a wide range of frequencies and temperatures. We observe a clear liquid-to-gel transition across the melting temperature region for which the Y-DNA bind to each other. Our measurements reveal a cross-over between the elastic [Formula: see text] and loss modulus [Formula: see text] around the melting temperature [Formula: see text] of the DNA building blocks, which coincides with the systems percolation transition. This transition can be easily shifted in temperature by changing the DNA bond length between the Y shapes. Using bulk rheology as well, we further show that, by reducing the flexibility between the Y-DNA bonds, we can go from a semiflexible transient network to a more energy-driven hydrogel with higher elasticity while keeping the microstructure the same. This level of control in mechanical properties will facilitate the design of more sensitive molecular sensing tools and controlled release systems.
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Affiliation(s)
- Zhongyang Xing
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom;
| | - Alessio Caciagli
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Tianyang Cao
- Department of Chemistry, University of Tsinghua, Beijing 100084, China
| | - Iliya Stoev
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Mykolas Zupkauskas
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Thomas O'Neill
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Tobias Wenzel
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Robin Lamboll
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Dongsheng Liu
- Department of Chemistry, University of Tsinghua, Beijing 100084, China
| | - Erika Eiser
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom;
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35
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Cai J, Sweeney AM. The Proof Is in the Pidan: Generalizing Proteins as Patchy Particles. ACS CENTRAL SCIENCE 2018; 4:840-853. [PMID: 30062112 PMCID: PMC6062823 DOI: 10.1021/acscentsci.8b00187] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Indexed: 05/07/2023]
Abstract
The Chinese century egg, or pidan, is a traditional preparation of duck eggs that can be stored for months at room temperature without degradation. Raw eggs are soaked in a strong alkaline and salt solution, and the albumin gradually forms a stable, transparent gel. Here, we show that pidan gels belong to the class of materials formed from "patchy particles". We found that the β-sheet structure of ovalbumin, the major protein constituent of egg white, is preserved during gelation, while α-helical regions undergo a degree of unfolding into unstructured random coils that may form attractive patches. Upon dilution in additional strong base, the phase behavior of pidan gels is consistent with patchy-particle thermodynamics. This protein gel is also physically and structurally similar to the protein gels that form the squid lens. Both systems exhibit patchy thermodynamics, and the constituent proteins share physical features including a structured, charged core, and polar, unstructured "arms" that form attractive patches. Our work provides a path toward rational design of proteins for precisely structured, volume-spanning materials.
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Affiliation(s)
- Jing Cai
- Department of Physics and
Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alison M. Sweeney
- Department of Physics and
Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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36
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Rovigatti L, Russo J, Romano F. How to simulate patchy particles ⋆. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:59. [PMID: 29748868 DOI: 10.1140/epje/i2018-11667-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed significantly to our understanding of the behaviour of patchy particles, but, although simple in principle, advanced simulation techniques are often required to sample the low temperatures and long time-scales associated with their self-assembly behaviour. In this work we review the most popular simulation techniques that have been used to study patchy particles, with a special focus on Monte Carlo methods. We cover many of the tools required to simulate patchy systems, from interaction potentials to biased moves, cluster moves, and free-energy methods. The review is complemented by an educationally oriented Monte Carlo computer code that implements all the techniques described in the text to simulate a well-known tetrahedral patchy particle model.
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Affiliation(s)
- Lorenzo Rovigatti
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185, Roma, Italy.
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185, Roma, Italy.
| | - John Russo
- School of Mathematics, University of Bristol, BS8 1TW, Bristol, UK
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, 30172, Venezia Mestre, Italy
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37
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Henrich O, Gutiérrez Fosado YA, Curk T, Ouldridge TE. Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:57. [PMID: 29748779 DOI: 10.1140/epje/i2018-11669-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/19/2018] [Indexed: 05/25/2023]
Abstract
During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.
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Affiliation(s)
- Oliver Henrich
- Department of Physics, SUPA, University of Strathclyde, G4 0NG, Glasgow, Scotland, UK.
| | | | - Tine Curk
- CAS Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190, Beijing, China
- Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Thomas E Ouldridge
- Department of Bioengineering, Imperial College London, SW7 2AZ, London, UK
- Centre of Synthetic Biology, Imperial College London, SW7 2AZ, London, UK
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38
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Condon JE, Jayaraman A. Effect of oligonucleic acid (ONA) backbone features on assembly of ONA-star polymer conjugates: a coarse-grained molecular simulation study. SOFT MATTER 2017; 13:6770-6783. [PMID: 28825068 DOI: 10.1039/c7sm01534h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the impact of incorporating new physical and chemical features in oligomeric DNA mimics, termed generally as "oligonucleic acids" (ONAs), on their structure and thermodynamics will be beneficial in designing novel materials for a variety of applications. In this work, we conduct coarse-grained molecular simulations of ONA-star polymer conjugates with varying ONA backbone flexibility, ONA backbone charge, and number of arms in the star polymer at a constant ONA strand volume fraction to elucidate the effect of these design parameters on the thermodynamics and assembly of multi-arm ONA-star polymer conjugates. We quantify the thermo-reversible behavior of the ONA-star polymer conjugates by quantifying the hybridization of the ONA strands in the system as a function of temperature (i.e. melting curve). Additionally, we characterize the assembly of the ONA-star polymer conjugates by tracking cluster formation and percolation as a function of temperature, as well as cluster size distribution at temperatures near the assembly transition region. The key results are as follows. The melting temperature (Tm) of the ONA strands decreases upon going from a neutral to a charged ONA backbone and upon increasing flexibility of the ONA backbone. Similar behavior is seen for the assembly transition temperature (Ta) with varying ONA backbone charge and flexibility. While the number of arms in the ONA-star polymer conjugate has a negligible effect on the ONA Tm in these systems, as the number of ONA-star polymer arms increase, the assembly temperature Ta increases and local ordering in the assembled state improves. By understanding how factors like ONA backbone charge, backbone flexibility, and ONA-star polymer conjugate architecture impact the behavior of ONA-star polymer conjugate systems, we can better inform how the selection of ONA chemistry will influence resulting ONA-star polymer assembly.
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Affiliation(s)
- Joshua E Condon
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA.
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39
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Nöll T, Wenderhold-Reeb S, Schönherr H, Nöll G. DNA-Hydrogele aus Plasmid-DNA. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Tanja Nöll
- Nachwuchsforschergruppe Nöll; Organische Chemie; Department Chemie und Biologie; Universität Siegen; Adolf-Reichwein-Straße 2 57068 Siegen Deutschland
| | - Sabine Wenderhold-Reeb
- Nachwuchsforschergruppe Nöll; Organische Chemie; Department Chemie und Biologie; Universität Siegen; Adolf-Reichwein-Straße 2 57068 Siegen Deutschland
| | - Holger Schönherr
- Physikalische Chemie I; Research Center of Micro and Nanochemistry and Engineering (Cμ); Department Chemie und Biologie; Universität Siegen; Adolf-Reichwein-Straße 2 57076 Siegen Deutschland
| | - Gilbert Nöll
- Nachwuchsforschergruppe Nöll; Organische Chemie; Department Chemie und Biologie; Universität Siegen; Adolf-Reichwein-Straße 2 57068 Siegen Deutschland
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40
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Nöll T, Wenderhold-Reeb S, Schönherr H, Nöll G. Pristine DNA Hydrogels from Biotechnologically Derived Plasmid DNA. Angew Chem Int Ed Engl 2017; 56:12004-12008. [DOI: 10.1002/anie.201705001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Tanja Nöll
- Nöll Research Group; Organic Chemistry; Department of Chemistry and Biology, School of Science and Technology; University of Siegen; Adolf-Reichwein-Strasse 2 57068 Siegen Germany
| | - Sabine Wenderhold-Reeb
- Nöll Research Group; Organic Chemistry; Department of Chemistry and Biology, School of Science and Technology; University of Siegen; Adolf-Reichwein-Strasse 2 57068 Siegen Germany
| | - Holger Schönherr
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ); Department of Chemistry and Biology; University of Siegen; Adolf-Reichwein-Strasse 2 57076 Siegen Germany
| | - Gilbert Nöll
- Nöll Research Group; Organic Chemistry; Department of Chemistry and Biology, School of Science and Technology; University of Siegen; Adolf-Reichwein-Strasse 2 57068 Siegen Germany
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41
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Chremos A, Douglas JF. Solution properties of star polyelectrolytes having a moderate number of arms. J Chem Phys 2017; 147:044906. [PMID: 28764357 PMCID: PMC5702915 DOI: 10.1063/1.4995534] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate polyelectrolyte stars having a moderate number of arms by molecular dynamics simulations of a coarse-grained model over a range of polyelectrolyte concentrations, where both the counter-ions and solvent are treated explicitly. This class of polymeric materials is found to exhibit rather distinct static and dynamic properties from linear and highly branched star polyelectrolyte solutions emphasized in past studies. Moderately branched polymers are particle-like in many of their properties, while at the same time they exhibit large fluctuations in size and shape as in the case of linear chain polymers. Correspondingly, these fluctuations suppress crystallization at high polymer concentrations, leading apparently to an amorphous rather than crystalline solid state at high polyelectrolyte concentrations. We quantify the onset of this transition by measuring the polymer size and shape fluctuations of our model star polyelectrolytes and the static and dynamic structure factor of these solutions over a wide range of polyelectrolyte concentration. Our findings for star polyelectrolytes are similar to those of polymer-grafted nanoparticles having a moderate grafting density, which is natural given the soft and highly deformable nature of both of these "particles."
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Affiliation(s)
- Alexandros Chremos
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Jack F Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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42
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Kurokawa C, Fujiwara K, Morita M, Kawamata I, Kawagishi Y, Sakai A, Murayama Y, Nomura SIM, Murata S, Takinoue M, Yanagisawa M. DNA cytoskeleton for stabilizing artificial cells. Proc Natl Acad Sci U S A 2017; 114:7228-7233. [PMID: 28652345 PMCID: PMC5514726 DOI: 10.1073/pnas.1702208114] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cell-sized liposomes and droplets coated with lipid layers have been used as platforms for understanding live cells, constructing artificial cells, and implementing functional biomedical tools such as biosensing platforms and drug delivery systems. However, these systems are very fragile, which results from the absence of cytoskeletons in these systems. Here, we construct an artificial cytoskeleton using DNA nanostructures. The designed DNA oligomers form a Y-shaped nanostructure and connect to each other with their complementary sticky ends to form networks. To undercoat lipid membranes with this DNA network, we used cationic lipids that attract negatively charged DNA. By encapsulating the DNA into the droplets, we successfully created a DNA shell underneath the membrane. The DNA shells increased interfacial tension, elastic modulus, and shear modulus of the droplet surface, consequently stabilizing the lipid droplets. Such drastic changes in stability were detected only when the DNA shell was in the gel phase. Furthermore, we demonstrate that liposomes with the DNA gel shell are substantially tolerant against outer osmotic shock. These results clearly show the DNA gel shell is a stabilizer of the lipid membrane akin to the cytoskeleton in live cells.
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Affiliation(s)
- Chikako Kurokawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Kanagawa 223-8522, Japan
| | - Masamune Morita
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
| | - Ibuki Kawamata
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | - Yui Kawagishi
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | - Atsushi Sakai
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan
| | - Yoshihiro Murayama
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan
| | | | - Satoshi Murata
- Department of Robotics, Tohoku University, Sendai 980-8579, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan;
| | - Miho Yanagisawa
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Tokyo 184-8588 Japan;
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43
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C. Gârlea I, Bianchi E, Capone B, Rovigatti L, N. Likos C. Hierarchical self-organization of soft patchy nanoparticles into morphologically diverse aggregates. Curr Opin Colloid Interface Sci 2017. [DOI: 10.1016/j.cocis.2017.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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44
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Bianchi E, van Oostrum PD, Likos CN, Kahl G. Inverse patchy colloids: Synthesis, modeling and self-organization. Curr Opin Colloid Interface Sci 2017. [DOI: 10.1016/j.cocis.2017.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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45
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Porter CL, Crocker JC. Directed assembly of particles using directional DNA interactions. Curr Opin Colloid Interface Sci 2017. [DOI: 10.1016/j.cocis.2017.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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46
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47
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Brady RA, Brooks NJ, Cicuta P, Di Michele L. Crystallization of Amphiphilic DNA C-Stars. NANO LETTERS 2017; 17:3276-3281. [PMID: 28417635 DOI: 10.1021/acs.nanolett.7b00980] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Many emerging technologies require materials with well-defined three-dimensional nanoscale architectures. Production of these structures is currently underpinned by self-assembling amphiphilic macromolecules or engineered all-DNA building blocks. Both of these approaches produce restricted ranges of crystal geometries due to synthetic amphiphiles' simple shape and limited specificity, or the technical difficulties in designing space-filling DNA motifs with targeted shapes. We have overcome these limitations with amphiphilic DNA nanostructures, or "C-Stars", that combine the design freedom and facile functionalization of DNA-based materials with robust hydrophobic interactions. C-Stars self-assemble into single crystals exceeding 40 μm in size with lattice parameters exceeding 20 nm.
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Affiliation(s)
- Ryan A Brady
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Nicholas J Brooks
- Department of Chemistry, Imperial College London , London SW7 2AZ, U.K
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge , Cambridge CB3 0HE, U.K
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48
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Simon AJ, Walls-Smith LT, Freddi MJ, Fong FY, Gubala V, Plaxco KW. Simultaneous Measurement of the Dissolution Kinetics of Responsive DNA Hydrogels at Multiple Length Scales. ACS NANO 2017; 11:461-468. [PMID: 28006092 DOI: 10.1021/acsnano.6b06414] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Recent years have seen increasing study of stimulus-responsive hydrogels constructed from aptamer-connected DNA building blocks. Presumably due to a lack of simple, quantitative tools with which to measure gel responsiveness, however, the literature describing these materials is largely qualitative. In response, we demonstrate here simple, time-resolved, multiscale methods for measuring the response kinetics of these materials. Specifically, by employing trace amounts of fluorophore-quencher labeled cross-linkers and the rheology of entrapped fluorescent particles, we simultaneously measure dissolution at molecular, hundred-nanometer, and hundred-micron length-scales. For our test-bed system, an adenine-responsive hydrogel, we find biphasic response kinetics dependent on both effector concentration and depth within the gel and a dissolution pattern uniform at scales longer than a few times the monomer-monomer distance. Likewise, we find that, in agreement with theoretical predictions, dissolution kinetics over the hundred nanometer length scale exhibit a power-law-like dependence on the fraction of disrupted cross-links before a distinct crossover from solid-like to liquid-like behavior.
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Affiliation(s)
| | | | - Matthew J Freddi
- Medway School of Pharmacy, University of Kent , Central Avenue, Chatham Maritime, Chatham, ME4 4TB Kent, U.K
| | | | - Vladimir Gubala
- Medway School of Pharmacy, University of Kent , Central Avenue, Chatham Maritime, Chatham, ME4 4TB Kent, U.K
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49
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Bianchi E, Capone B, Coluzza I, Rovigatti L, van Oostrum PDJ. Limiting the valence: advancements and new perspectives on patchy colloids, soft functionalized nanoparticles and biomolecules. Phys Chem Chem Phys 2017; 19:19847-19868. [DOI: 10.1039/c7cp03149a] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Artistic representation of limited valance units consisting of a soft core (in blue) and a small number of flexible bonding patches (in orange).
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Affiliation(s)
- Emanuela Bianchi
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Institute for Theoretical Physics
| | - Barbara Capone
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Dipartimento di Scienze
| | - Ivan Coluzza
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
| | - Lorenzo Rovigatti
- Faculty of Physics
- University of Vienna
- A-1090 Vienna
- Austria
- Rudolf Peierls Centre for Theoretical Physics
| | - Peter D. J. van Oostrum
- Department of Nanobiotechnology
- Institute for Biologically Inspired Materials
- University of Natural Resources and Life Sciences
- A-1190 Vienna
- Austria
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Lindquist BA, Jadrich RB, Milliron DJ, Truskett TM. On the formation of equilibrium gels via a macroscopic bond limitation. J Chem Phys 2016; 145:074906. [DOI: 10.1063/1.4960773] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- B. A. Lindquist
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - R. B. Jadrich
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - D. J. Milliron
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - T. M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
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