1
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Shi Z, Li Y, Du X, Liu D, Dong Y. Constructing Stiffness Tunable DNA Hydrogels Based on DNA Modules with Adjustable Rigidity. NANO LETTERS 2024; 24:8634-8641. [PMID: 38950146 DOI: 10.1021/acs.nanolett.4c01870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
DNA hydrogel represents a potent material for crafting biological scaffolds, but the toolbox to systematically regulate the mechanical property is still limited. Herein, we have provided a strategy to tune the stiffness of DNA hydrogel through manipulating the rigidity of DNA modules. By introducing building blocks with higher molecular rigidity and proper connecting fashion, DNA hydrogel stiffness could be systematically elevated. These hydrogels showed excellent dynamic properties and biocompatibility, thus exhibiting great potential in three-dimensional (3D) cell culture. This study has offered a systematic method to explore the structure-property relationship, which may contribute to the development of more intelligent and personalized biomedical platforms.
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Affiliation(s)
- Ziwei Shi
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yujie Li
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xiuji Du
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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2
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Douglas JF, Horkay F. Influence of swelling on the elasticity of polymer networks cross-linked in the melt state: Test of the localization model of rubber elasticity. J Chem Phys 2024; 160:224903. [PMID: 38856072 PMCID: PMC11305141 DOI: 10.1063/5.0212901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
The elasticity of polymer networks, formed by cross-linking high molecular mass polymers in the melt state and then swollen by a solvent, involves contributions from both the presence of cross-link network junctions and the interchain interactions associated with the combined effect of excluded volume interactions and topological constraints that become modified when the network is swollen. We test the capacity of the previously developed localization model of rubber elasticity, a mean field "tube model," to describe changes in elasticity observed in classical experimental studies of the mechanical properties of this type of network. In order to obtain a satisfactory comparison to the experiments, it was found to be necessary to account for the independently observed tendency of the network junctions to become localized in the network with appreciable swelling, as well as the interchain interactions emphasized in previous discussions of the localization model.
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Affiliation(s)
- Jack F. Douglas
- Material Measurement Laboratory, Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Ferenc Horkay
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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3
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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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4
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Harnett J, Weir S, Michieletto D. Effects of monovalent and divalent cations on the rheology of entangled DNA. SOFT MATTER 2024; 20:3980-3986. [PMID: 38686506 PMCID: PMC11095498 DOI: 10.1039/d3sm00957b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.
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Affiliation(s)
- Jennifer Harnett
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Simon Weir
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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5
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Daly ML, Nishi K, Klawa SJ, Hinton KY, Gao Y, Freeman R. Designer peptide-DNA cytoskeletons regulate the function of synthetic cells. Nat Chem 2024:10.1038/s41557-024-01509-w. [PMID: 38654104 DOI: 10.1038/s41557-024-01509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
The bottom-up engineering of artificial cells requires a reconfigurable cytoskeleton that can organize at distinct locations and dynamically modulate its structural and mechanical properties. Here, inspired by the vast array of actin-binding proteins and their ability to reversibly crosslink or bundle filaments, we have designed a library of peptide-DNA crosslinkers varying in length, valency and geometry. Peptide filaments conjoint through DNA hybridization give rise to tactoid-shaped bundles with tunable aspect ratios and mechanics. When confined in cell-sized water-in-oil droplets, the DNA crosslinker design guides the localization of cytoskeletal structures at the cortex or within the lumen of the synthetic cells. The tunable spatial arrangement regulates the passive diffusion of payloads within the droplets and complementary DNA handles allow for the reversible recruitment and release of payloads on and off the cytoskeleton. Heat-induced reconfiguration of peptide-DNA architectures triggers shape deformations of droplets, regulated by DNA melting temperatures. Altogether, the modular design of peptide-DNA architectures is a powerful strategy towards the bottom-up assembly of synthetic cells.
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Affiliation(s)
- Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kengo Nishi
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kameryn Y Hinton
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA.
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6
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Agarwal S, Osmanovic D, Dizani M, Klocke MA, Franco E. Dynamic control of DNA condensation. Nat Commun 2024; 15:1915. [PMID: 38429336 PMCID: PMC10907372 DOI: 10.1038/s41467-024-46266-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/21/2024] [Indexed: 03/03/2024] Open
Abstract
Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics.
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Affiliation(s)
- Siddharth Agarwal
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Bioengineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Dino Osmanovic
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Mahdi Dizani
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Melissa A Klocke
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Elisa Franco
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Bioengineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
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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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Tayar AM, Caballero F, Anderberg T, Saleh OA, Cristina Marchetti M, Dogic Z. Controlling liquid-liquid phase behaviour with an active fluid. NATURE MATERIALS 2023; 22:1401-1408. [PMID: 37679525 DOI: 10.1038/s41563-023-01660-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Demixing binary liquids is a ubiquitous transition explained using a well-established thermodynamic formalism that requires the equality of intensive thermodynamics parameters across phase boundaries. Demixing transitions also occur when binary fluid mixtures are driven away from equilibrium, but predicting and designing such out-of-equilibrium transitions remains a challenge. Here we study the liquid-liquid phase separation of attractive DNA nanostars driven away from equilibrium using a microtubule-based active fluid. We find that activity lowers the critical temperature and narrows the range of coexistence concentrations, but only in the presence of mechanical bonds between the liquid droplets and reconfiguring active fluid. Similar behaviours are observed in numerical simulations, suggesting that the activity suppression of the critical point is a generic feature of active liquid-liquid phase separation. Our work describes a versatile platform for building soft active materials with feedback control and providing an insight into self-organization in cell biology.
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Affiliation(s)
- Alexandra M Tayar
- Department of Physics, University of California, Santa Barbara, CA, USA.
| | | | - Trevor Anderberg
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Omar A Saleh
- Department of Physics, University of California, Santa Barbara, CA, USA
- Materials Department, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - M Cristina Marchetti
- Department of Physics, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA.
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9
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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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10
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Saleh OA, Wilken S, Squires TM, Liedl T. Vacuole dynamics and popping-based motility in liquid droplets of DNA. Nat Commun 2023; 14:3574. [PMID: 37328453 PMCID: PMC10275875 DOI: 10.1038/s41467-023-39175-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 06/01/2023] [Indexed: 06/18/2023] Open
Abstract
Liquid droplets of biomolecules play key roles in organizing cellular behavior, and are also technologically relevant, yet physical studies of dynamic processes of such droplets have generally been lacking. Here, we investigate and quantify the dynamics of formation of dilute internal inclusions, i.e., vacuoles, within a model system consisting of liquid droplets of DNA 'nanostar' particles. When acted upon by DNA-cleaving restriction enzymes, these DNA droplets exhibit cycles of appearance, growth, and bursting of internal vacuoles. Analysis of vacuole growth shows their radius increases linearly in time. Further, vacuoles pop upon reaching the droplet interface, leading to droplet motion driven by the osmotic pressure of restriction fragments captured in the vacuole. We develop a model that accounts for the linear nature of vacuole growth, and the pressures associated with motility, by describing the dynamics of diffusing restriction fragments. The results illustrate the complex non-equilibrium dynamics possible in biomolecular condensates.
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Affiliation(s)
- Omar A Saleh
- Materials Department and Physics Department, University of California, Santa Barbara, CA, 93106, USA.
| | - Sam Wilken
- Materials Department and Physics Department, University of California, Santa Barbara, CA, 93106, USA
| | - Todd M Squires
- Chemical Engineering Department, University of California, Santa Barbara, CA, 93106, USA
| | - Tim Liedl
- Physics Department, Ludwig-Maximilians University, Munich, Germany
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11
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Sato Y, Takinoue M. Sequence-dependent fusion dynamics and physical properties of DNA droplets. NANOSCALE ADVANCES 2023; 5:1919-1925. [PMID: 36998664 PMCID: PMC10044877 DOI: 10.1039/d3na00073g] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/12/2023] [Indexed: 06/19/2023]
Abstract
Liquid-liquid phase separation (LLPS) of biopolymer molecules generates liquid-like droplets. Physical properties such as viscosity and surface tension play important roles in the functions of these droplets. DNA-nanostructure-based LLPS systems provide useful model tools to investigate the influence of molecular design on the physical properties of the droplets, which has so far remained unclear. Herein, we report changes in the physical properties of DNA droplets by sticky end (SE) design in DNA nanostructures. We used a Y-shaped DNA nanostructure (Y-motif) with three SEs as a model structure. Seven different SE designs were used. The experiments were performed at the phase transition temperature where the Y-motifs self-assembled into droplets. We found that the DNA droplets assembled from the Y-motifs with longer SEs exhibited a longer coalescence period. In addition, the Y-motifs with the same length but different sequence SEs showed slight variations in the coalescence period. Our results suggest that the SE length greatly affected the surface tension at the phase transition temperature. We believe that these findings will accelerate our understanding of the relationship between molecular design and the physical properties of droplets formed via LLPS.
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Affiliation(s)
- Yusuke Sato
- Department of Computer Science, Tokyo Institute of Technology 4259, Nagatsuta-cho, Midori-ku Yokoham Kanagawa 226-8502 Japan
- 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 Yokoham 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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12
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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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13
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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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14
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Do S, Lee C, Lee T, Kim DN, Shin Y. Engineering DNA-based synthetic condensates with programmable material properties, compositions, and functionalities. SCIENCE ADVANCES 2022; 8:eabj1771. [PMID: 36240277 PMCID: PMC9565806 DOI: 10.1126/sciadv.abj1771] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/29/2022] [Indexed: 05/21/2023]
Abstract
Biomolecular condensates participate in diverse cellular processes, ranging from gene regulation to stress survival. Bottom-up engineering of synthetic condensates advances our understanding of the organizing principle of condensates. It also enables the synthesis of artificial systems with novel functions. However, building synthetic condensates with a predictable organization and function remains challenging. Here, we use DNA as a building block to create synthetic condensates that are assembled through phase separation. The programmability of intermolecular interactions between DNA molecules enables the control over various condensate properties including assembly, composition, and function. Similar to the way intracellular condensates are organized, DNA clients are selectively partitioned into cognate condensates. We demonstrate that the synthetic condensates can accelerate DNA strand displacement reactions and logic gate operation by concentrating specific reaction components. We envision that the DNA-based condensates could help the realization of the high-order functions required to build more life-like artificial systems.
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Affiliation(s)
- Sungho Do
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
| | - Taehyun 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
- Corresponding author. (Y.S.); (D.-N.K.)
| | - Yongdae Shin
- 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
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea
- Corresponding author. (Y.S.); (D.-N.K.)
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15
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Agarwal S, Osmanovic D, Klocke MA, Franco E. The Growth Rate of DNA Condensate Droplets Increases with the Size of Participating Subunits. ACS NANO 2022; 16:11842-11851. [PMID: 35867936 DOI: 10.1021/acsnano.2c00084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Liquid-liquid phase separation (LLPS) is a common phenomenon underlying the formation of dynamic membraneless organelles in biological cells, which are emerging as major players in controlling cellular functions and health. The bottom-up synthesis of biomolecular liquid systems with simple constituents, like nucleic acids and peptides, is useful to understand LLPS in nature as well as to develop programmable means to build new amorphous materials with properties matching or surpassing those observed in natural condensates. In particular, understanding which parameters determine condensate growth kinetics is essential for the synthesis of condensates with the capacity for active, dynamic behaviors. Here we use DNA nanotechnology to study artificial liquid condensates through programmable star-shaped subunits, focusing on the effects of changing subunit size. First, we show that LLPS is achieved in a 6-fold range of subunit size. Second, we demonstrate that the rate of growth of condensate droplets scales with subunit size. Our investigation is supported by a general model that describes how coarsening and coalescence are expected to scale with subunit size under ideal assumptions. Beyond suggesting a route toward achieving control of LLPS kinetics via design of subunit size in synthetic liquids, our work suggests that particle size may be a key parameter in biological condensation processes.
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Affiliation(s)
- Siddharth Agarwal
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90024, United States
| | - Dino Osmanovic
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90024, United States
| | - Melissa A Klocke
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90024, United States
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90024, United States
- Bioengineering, University of California at Los Angeles, Los Angeles, California 90024, United States
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16
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Tauber J, van der Gucht J, Dussi S. Stretchy and disordered: Toward understanding fracture in soft network materials via mesoscopic computer simulations. J Chem Phys 2022; 156:160901. [PMID: 35490006 DOI: 10.1063/5.0081316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Soft network materials exist in numerous forms ranging from polymer networks, such as elastomers, to fiber networks, such as collagen. In addition, in colloidal gels, an underlying network structure can be identified, and several metamaterials and textiles can be considered network materials as well. Many of these materials share a highly disordered microstructure and can undergo large deformations before damage becomes visible at the macroscopic level. Despite their widespread presence, we still lack a clear picture of how the network structure controls the fracture processes of these soft materials. In this Perspective, we will focus on progress and open questions concerning fracture at the mesoscopic scale, in which the network architecture is clearly resolved, but neither the material-specific atomistic features nor the macroscopic sample geometries are considered. We will describe concepts regarding the network elastic response that have been established in recent years and turn out to be pre-requisites to understand the fracture response. We will mostly consider simulation studies, where the influence of specific network features on the material mechanics can be cleanly assessed. Rather than focusing on specific systems, we will discuss future challenges that should be addressed to gain new fundamental insights that would be relevant across several examples of soft network materials.
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Affiliation(s)
- Justin Tauber
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Simone Dussi
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
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17
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Ronceray P, Zhang Y, Liu X, Wingreen NS. Stoichiometry Controls the Dynamics of Liquid Condensates of Associative Proteins. PHYSICAL REVIEW LETTERS 2022; 128:038102. [PMID: 35119898 PMCID: PMC10497325 DOI: 10.1103/physrevlett.128.038102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 01/04/2022] [Indexed: 05/12/2023]
Abstract
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprising two complementary proteins via scaling analysis and molecular dynamics. We find that when stoichiometry is balanced, relaxation slows down dramatically due to a scarcity of alternative binding partners following bond breakage. This microscopic slow-down strongly affects the bulk diffusivity, viscosity, and mixing, which provides a means to experimentally test this prediction.
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Affiliation(s)
- Pierre Ronceray
- Center for the Physics of Biological Function, Princeton University, Princeton, New Jersey 08544, USA
- Aix Marseille Univ, CNRS, CINAM, Turing Center for Living Systems, Marseille, France
| | - Yaojun Zhang
- Center for the Physics of Biological Function, Princeton University, Princeton, New Jersey 08544, USA
- Department of Physics and Astronomy and Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xichong Liu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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18
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Lattuada E, Caprara D, Piazza R, Sciortino F. Spatially uniform dynamics in equilibrium colloidal gels. SCIENCE ADVANCES 2021; 7:eabk2360. [PMID: 34860553 PMCID: PMC8641940 DOI: 10.1126/sciadv.abk2360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Gels of DNA nanostars, besides providing a compatible scaffold for biomedical applications, are ideal model systems for testing the physics of equilibrium colloidal gels. Here, using dynamic light scattering and photon correlation imaging (a recent technique that, by blending light scattering and imaging, provides space-resolved quantification of the dynamics), we follow the process of gel formation over 10 orders of magnitude in time in a model system of tetravalent DNA nanostars in solution, a realization of limited-valence colloids. Such a system, depending on the nanostar concentration, can form either equilibrium or phase separation gels. In stark contrast to the heterogeneity of concentration and dynamics displayed by the phase separation gel, the equilibrium gel shows absence of aging and a remarkable spatially uniform dynamics.
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Affiliation(s)
- Enrico Lattuada
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Debora Caprara
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Roberto Piazza
- Department of Chemistry, Materials Science, and Chemical Engineering (CMIC), Politecnico di Milano, Edificio 6, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Francesco Sciortino
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Roma, Italy
- Corresponding author.
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19
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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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20
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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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21
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Lattuada E, Caprara D, Lamberti V, Sciortino F. Hyperbranched DNA clusters. NANOSCALE 2020; 12:23003-23012. [PMID: 33180079 DOI: 10.1039/d0nr04840b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Taking advantage of the base-pairing specificity and tunability of DNA interactions, we investigate the spontaneous formation of hyperbranched clusters starting from purposely designed DNA tetravalent nanostar monomers, encoding in their four sticky ends the desired binding rules. Specifically, we combine molecular dynamics simulations and Dynamic Light Scattering experiments to follow the aggregation process of DNA nanostars at different concentrations and temperatures. At odds with the Flory-Stockmayer predictions, we find that, even when all possible bonds are formed, the system does not reach percolation due to the presence of intracluster bonds. We present an extension of the Flory-Stockmayer theory that properly describes the numerical and experimental results.
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Affiliation(s)
- Enrico Lattuada
- Physics Department, Sapienza University, P.le Aldo Moro 5, 00185, Rome, Italy.
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22
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Creusen G, Akintayo CO, Schumann K, Walther A. Scalable One-Pot-Liquid-Phase Oligonucleotide Synthesis for Model Network Hydrogels. J Am Chem Soc 2020; 142:16610-16621. [PMID: 32902960 PMCID: PMC7612451 DOI: 10.1021/jacs.0c05488] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Solid-phase oligonucleotide synthesis (SPOS) based on phosphoramidite chemistry is currently the most widespread technique for DNA and RNA synthesis but suffers from scalability limitations and high reagent consumption. Liquid-phase oligonucleotide synthesis (LPOS) uses soluble polymer supports and has the potential of being scalable. However, at present, LPOS requires 3 separate reaction steps and 4-5 precipitation steps per nucleotide addition. Moreover, long acid exposure times during the deprotection step degrade sequences with high A content (adenine) due to depurination and chain cleavage. In this work, we present the first one-pot liquid-phase DNA synthesis technique which allows the addition of one nucleotide in a one-pot reaction of sequential coupling, oxidation, and deprotection followed by a single precipitation step. Furthermore, we demonstrate how to suppress depurination during the addition of adenine nucleotides. We showcase the potential of this technique to prepare high-purity 4-arm PEG-T20 (T = thymine) and 4-arm PEG-A20 building blocks in multigram scale. Such complementary 4-arm PEG-DNA building blocks reversibly self-assemble into supramolecular model network hydrogels and facilitate the elucidation of bond lifetimes. These model network hydrogels exhibit new levels of mechanical properties (storage modulus, bond lifetimes) in DNA bonds at room temperature (melting at 44 °C) and thus open up pathways to next-generation DNA materials programmable through sequence recognition and available for macroscale applications.
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Affiliation(s)
- Guido Creusen
- ABMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler- Allee 105, 79110 Freiburg, Germany
| | - Cecilia Oluwadunsin Akintayo
- ABMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler- Allee 105, 79110 Freiburg, Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), 79110 Freiburg, Germany
| | - Katja Schumann
- ABMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
| | - Andreas Walther
- ABMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, 79104 Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler- Allee 105, 79110 Freiburg, Germany
- DFG Cluster of Excellence “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), 79110 Freiburg, Germany
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23
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Spinozzi F, Ortore MG, Nava G, Bomboi F, Carducci F, Amenitsch H, Bellini T, Sciortino F, Mariani P. Gelling without Structuring: A SAXS Study of the Interactions among DNA Nanostars. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10387-10396. [PMID: 32787014 PMCID: PMC8010795 DOI: 10.1021/acs.langmuir.0c01520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/25/2020] [Indexed: 06/11/2023]
Abstract
We evaluate, by means of synchrotron small-angle X-ray scattering, the shape and mutual interactions of DNA tetravalent nanostars as a function of temperature in both the gas-like state and across the gel transition. To this end, we calculate the form factor from coarse-grained molecular dynamics simulations with a novel method that includes hydration effects; we approximate the radial interaction of DNA nanostars as a hard-sphere potential complemented by a repulsive and an attractive Yukawa term; and we predict the structure factors by exploiting the perturbative random phase approximation of the Percus-Yevick equation. Our approach enables us to fit all the data by selecting the particle radius and the width and amplitude of the attractive potential as free parameters. We determine the evolution of the structure factor across gelation and detect subtle changes of the effective interparticle interactions, that we associate to the temperature and concentration dependence of the particle size. Despite the approximations, the approach here adopted offers new detailed insights into the structure and interparticle interactions of this fascinating system.
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Affiliation(s)
- Francesco Spinozzi
- Department
of Life and Environmental Sciences, Polytechnic
University of Marche, 60131 Ancona, Italy
| | - Maria Grazia Ortore
- Department
of Life and Environmental Sciences, Polytechnic
University of Marche, 60131 Ancona, Italy
| | - Giovanni Nava
- Department
of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20133 Milan, Italy
| | - Francesca Bomboi
- Department
of Physics, Sapienza, Università
di Roma, 00185 Rome, Italy
| | - Federica Carducci
- Department
of Life and Environmental Sciences, Polytechnic
University of Marche, 60131 Ancona, Italy
| | - Heinz Amenitsch
- Institute
for Inorganic Chemistry, Graz University
of Technology, 8010 Graz, Austria
| | - Tommaso Bellini
- Department
of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20133 Milan, Italy
| | | | - Paolo Mariani
- Department
of Life and Environmental Sciences, Polytechnic
University of Marche, 60131 Ancona, Italy
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24
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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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25
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Ozaki H, Koga T. Theory of transient networks with a well-defined junction structure. J Chem Phys 2020; 152:184902. [PMID: 32414249 DOI: 10.1063/5.0003799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The present study constructs a theory of physical gels consisting of bifunctional molecules, f-functional molecules, and solvent. This theory considered the formation of loops (i.e., the smallest cycles). First, the association state in the equilibrium state was investigated. Unlike the previous theory proposed by the authors, the present theory was able to describe the effect of functionality on the association state. Second, the dynamics of gelation was studied. As a result, the authors found two regimes: one where the characteristic time of gelation is governed by the association of associative groups and another where it is governed by the dissociation of them. Finally, theoretical results and the existing experimental results were compared in terms of gelation time and the time development of elasticity. With parameters set reasonably, the theory succeeded in the quantitative description of the experimental results.
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Affiliation(s)
- Hiroto Ozaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Tsuyoshi Koga
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
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26
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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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27
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Howard MP, Jadrich RB, Lindquist BA, Khabaz F, Bonnecaze RT, Milliron DJ, Truskett TM. Structure and phase behavior of polymer-linked colloidal gels. J Chem Phys 2019; 151:124901. [DOI: 10.1063/1.5119359] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael P. Howard
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Ryan B. Jadrich
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Beth A. Lindquist
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Fardin Khabaz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Roger T. Bonnecaze
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Delia J. Milliron
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Thomas M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA
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28
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Bomboi F, Caprara D, Fernandez-Castanon J, Sciortino F. Cold-swappable DNA gels. NANOSCALE 2019; 11:9691-9697. [PMID: 31066406 DOI: 10.1039/c9nr01156k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report an experimental investigation of an all-DNA gel composed by tetra-functional DNA nanoparticles acting as network nodes and bi-functional ones acting as links. The DNA binding sequence is designed to generate at room and lower temperatures a persistent long-lived network. Exploiting ideas from DNA-nanotechnology, we implement in the binding base sequences an appropriate exchange reaction which allows links to swap, constantly retaining the total number of network links. The DNA gel is thus able to rearrange its topology at low temperature while preserving its fully-bonded configuration.
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Affiliation(s)
- Francesca Bomboi
- Physics Department, Sapienza University, P.le Aldo Moro 5, 00185, Rome, Italy.
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