1
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Stewart JM, Li S, Tang AA, Klocke MA, Gobry MV, Fabrini G, Di Michele L, Rothemund PWK, Franco E. Modular RNA motifs for orthogonal phase separated compartments. Nat Commun 2024; 15:6244. [PMID: 39080253 PMCID: PMC11289419 DOI: 10.1038/s41467-024-50003-x] [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: 10/12/2023] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
Recent discoveries in biology have highlighted the importance of protein and RNA-based condensates as an alternative to classical membrane-bound organelles. Here, we demonstrate the design of pure RNA condensates from nanostructured, star-shaped RNA motifs. We generate condensates using two different RNA nanostar architectures: multi-stranded nanostars whose binding interactions are programmed via linear overhangs, and single-stranded nanostars whose interactions are programmed via kissing loops. Through systematic sequence design, we demonstrate that both architectures can produce orthogonal (distinct and immiscible) condensates, which can be individually tracked via fluorogenic aptamers. We also show that aptamers make it possible to recruit peptides and proteins to the condensates with high specificity. Successful co-transcriptional formation of condensates from single-stranded nanostars suggests that they may be genetically encoded and produced in living cells. We provide a library of orthogonal RNA condensates that can be modularly customized and offer a route toward creating systems of functional artificial organelles for the task of compartmentalizing molecules and biochemical reactions.
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Affiliation(s)
- Jaimie Marie Stewart
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Shiyi Li
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Anli A Tang
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
| | - Melissa Ann Klocke
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
| | - Martin Vincent Gobry
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Giacomo Fabrini
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London, UK
| | - Paul W K Rothemund
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
- Department of Bioengineering, California Institute of Technology, Pasadena, USA.
- Department of Computation & Neural Systems, California Institute of Technology, Pasadena, USA.
| | - Elisa Franco
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA.
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2
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Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024; 124:8550-8595. [PMID: 38885177 PMCID: PMC11260227 DOI: 10.1021/acs.chemrev.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
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3
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Udono H, Fan M, Saito Y, Ohno H, Nomura SIM, Shimizu Y, Saito H, Takinoue M. Programmable Computational RNA Droplets Assembled via Kissing-Loop Interaction. ACS NANO 2024; 18:15477-15486. [PMID: 38831645 PMCID: PMC11191694 DOI: 10.1021/acsnano.3c12161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 06/05/2024]
Abstract
DNA droplets, artificial liquid-like condensates of well-engineered DNA sequences, allow the critical aspects of phase-separated biological condensates to be harnessed programmably, such as molecular sensing and phase-state regulation. In contrast, their RNA-based counterparts remain less explored despite more diverse molecular structures and functions ranging from DNA-like to protein-like features. Here, we design and demonstrate computational RNA droplets capable of two-input AND logic operations. We use a multibranched RNA nanostructure as a building block comprising multiple single-stranded RNAs. Its branches engaged in RNA-specific kissing-loop (KL) interaction enables the self-assembly into a network-like microstructure. Upon two inputs of target miRNAs, the nanostructure is programmed to break up into lower-valency structures that are interconnected in a chain-like manner. We optimize KL sequences adapted from viral sequences by numerically and experimentally studying the base-wise adjustability of the interaction strength. Only upon receiving cognate microRNAs, RNA droplets selectively show a drastic phase-state change from liquid to dispersed states due to dismantling of the network-like microstructure. This demonstration strongly suggests that the multistranded motif design offers a flexible means to bottom-up programming of condensate phase behavior. Unlike submicroscopic RNA-based logic operators, the macroscopic phase change provides a naked-eye-distinguishable readout of molecular sensing. Our computational RNA droplets can be applied to in situ programmable assembly of computational biomolecular devices and artificial cells from transcriptionally derived RNA within biological/artificial cells.
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Affiliation(s)
- Hirotake Udono
- Department
of Computer Science, Tokyo Institute of
Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minzhi Fan
- Department
of Computer Science, Tokyo Institute of
Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yoko Saito
- Department
of Computer Science, Tokyo Institute of
Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Hirohisa Ohno
- Department
of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shin-ichiro M. Nomura
- Department
of Robotics, Graduate School of Engineering, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yoshihiro Shimizu
- Laboratory
for Cell-Free Protein Synthesis, RIKEN Center
for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Hirohide Saito
- Department
of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masahiro Takinoue
- Department
of Computer Science, Tokyo Institute of
Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Department
of Life Science and Technology, Tokyo Institute
of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Research
Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative
Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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4
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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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5
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Hegde O, Li T, Sharma A, Borja M, Jacobs WM, Rogers WB. Competition between Self-Assembly and Phase Separation Governs High-Temperature Condensation of a DNA Liquid. PHYSICAL REVIEW LETTERS 2024; 132:208401. [PMID: 38829088 DOI: 10.1103/physrevlett.132.208401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2024] [Accepted: 04/19/2024] [Indexed: 06/05/2024]
Abstract
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite behavior, whereby self-assembly of DNA oligonucleotides into finite-sized, stoichiometric clusters tends to inhibit phase separation. We first use microfluidics-based experiments to map a novel phase transition in which the oligonucleotides condense as the temperature increases at high concentrations of divalent cations. We then show that a theoretical model of competition between self-assembly and phase separation quantitatively predicts changes in experimental phase diagrams arising from DNA sequence perturbations. Our results point to a general mechanism by which self-assembly shapes phase boundaries in complex biopolymer solutions.
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Affiliation(s)
- Omkar Hegde
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Tianhao Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Anjali Sharma
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Marco Borja
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - W Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
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6
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Naz M, Zhang L, Chen C, Yang S, Dou H, Mann S, Li J. Self-assembly of stabilized droplets from liquid-liquid phase separation for higher-order structures and functions. Commun Chem 2024; 7:79. [PMID: 38594355 PMCID: PMC11004187 DOI: 10.1038/s42004-024-01168-5] [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: 12/31/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
Dynamic microscale droplets produced by liquid-liquid phase separation (LLPS) have emerged as appealing biomaterials due to their remarkable features. However, the instability of droplets limits the construction of population-level structures with collective behaviors. Here we first provide a brief background of droplets in the context of materials properties. Subsequently, we discuss current strategies for stabilizing droplets including physical separation and chemical modulation. We also discuss the recent development of LLPS droplets for various applications such as synthetic cells and biomedical materials. Finally, we give insights on how stabilized droplets can self-assemble into higher-order structures displaying coordinated functions to fully exploit their potentials in bottom-up synthetic biology and biomedical applications.
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Affiliation(s)
- Mehwish Naz
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China
| | - Lin Zhang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China
| | - Chong Chen
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, Turku, 20520, Finland
| | - Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China.
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China.
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, 429 Zhangheng Road, Shanghai, 201203, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.
| | - Jianwei Li
- MediCity Research Laboratory, University of Turku, Tykistökatu 6, Turku, 20520, Finland.
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7
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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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8
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Sato Y, Takinoue M. Pioneering artificial cell-like structures with DNA nanotechnology-based liquid-liquid phase separation. Biophys Physicobiol 2024; 21:e210010. [PMID: 38803334 PMCID: PMC11128300 DOI: 10.2142/biophysico.bppb-v21.0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/26/2024] [Indexed: 05/29/2024] Open
Abstract
Recent studies have revealed that liquid-liquid phase separation (LLPS) plays crucial roles in various cellular functions. Droplets formed via LLPS within cells, often referred to as membraneless organelles, serve to concentrate specific molecules, thus enhancing biochemical reactions. Artificial LLPS systems have been utilized to construct synthetic cell models, employing a range of synthetic molecules. LLPS systems based on DNA nanotechnology are particularly notable for their designable characteristics in droplet formation, dynamics, properties, and functionalities. This review surveys recent advancements in DNA-based LLPS systems, underscoring the programmability afforded by DNA's base-pair specific interactions. We discuss the fundamentals of DNA droplet formation, including temperature-dependence and physical properties, along with the precise control achievable through sequence design. Attention is given to the phase separation of DNA nanostructures on two-dimensional closed interfaces, which results in spatial pattern formation at the interface. Furthermore, we spotlight the potential of DNA droplet computing for cancer diagnostics through specific microRNA pattern recognition. We envision that DNA-based LLPS presents a versatile platform for the exploration of cellular mimicry and opens innovative ways for the development of functional synthetic cells.
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Affiliation(s)
- Yusuke Sato
- Department of Intelligent and Control Systems, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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9
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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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10
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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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11
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Bartolucci G, Calaça Serrão A, Schwintek P, Kühnlein A, Rana Y, Janto P, Hofer D, Mast CB, Braun D, Weber CA. Sequence self-selection by cyclic phase separation. Proc Natl Acad Sci U S A 2023; 120:e2218876120. [PMID: 37847736 PMCID: PMC10614837 DOI: 10.1073/pnas.2218876120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 09/06/2023] [Indexed: 10/19/2023] Open
Abstract
The emergence of functional oligonucleotides on early Earth required a molecular selection mechanism to screen for specific sequences with prebiotic functions. Cyclic processes such as daily temperature oscillations were ubiquitous in this environment and could trigger oligonucleotide phase separation. Here, we propose sequence selection based on phase separation cycles realized through sedimentation in a system subjected to the feeding of oligonucleotides. Using theory and experiments with DNA, we show sequence-specific enrichment in the sedimented dense phase, in particular of short 22-mer DNA sequences. The underlying mechanism selects for complementarity, as it enriches sequences that tightly interact in the dense phase through base-pairing. Our mechanism also enables initially weakly biased pools to enhance their sequence bias or to replace the previously most abundant sequences as the cycles progress. Our findings provide an example of a selection mechanism that may have eased screening for auto-catalytic self-replicating oligonucleotides.
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Affiliation(s)
- Giacomo Bartolucci
- Division Biological Physics, Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Adriana Calaça Serrão
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Philipp Schwintek
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Alexandra Kühnlein
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Yash Rana
- Division Biological Physics, Max Planck Institute for the Physics of Complex Systems, Dresden01187, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
| | - Philipp Janto
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Dorothea Hofer
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Christof B. Mast
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Dieter Braun
- Ludwigs-Maximilian-Universität München and Center for NanoScience, Munich80799, Germany
| | - Christoph A. Weber
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Augsburg86159, Germany
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12
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Testa A, Spanke HT, Jambon-Puillet E, Yasir M, Feng Y, Küffner AM, Arosio P, Dufresne ER, Style RW, Rebane AA. Surface Passivation Method for the Super-repellence of Aqueous Macromolecular Condensates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:14626-14637. [PMID: 37797324 PMCID: PMC10586374 DOI: 10.1021/acs.langmuir.3c01886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/21/2023] [Indexed: 10/07/2023]
Abstract
Solutions of macromolecules can undergo liquid-liquid phase separation to form droplets with ultralow surface tension. Droplets with such low surface tension wet and spread over common surfaces such as test tubes and microscope slides, complicating in vitro experiments. The development of a universal super-repellent surface for macromolecular droplets has remained elusive because their ultralow surface tension requires low surface energies. Furthermore, the nonwetting of droplets containing proteins poses additional challenges because the surface must remain inert to a wide range of chemistries presented by the various amino acid side chains at the droplet surface. Here, we present a method to coat microscope slides with a thin transparent hydrogel that exhibits complete dewetting (contact angles θ ≈ 180°) and minimal pinning of phase-separated droplets in aqueous solution. The hydrogel is based on a swollen matrix of chemically cross-linked polyethylene glycol diacrylate of molecular weight 12 kDa (PEGDA), and can be prepared with basic chemistry laboratory equipment. The PEGDA hydrogel is a powerful tool for in vitro studies of weak interactions, dynamics, and the internal organization of phase-separated droplets in aqueous solutions.
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Affiliation(s)
- Andrea Testa
- Department
of Materials, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Etienne Jambon-Puillet
- Department
of Materials, ETH Zürich, 8093 Zürich, Switzerland
- LadHyX,
CNRS, Ecole Polytechnique, Institut Polytechnique
de Paris, Palaiseau 91120, France
| | - Mohammad Yasir
- Department
of Materials, ETH Zürich, 8093 Zürich, Switzerland
| | - Yanxia Feng
- Department
of Materials, ETH Zürich, 8093 Zürich, Switzerland
| | - Andreas M. Küffner
- Department
of Chemistry and Applied Biosciences, Institute
for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Paolo Arosio
- Department
of Chemistry and Applied Biosciences, Institute
for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Robert W. Style
- Department
of Materials, ETH Zürich, 8093 Zürich, Switzerland
| | - Aleksander A. Rebane
- Department
of Materials, ETH Zürich, 8093 Zürich, Switzerland
- Life
Molecules and Materials Laboratory, Programs in Chemistry and in Physics, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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13
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Agarwal S, Dizani M, Osmanovic D, Franco E. Light-controlled growth of DNA organelles in synthetic cells. Interface Focus 2023; 13:20230017. [PMID: 37577006 PMCID: PMC10415744 DOI: 10.1098/rsfs.2023.0017] [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: 04/05/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
Living cells regulate many of their vital functions through dynamic, membraneless compartments that phase separate (condense) in response to different types of stimuli. In synthetic cells, responsive condensates could similarly play a crucial role in sustaining their operations. Here we use DNA nanotechnology to design and characterize artificial condensates that respond to light. These condensates form via the programmable interactions of star-shaped DNA subunits (nanostars), which are engineered to include photo-responsive protection domains. In the absence of UV irradiation, the nanostar interactions are not conducive to the formation of condensates. UV irradiation cleaves the protection domains, increases the nanostar valency and enables condensation. We demonstrate that this approach makes it possible to tune precisely the kinetics of condensate formation by dosing UV exposure time. Our experimental observations are complemented by a computational model that characterizes phase transitions of mixtures of particles of different valency, under changes in the mixture composition and bond interaction energy. In addition, we illustrate how UV activation is a useful tool to control the formation and size of DNA condensates in emulsion droplets, as a prototype organelle in a synthetic cell. This research expands our capacity to remotely control the dynamics of DNA-based components via physical stimuli and is particularly relevant to the development of minimal artificial cells and responsive biomaterials.
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Affiliation(s)
- Siddharth Agarwal
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90024, USA
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, CA 90024, USA
| | - Mahdi Dizani
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90024, USA
| | - Dino Osmanovic
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90024, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA 90024, USA
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, CA 90024, USA
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA 90024, USA
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14
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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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15
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Tschurikow X, Gadzekpo A, Tran MP, Chatterjee R, Sobucki M, Zaburdaev V, Göpfrich K, Hilbert L. Amphiphiles Formed from Synthetic DNA-Nanomotifs Mimic the Stepwise Dispersal of Transcriptional Clusters in the Cell Nucleus. NANO LETTERS 2023; 23:7815-7824. [PMID: 37586706 PMCID: PMC10510709 DOI: 10.1021/acs.nanolett.3c01301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and we achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Increasing amphiphile concentrations induce rounding of droplets, prevent droplet fusion, and, at high concentrations, cause full dispersal of droplets. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that the addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of transcriptional cluster formation in biological cells using relatively simple DNA sequence-programmable nanostructures, opening novel ways to control the mesoscopic organization of synthetic nanomaterials.
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Affiliation(s)
- Xenia Tschurikow
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Aaron Gadzekpo
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Mai P. Tran
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg 69120, Germany
- Max
Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Rakesh Chatterjee
- Max
Planck Zentrum für Physik und Medizin, Erlangen 91058, Germany
- Chair
of Mathematics in Life Sciences, Friedrich-Alexander
Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Marcel Sobucki
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - Vasily Zaburdaev
- Max
Planck Zentrum für Physik und Medizin, Erlangen 91058, Germany
- Chair
of Mathematics in Life Sciences, Friedrich-Alexander
Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Kerstin Göpfrich
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg 69120, Germany
- Max
Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Lennart Hilbert
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
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16
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Galvanetto N, Ivanović MT, Chowdhury A, Sottini A, Nüesch MF, Nettels D, Best RB, Schuler B. Extreme dynamics in a biomolecular condensate. Nature 2023:10.1038/s41586-023-06329-5. [PMID: 37468629 DOI: 10.1038/s41586-023-06329-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/14/2023] [Indexed: 07/21/2023]
Abstract
Proteins and nucleic acids can phase-separate in the cell to form concentrated biomolecular condensates1-4. The functions of condensates span many length scales: they modulate interactions and chemical reactions at the molecular scale5, organize biochemical processes at the mesoscale6 and compartmentalize cells4. Understanding the underlying mechanisms of these processes will require detailed knowledge of the rich dynamics across these scales7. The mesoscopic dynamics of biomolecular condensates have been extensively characterized8, but their behaviour at the molecular scale has remained more elusive. Here, as an example of biomolecular phase separation, we study complex coacervates of two highly and oppositely charged disordered human proteins9. Their dense phase is 1,000 times more concentrated than the dilute phase, and the resulting percolated interaction network10 leads to a bulk viscosity 300 times greater than that of water. However, single-molecule spectroscopy optimized for measurements within individual droplets reveals that at the molecular scale, the disordered proteins remain exceedingly dynamic, with their chain configurations interconverting on submicrosecond timescales. Massive all-atom molecular dynamics simulations reproduce the experimental observations and explain this apparent discrepancy: the underlying interactions between individual charged side chains are short-lived and exchange on a pico- to nanosecond timescale. Our results indicate that, despite the high macroscopic viscosity of phase-separated systems, local biomolecular rearrangements required for efficient reactions at the molecular scale can remain rapid.
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Affiliation(s)
- Nicola Galvanetto
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
| | - Miloš T Ivanović
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Aritra Chowdhury
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Mark F Nüesch
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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17
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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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18
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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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19
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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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20
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Tran MP, Chatterjee R, Dreher Y, Fichtler J, Jahnke K, Hilbert L, Zaburdaev V, Göpfrich K. A DNA Segregation Module for Synthetic Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202711. [PMID: 35971190 DOI: 10.1002/smll.202202711] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/01/2022] [Indexed: 06/15/2023]
Abstract
The bottom-up construction of an artificial cell requires the realization of synthetic cell division. Significant progress has been made toward reliable compartment division, yet mechanisms to segregate the DNA-encoded informational content are still in their infancy. Herein, droplets of DNA Y-motifs are formed by liquid-liquid phase separation. DNA droplet segregation is obtained by cleaving the linking component between two populations of DNA Y-motifs. In addition to enzymatic cleavage, photolabile sites are introduced for spatio-temporally controlled DNA segregation in bulk as well as in cell-sized water-in-oil droplets and giant unilamellar lipid vesicles (GUVs). Notably, the segregation process is slower in confinement than in bulk. The ionic strength of the solution and the nucleobase sequences are employed to regulate the segregation dynamics. The experimental results are corroborated in a lattice-based theoretical model which mimics the interactions between the DNA Y-motif populations. Altogether, engineered DNA droplets, reconstituted in GUVs, can represent a strategy toward a DNA segregation module within bottom-up assembled synthetic cells.
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Affiliation(s)
- Mai P Tran
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Rakesh Chatterjee
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 11, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Yannik Dreher
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
| | - Julius Fichtler
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
| | - Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
| | - Lennart Hilbert
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Zoological Institute, Department of Systems Biology / Bioinformatics, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Vasily Zaburdaev
- Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 11, 91058, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
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21
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Meier SM, Farcas AM, Kumar A, Ijavi M, Bill RT, Stelling J, Dufresne ER, Steinmetz MO, Barral Y. Multivalency ensures persistence of a +TIP body at specialized microtubule ends. Nat Cell Biol 2023; 25:56-67. [PMID: 36536177 PMCID: PMC9859758 DOI: 10.1038/s41556-022-01035-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/21/2022] [Indexed: 12/24/2022]
Abstract
Microtubule plus-end tracking proteins (+TIPs) control microtubule specialization and are as such essential for cell division and morphogenesis. Here we investigated interactions and functions of the budding yeast Kar9 network consisting of the core +TIP proteins Kar9 (functional homologue of APC, MACF and SLAIN), Bim1 (orthologous to EB1) and Bik1 (orthologous to CLIP-170). A multivalent web of redundant interactions links the three +TIPs together to form a '+TIP body' at the end of chosen microtubules. This body behaves as a liquid condensate that allows it to persist on both growing and shrinking microtubule ends, and to function as a mechanical coupling device between microtubules and actin cables. Our study identifies nanometre-scale condensates as effective cellular structures and underlines the power of dissecting the web of low-affinity interactions driving liquid-liquid phase separation in order to establish how condensation processes support cell function.
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Affiliation(s)
- Sandro M Meier
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.,Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland
| | - Ana-Maria Farcas
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland
| | - Anil Kumar
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland.,ImmunOs Therapeutics AG, Schlieren, Switzerland
| | - Mahdiye Ijavi
- Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland.,Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Robert T Bill
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel, Switzerland
| | - Eric R Dufresne
- Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland.,Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, Villigen, Switzerland. .,University of Basel, Biozentrum, Basel, Switzerland.
| | - Yves Barral
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich, Switzerland. .,Bringing Materials to Life Initiative, ETH Zürich, Zürich, Switzerland.
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22
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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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23
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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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24
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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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25
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Liu J, Zhorabek F, Chau Y. Nucleic Acids Modulate Liquidity and Dynamics of Artificial Membraneless Organelles. ACS Macro Lett 2022; 11:562-567. [PMID: 35575335 DOI: 10.1021/acsmacrolett.2c00167] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid-liquid phase separation (LLPS) emerges as a fundamental underlying mechanism for the biological organization, especially the formation of membraneless organelles (MLOs) hosting intrinsically disordered proteins (IDPs) as scaffolds. Nucleic acids are compositional biomacromolecules of MLOs with wide implications in normal cell functions as well as in pathophysiology caused by aberrant phase behavior. Exploiting a minimalist artificial membraneless organelles (AMLO) from LLPS of IDP-mimicking polymer-oligopeptide hybrid (IPH), we investigated the effect of nucleic acids with different lengths and sequence variations on AMLO. The behavior of this AMLO in the presence of DNAs and RNAs resembled natural MLOs in multiple aspects, namely, modulated propensity of formation, morphology, liquidity, and dynamics. Both DNA and RNA could enhance the LLPS of AMLO, while compared with RNA, DNA had a higher tendency to solidify and diminish dynamics thereof. These findings suggest its potential as a concise model system for the understanding of the interaction between nucleic acids and natural MLOs and for studying the molecular mechanism of diseases involving MLOs.
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Affiliation(s)
- Jianhui Liu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Fariza Zhorabek
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
| | - Ying Chau
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR 999077, China
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26
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Lee C, Do S, Lee JY, Kim M, Kim SM, Shin Y, Kim DN. Formation of non-base-pairing DNA microgels using directed phase transition of amphiphilic monomers. Nucleic Acids Res 2022; 50:4187-4196. [PMID: 35390157 PMCID: PMC9023257 DOI: 10.1093/nar/gkac232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/27/2022] [Accepted: 03/26/2022] [Indexed: 11/22/2022] Open
Abstract
Programmability of DNA sequences enables the formation of synthetic DNA nanostructures and their macromolecular assemblies such as DNA hydrogels. The base pair-level interaction of DNA is a foundational and powerful mechanism to build DNA structures at the nanoscale; however, its temperature sensitivity and weak interaction force remain a barrier for the facile and scalable assembly of DNA structures toward higher-order structures. We conducted this study to provide an alternative, non-base-pairing approach to connect nanoscale DNA units to yield micrometer-sized gels based on the sequential phase transition of amphiphilic unit structures. Strong electrostatic interactions between DNA nanostructures and polyelectrolyte spermines led to the formation of giant phase-separated aggregates of monomer units. Gelation could be initiated by the addition of NaCl, which weakened the electrostatic DNA-spermine interaction while attractive interactions between cholesterols created stable networks by crosslinking DNA monomers. In contrast to the conventional DNA gelation techniques, our system used solid aggregates as a precursor for DNA microgels. Therefore, in situ gelation could be achieved by depositing aggregates on the desired substrate and subsequently initiating a phase transition. Our approach can expand the utility and functionality of DNA hydrogels by using more complex nucleic acid assemblies as unit structures and combining the technique with top-down microfabrication methods.
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Affiliation(s)
- Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Sungho Do
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea
| | - Minju Kim
- Department of Mechanical Engineering, Incheon National University, Incheon 22012, Korea
| | - Sang Moon Kim
- Department of Mechanical Engineering, Incheon National University, Incheon 22012, Korea
| | - Yongdae Shin
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Korea.,Department of Mechanical Engineering, Seoul National University, Seoul 08826, Korea.,Institute of Engineering Research, Seoul National University, Seoul 08826, Korea
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27
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Nishida K, Nishimura SN, Tanaka M. Selective Accumulation to Tumor Cells with Coacervate Droplets Formed from a Water-Insoluble Acrylate Polymer. Biomacromolecules 2022; 23:1569-1580. [PMID: 35089709 DOI: 10.1021/acs.biomac.1c01343] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Selective targeting of specific cells without the use of biological ligands has not been achieved. In the present study, we revealed that the coacervate droplets formed from poly(2-methoxyethyl acrylate) (PMEA) and its derivatives selectively accumulated to tumor cells. PMEA derivatives, which are insoluble acrylate polymers, induced coacervation in water to form polymer-dense droplets via hydrophobic interaction. Interestingly, the accumulation of coacervate droplets to tumor cells was involved in the bound water content of PMEA derivatives. Coacervate droplets with a high bound water content accumulated and internalized up to 36.6-fold higher in HeLa cervical tumor cells than in normal human fibroblasts (NHDF). Moreover, the interactions between coacervate droplets and plasma membrane components such as CD44 played a key role in this accumulation process. Therefore, coacervate droplets formed from PMEA derivatives have great clinical potential in tumor cell detection, development of alternative tumor-targeting ligands, and optimization of drug delivery carriers.
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Affiliation(s)
- Kei Nishida
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shin-Nosuke Nishimura
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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28
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Sato Y, Takinoue M. Capsule-like DNA Hydrogels with Patterns Formed by Lateral Phase Separation of DNA Nanostructures. JACS AU 2022; 2:159-168. [PMID: 35098232 PMCID: PMC8790810 DOI: 10.1021/jacsau.1c00450] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 05/03/2023]
Abstract
Phase separation is a key phenomenon in artificial cell construction. Recent studies have shown that the liquid-liquid phase separation of designed-DNA nanostructures induces the formation of liquid-like condensates that eventually become hydrogels by lowering the solution temperature. As a compartmental capsule is an essential artificial cell structure, many studies have focused on the lateral phase separation of artificial lipid vesicles. However, controlling phase separation using a molecular design approach remains challenging. Here, we present the lateral liquid-liquid phase separation of DNA nanostructures that leads to the formation of phase-separated capsule-like hydrogels. We designed three types of DNA nanostructures (two orthogonal and a linker nanostructure) that were adsorbed onto an interface of water-in-oil (W/O) droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels with bicontinuous, patch, and mix patterns, due to the immiscibility of liquid-like DNA during the self-assembly process. The frequency of appearance of these patterns was altered by designing DNA sequences and altering the mixing ratio of the nanostructures. We constructed a phase diagram for the capsule-like DNA hydrogels by investigating pattern formation under various conditions. The phase-separated DNA hydrogels did not only form on the W/O droplet interface but also on the inner leaflet of lipid vesicles. Notably, the capsule-like hydrogels were extracted into an aqueous solution, maintaining the patterns formed by the lateral phase separation. In addition, the extracted hydrogels were successfully combined with enzymatic reactions, which induced their degradation. Our results provide a method for the design and control of phase-separated hydrogel capsules using sequence-designed DNAs. We envision that by incorporating various DNA nanodevices into DNA hydrogel capsules, the capsules will gain molecular sensing, chemical-information processing, and mechanochemical actuating functions, allowing the construction of functional molecular systems.
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Affiliation(s)
- Yusuke Sato
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Miyagi 980-8579, Japan
- Department
of Computer Science, Tokyo Institute of
Technology, Kanagawa 226-8502, Japan
| | - Masahiro Takinoue
- Department
of Computer Science, Tokyo Institute of
Technology, Kanagawa 226-8502, Japan
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29
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Bartolucci G, Adame-Arana O, Zhao X, Weber CA. Controlling composition of coexisting phases via molecular transitions. Biophys J 2021; 120:4682-4697. [PMID: 34600899 DOI: 10.1016/j.bpj.2021.09.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/10/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely unexplored how the behavior of phase-separating systems with molecular transitions differs between thermodynamic equilibrium and cases in which the detailed balance of the molecular transition rates is broken because of the presence of fuel. Here, we present a model of a phase-separating ternary mixture in which two components can convert into each other. At thermodynamic equilibrium, we find that molecular transitions can give rise to a lower dissolution temperature and thus reentrant phase behavior. Moreover, we find a discontinuous thermodynamic phase transition in the composition of the droplet phase if both converting molecules attract themselves with similar interaction strength. Breaking the detailed balance of the molecular transition leads to quasi-discontinuous changes in droplet composition by varying the fuel amount for a larger range of intermolecular interactions. Our findings showcase that phase separation with molecular transitions provides a versatile mechanism to control properties of intracellular and synthetic condensates via discontinuous switches in droplet composition.
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Affiliation(s)
- Giacomo Bartolucci
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | - Omar Adame-Arana
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Xueping Zhao
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | - Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany.
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30
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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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31
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Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021. [PMID: 34185516 DOI: 10.1101/2021.02.24.432456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
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Affiliation(s)
| | - Federico Fanalista
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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32
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Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021; 10:1690-1702. [PMID: 34185516 PMCID: PMC8291763 DOI: 10.1021/acssynbio.1c00068] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 12/17/2022]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
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Affiliation(s)
| | - Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department
of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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33
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Floris E, Piras A, Dall’Asta L, Gamba A, Hirsch E, Campa CC. Physics of compartmentalization: How phase separation and signaling shape membrane and organelle identity. Comput Struct Biotechnol J 2021; 19:3225-3233. [PMID: 34141141 PMCID: PMC8190439 DOI: 10.1016/j.csbj.2021.05.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/15/2021] [Indexed: 11/29/2022] Open
Abstract
Compartmentalization of cellular functions is at the core of the physiology of eukaryotic cells. Recent evidences indicate that a universal organizing process - phase separation - supports the partitioning of biomolecules in distinct phases from a single homogeneous mixture, a landmark event in both the biogenesis and the maintenance of membrane and non-membrane-bound organelles. In the cell, 'passive' (non energy-consuming) mechanisms are flanked by 'active' mechanisms of separation into phases of distinct density and stoichiometry, that allow for increased partitioning flexibility and programmability. A convergence of physical and biological approaches is leading to new insights into the inner functioning of this driver of intracellular order, holding promises for future advances in both biological research and biotechnological applications.
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Affiliation(s)
- Elisa Floris
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Andrea Piras
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
| | - Luca Dall’Asta
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Collegio Carlo Alberto, Piazza Arbarello 8, 10122 Torino, Italy
| | - Andrea Gamba
- Institute of Condensed Matter Physics and Complex Systems, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), sezione di Torino, Via Giuria 1, 10125 Torino, Italy
| | - Emilio Hirsch
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Via Nizza 52, 10126 Torino, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
- Candiolo Cancer Institute, FPO - IRCCS, Str.Prov.le 142, km 3.95, Candiolo (TO) 10060, Italy
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34
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Alshareedah I, Thurston GM, Banerjee PR. Quantifying viscosity and surface tension of multicomponent protein-nucleic acid condensates. Biophys J 2021; 120:1161-1169. [PMID: 33453268 PMCID: PMC8059090 DOI: 10.1016/j.bpj.2021.01.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/27/2020] [Accepted: 01/07/2021] [Indexed: 01/08/2023] Open
Abstract
Living cells organize their internal space into dynamic condensates through liquid-liquid phase separation of multivalent proteins in association with cellular nucleic acids. Here, we study how variations in nucleic acid (NA)-to-protein stoichiometry modulate the condensed phase organization and fluid dynamics in a model system of multicomponent heterotypic condensates. Employing a multiparametric approach comprised of video particle tracking microscopy and optical tweezer-induced droplet fusion, we show that the interfacial tension, but not viscosity, of protein-NA condensates is controlled by the NA/protein ratio across the two-phase regime. In parallel, we utilize fluorescence correlation spectroscopy to quantify protein and NA diffusion in the condensed phase. Fluorescence correlation spectroscopy measurements reveal that the diffusion of the component protein and NA within the condensate core is governed by the viscosity, and hence, also remains insensitive to the changes in NA-to-protein stoichiometry. Collectively, our results provide insights into the regulation of multicomponent heterotypic liquid condensates, reflecting how the bulk mixture composition affects their core versus surface organization and dynamical properties.
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Affiliation(s)
| | - George M Thurston
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York
| | - Priya R Banerjee
- Department of Physics, University at Buffalo SUNY, Buffalo, New York.
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35
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Deng J, Walther A. Programmable ATP-Fueled DNA Coacervates by Transient Liquid-Liquid Phase Separation. Chem 2020; 6:3329-3343. [DOI: 10.1016/j.chempr.2020.09.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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36
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Kaushik P, Pandey PK, Aswal VK, Bohidar HB. Ubiquity of complex coacervation of DNA and proteins in aqueous solution. SOFT MATTER 2020; 16:9525-9533. [PMID: 32966529 DOI: 10.1039/d0sm00543f] [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
We report complex coacervation between a primarily hydrophobic protein, elastin, and a strong polyanion DNA (2 kbp) in aqueous and salty solutions at room temperature, 25 °C. The associative interaction at fixed elastin and varying DNA concentration, thereby maintaining a mixing ratio of r = [DNA] : [elastin] = 0.0027 to 0.093, was probed. What distinguishes this study from protein-DNA coacervation reported earlier is that the protein used here was mostly a hydrophobic polyampholyte with low linear charge density, and its complementary polyelectrolyte, DNA, concentration was chosen to be extremely small (1-35 ppm). The interaction profile was found to be strongly hierarchical in the mixing ratio, defined by three distinct regions: (i) Region I (r < 0.02) was defined as the onset of primary binding leading to condensation of DNA; (ii) Region II (0.02 < r < 0.08) indicated secondary binding which led to the formation of fully charge neutralized complexes signaling the onset of coacervation; and (iii) Region III (0.08 < r < 0.12) revealed growth of insoluble complexes of large size facilitating liquid-solid phase separation. The degree of complex coacervation was suppressed in the presence of a monovalent salt implying that screened Coulomb interactions governed the binding. Small angle neutron scattering data attributed an amorphous structure to the coacervates. The elastin-DNA system belongs to a rare class of interacting biopolymers where very weak electrostatic interactions may drive coacervation, thereby implying that coacervation between DNA and proteins may be ubiquitous.
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Affiliation(s)
- Priyanka Kaushik
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Pankaj K Pandey
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India. and Experimental Physics, Saarland University, Saarbrücken 66123, Germany
| | - V K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - H B Bohidar
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, India.
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37
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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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38
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Alshareedah I, Kaur T, Banerjee PR. Methods for characterizing the material properties of biomolecular condensates. Methods Enzymol 2020; 646:143-183. [PMID: 33453924 PMCID: PMC7849318 DOI: 10.1016/bs.mie.2020.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are membrane-less sub-cellular compartments that perform a plethora of important functions in signaling and storage. The material properties of biomolecular condensates such as viscosity, surface tension, viscoelasticity, and macromolecular diffusion play important roles in regulating their biological functions. Aberrations in these properties have been implicated in various neurodegenerative disorders and certain types of cancer. Unraveling the molecular driving forces that control the fluid structure and dynamics of biomolecular condensates across different length- and time-scales necessitates the application of innovative biophysical methodologies. In this chapter, we discuss major experimental techniques that are widely used to study the material states and dynamics of biomolecular condensates as well as their practical and conceptual limitations. We end this chapter with a discussion on more advanced tools that are currently emerging to address the complex fluid dynamics of these condensates.
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Affiliation(s)
| | - Taranpreet Kaur
- Department of Physics, University at Buffalo, Buffalo, NY, United States
| | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, United States.
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39
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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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40
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Park S, Barnes R, Lin Y, Jeon BJ, Najafi S, Delaney KT, Fredrickson GH, Shea JE, Hwang DS, Han S. Dehydration entropy drives liquid-liquid phase separation by molecular crowding. Commun Chem 2020; 3:83. [PMID: 36703474 PMCID: PMC9814391 DOI: 10.1038/s42004-020-0328-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 05/15/2020] [Indexed: 01/29/2023] Open
Abstract
Complex coacervation driven liquid-liquid phase separation (LLPS) of biopolymers has been attracting attention as a novel phase in living cells. Studies of LLPS in this context are typically of proteins harboring chemical and structural complexity, leaving unclear which properties are fundamental to complex coacervation versus protein-specific. This study focuses on the role of polyethylene glycol (PEG)-a widely used molecular crowder-in LLPS. Significantly, entropy-driven LLPS is recapitulated with charged polymers lacking hydrophobicity and sequence complexity, and its propensity dramatically enhanced by PEG. Experimental and field-theoretic simulation results are consistent with PEG driving LLPS by dehydration of polymers, and show that PEG exerts its effect without partitioning into the dense coacervate phase. It is then up to biology to impose additional variations of functional significance to the LLPS of biological systems.
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Affiliation(s)
- Sohee Park
- grid.49100.3c0000 0001 0742 4007Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Chengam-ro, Nam-gu, Pohang 37673 Republic of Korea
| | - Ryan Barnes
- grid.133342.40000 0004 1936 9676Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA
| | - Yanxian Lin
- grid.133342.40000 0004 1936 9676Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Byoung-jin Jeon
- grid.133342.40000 0004 1936 9676Materials Department, University of California, Santa Barbara, CA 93106 USA
| | - Saeed Najafi
- grid.133342.40000 0004 1936 9676Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA ,grid.133342.40000 0004 1936 9676Materials Research Laboratory, University of California, Santa Barbara, CA 93106 USA
| | - Kris T. Delaney
- grid.133342.40000 0004 1936 9676Materials Research Laboratory, University of California, Santa Barbara, CA 93106 USA
| | - Glenn H. Fredrickson
- grid.133342.40000 0004 1936 9676Materials Department, University of California, Santa Barbara, CA 93106 USA ,grid.133342.40000 0004 1936 9676Materials Research Laboratory, University of California, Santa Barbara, CA 93106 USA ,grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
| | - Joan-Emma Shea
- grid.133342.40000 0004 1936 9676Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA ,grid.133342.40000 0004 1936 9676Department of Physics, University of California, Santa Barbara, CA 93106 USA
| | - Dong Soo Hwang
- grid.49100.3c0000 0001 0742 4007Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Chengam-ro, Nam-gu, Pohang 37673 Republic of Korea ,grid.49100.3c0000 0001 0742 4007Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), 77 Chengam-ro, Nam-gu, Pohang 37673 Republic of Korea
| | - Songi Han
- grid.133342.40000 0004 1936 9676Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 USA ,grid.133342.40000 0004 1936 9676Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA
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41
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Sato Y, Sakamoto T, Takinoue M. Sequence-based engineering of dynamic functions of micrometer-sized DNA droplets. SCIENCE ADVANCES 2020; 6:eaba3471. [PMID: 32537507 PMCID: PMC7269647 DOI: 10.1126/sciadv.aba3471] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/01/2020] [Indexed: 05/02/2023]
Abstract
DNA has the potential to achieve a controllable macromolecular structure, such as hydrogels or droplets formed through liquid-liquid phase separation (LLPS), as the design of its base sequence can result in programmable interactions. Here, we constructed "DNA droplets" via LLPS of sequence-designed DNA nanostructures and controlled their dynamic functions by designing their sequences. Specifically, we were able to adjust the temperature required for the formation of DNA droplets by designing the sequences. In addition, the fusion, fission, and formation of Janus-shaped droplets were controlled by sequence design and enzymatic reactions. Furthermore, modifications of proteins with sequence-designed DNAs allowed for their capture into specific droplets. Overall, our results provide a platform for designing and controlling macromolecular droplets via the information encoded in component molecules and pave the way for various applications of sequence-designed DNA such as cell mimics, synthetic membraneless organelles, and artificial molecular systems.
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Affiliation(s)
| | - Tetsuro Sakamoto
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
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42
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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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43
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Martin N. Dynamic Synthetic Cells Based on Liquid-Liquid Phase Separation. Chembiochem 2019; 20:2553-2568. [PMID: 31039282 DOI: 10.1002/cbic.201900183] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 12/16/2022]
Abstract
Living cells have long been a source of inspiration for chemists. Their capacity of performing complex tasks relies on the spatiotemporal coordination of matter and energy fluxes. Recent years have witnessed growing interest in the bottom-up construction of cell-like models capable of reproducing aspects of such dynamic organisation. Liquid-liquid phase-separation (LLPS) processes in water are increasingly recognised as representing a viable compartmentalisation strategy through which to produce dynamic synthetic cells. Herein, we highlight examples of the dynamic properties of LLPS used to assemble synthetic cells, including their biocatalytic activity, reversible condensation and dissolution, growth and division, and recent directions towards the design of higher-order structures and behaviour.
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Affiliation(s)
- Nicolas Martin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 Avenue du Dr. Albert Schweitzer, 33600, Pessac, France
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44
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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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45
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Kim H, Jeon BJ, Kim S, Jho Y, Hwang DS. Upper Critical Solution Temperature (UCST) Behavior of Coacervate of Cationic Protamine and Multivalent Anions. Polymers (Basel) 2019; 11:E691. [PMID: 30995741 PMCID: PMC6523134 DOI: 10.3390/polym11040691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 02/05/2023] Open
Abstract
Complex coacervation is an emerging liquid/liquid phase separation (LLPS) phenomenon that behaves as a membrane-less organelle in living cells. Yet while one of the critical factors for complex coacervation is temperature, little analysis and research has been devoted to the temperature effect on complex coacervation. Here, we performed a complex coacervation of cationic protamine and multivalent anions (citrate and tripolyphosphate (TPP)). Both mixtures (i.e., protamine/citrate and protamine/TPP) underwent coacervation in an aqueous solution, while a mixture of protamine and sodium chloride did not. Interestingly, the complex coacervation of protamine and multivalent anions showed upper critical solution temperature (UCST) behavior, and the coacervation of protamine and multivalent anions was reversible with solution temperature changes. The large asymmetry in molecular weight between positively charged protamine (~4 kDa) and the multivalent anions (<0.4 kDa) and strong electrostatic interactions between positively charged guanidine residues in protamine and multivalent anions were likely to contribute to UCST behavior in this coacervation system.
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Affiliation(s)
- Hyungbin Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea.
| | - Byoung-Jin Jeon
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
| | - Sangsik Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea.
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea.
| | - YongSeok Jho
- Department of Physics and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Korea.
| | - Dong Soo Hwang
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea.
- Division of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea.
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46
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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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