1
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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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2
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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3
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Abraham GR, Chaderjian AS, N Nguyen AB, Wilken S, Saleh OA. Nucleic acid liquids. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:066601. [PMID: 38697088 DOI: 10.1088/1361-6633/ad4662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by base-pairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.
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Affiliation(s)
- Gabrielle R Abraham
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Aria S Chaderjian
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Anna B N Nguyen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
| | - Sam Wilken
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
| | - Omar A Saleh
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
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4
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Liu W, Deng J, Song S, Sethi S, Walther A. A facile DNA coacervate platform for engineering wetting, engulfment, fusion and transient behavior. Commun Chem 2024; 7:100. [PMID: 38693272 PMCID: PMC11063173 DOI: 10.1038/s42004-024-01185-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/19/2024] [Indexed: 05/03/2024] Open
Abstract
Biomolecular coacervates are emerging models to understand biological systems and important building blocks for designer applications. DNA can be used to build up programmable coacervates, but often the processes and building blocks to make those are only available to specialists. Here, we report a simple approach for the formation of dynamic, multivalency-driven coacervates using long single-stranded DNA homopolymer in combination with a series of palindromic binders to serve as a synthetic coacervate droplet. We reveal details on how the length and sequence of the multivalent binders influence coacervate formation, how to introduce switching and autonomous behavior in reaction circuits, as well as how to engineer wetting, engulfment and fusion in multi-coacervate system. Our simple-to-use model DNA coacervates enhance the understanding of coacervate dynamics, fusion, phase transition mechanisms, and wetting behavior between coacervates, forming a solid foundation for the development of innovative synthetic and programmable coacervates for fundamental studies and applications.
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Affiliation(s)
- Wei Liu
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Jie Deng
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, 430074, Wuhan, China
| | - Siyu Song
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Soumya Sethi
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128, Mainz, Germany.
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5
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Agarwal S, Osmanovic D, Dizani M, Klocke MA, Franco E. Dynamic control of DNA condensation. Nat Commun 2024; 15:1915. [PMID: 38429336 PMCID: PMC10907372 DOI: 10.1038/s41467-024-46266-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 02/21/2024] [Indexed: 03/03/2024] Open
Abstract
Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics.
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Affiliation(s)
- Siddharth Agarwal
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Bioengineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Dino Osmanovic
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Mahdi Dizani
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Melissa A Klocke
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Elisa Franco
- Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Bioengineering, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
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6
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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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7
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Hanif W, Yadav I, Hasan E, Alsulaiman D. Programmable all-DNA hydrogels based on rolling circle and multiprimed chain amplification products. APL Bioeng 2023; 7:046106. [PMID: 37901137 PMCID: PMC10613091 DOI: 10.1063/5.0169063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023] Open
Abstract
Soft, biocompatible, and tunable materials offer biomedical engineers and material scientists programmable matrices for a variety of biomedical applications. In this regard, DNA hydrogels have emerged as highly promising biomaterials that offer programmable self-assembly, superior biocompatibility, and the presence of specific molecular identifiable structures. Many types of DNA hydrogels have been developed, yet the programmability of the DNA building blocks has not been fully exploited, and further efforts must be directed toward understanding how to finely tune their properties in a predictable manner. Herein, we develop physically crosslinked all-DNA hydrogels with tunable morphology and controllable biodegradation, based on rolling circle amplification and multiprimed chain amplification products. Through molecular engineering of the DNA sequences and their nano-/microscale architectures, the precursors self-assemble in a controlled manner to produce soft hydrogels in an efficient, cost-effective, and highly tunable manner. Notably, we develop a novel DNA microladder architecture that serves as a framework for modulating the hydrogel properties, including over an order of magnitude change in pore size and up to 50% change in biodegradation rate. Overall, we demonstrate how the properties of this DNA-based biomaterial can be tuned by modulating the amounts of rigid double-stranded DNA chains compared to flexible single-stranded DNA chains, as well as through the precursor architecture. Ultimately, this work opens new avenues for the development of programmable and biodegradable soft materials in which DNA functions not only as a store of genetic information but also as a versatile polymeric biomaterial and molecularly engineered macroscale scaffold.
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Affiliation(s)
- Wildan Hanif
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Indresh Yadav
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Erol Hasan
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Dana Alsulaiman
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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8
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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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9
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Cho Y, Jacobs WM. Nonequilibrium interfacial properties of chemically driven fluids. J Chem Phys 2023; 159:154101. [PMID: 37843057 DOI: 10.1063/5.0166824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
Chemically driven fluids can demix to form condensed droplets that exhibit phase behaviors not observed at equilibrium. In particular, nonequilibrium interfacial properties can emerge when the chemical reactions are driven differentially between the interior and exterior of the phase-separated droplets. Here, we use a minimal model to study changes in the interfacial tension between coexisting phases away from equilibrium. Simulations of both droplet nucleation and interface roughness indicate that the nonequilibrium interfacial tension can either be increased or decreased relative to its equilibrium value, depending on whether the driven chemical reactions are accelerated or decelerated within the droplets. Finally, we show that these observations can be understood using a predictive theory based on an effective thermodynamic equilibrium.
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Affiliation(s)
- Yongick Cho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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10
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Bergmann AM, Bauermann J, Bartolucci G, Donau C, Stasi M, Holtmannspötter AL, Jülicher F, Weber CA, Boekhoven J. Liquid spherical shells are a non-equilibrium steady state of active droplets. Nat Commun 2023; 14:6552. [PMID: 37848445 PMCID: PMC10582082 DOI: 10.1038/s41467-023-42344-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/06/2023] [Indexed: 10/19/2023] Open
Abstract
Liquid-liquid phase separation yields spherical droplets that eventually coarsen to one large, stable droplet governed by the principle of minimal free energy. In chemically fueled phase separation, the formation of phase-separating molecules is coupled to a fuel-driven, non-equilibrium reaction cycle. It thus yields dissipative structures sustained by a continuous fuel conversion. Such dissipative structures are ubiquitous in biology but are poorly understood as they are governed by non-equilibrium thermodynamics. Here, we bridge the gap between passive, close-to-equilibrium, and active, dissipative structures with chemically fueled phase separation. We observe that spherical, active droplets can undergo a morphological transition into a liquid, spherical shell. We demonstrate that the mechanism is related to gradients of short-lived droplet material. We characterize how far out of equilibrium the spherical shell state is and the chemical power necessary to sustain it. Our work suggests alternative avenues for assembling complex stable morphologies, which might already be exploited to form membraneless organelles by cells.
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Affiliation(s)
- Alexander M Bergmann
- School of Natural Sciences, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Jonathan Bauermann
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187, Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Giacomo Bartolucci
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187, Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Carsten Donau
- School of Natural Sciences, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Michele Stasi
- School of Natural Sciences, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Anna-Lena Holtmannspötter
- School of Natural Sciences, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Strasse 38, 01187, Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307, Dresden, Germany
- Cluster of Excellence Physics of Life, Technical University of Dresden, 01307, Dresden, Germany
| | - Christoph A Weber
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstrasse 1, 86159, Augsburg, Germany.
| | - Job Boekhoven
- School of Natural Sciences, Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany.
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11
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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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12
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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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13
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Kubota R, Hiroi T, Ikuta Y, Liu Y, Hamachi I. Visualizing Formation and Dynamics of a Three-Dimensional Sponge-like Network of a Coacervate in Real Time. J Am Chem Soc 2023; 145:18316-18328. [PMID: 37562059 DOI: 10.1021/jacs.3c03793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Coacervates, which are formed by liquid-liquid phase separation, have been extensively explored as models for synthetic cells and membraneless organelles, so their in-depth structural analysis is crucial. However, both the inner structure dynamics and formation mechanism of coacervates remain elusive. Herein, we demonstrate real-time confocal observation of a three-dimensional sponge-like network in a dipeptide-based coacervate. In situ generation of the dipeptide allowed us to capture the emergence of the sponge-like network via unprecedented membrane folding of vesicle-shaped intermediates. We also visualized dynamic fluctuation of the network, including reversible engagement/disengagement of cross-links and a stochastic network kissing event. Photoinduced transient formation of a multiphase coacervate was achieved with a thermally responsive phase transition. Our findings expand the fundamental understanding of synthetic coacervates and provide opportunities to manipulate their physicochemical properties by engineering the inner network for potential applications in development of artificial cells and life-like material fabrication.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Taro Hiroi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuriki Ikuta
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuchong Liu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Nishikyo-ku, Katsura 615-8530, Japan
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14
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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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15
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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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16
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Cho Y, Jacobs WM. Tuning Nucleation Kinetics via Nonequilibrium Chemical Reactions. PHYSICAL REVIEW LETTERS 2023; 130:128203. [PMID: 37027881 DOI: 10.1103/physrevlett.130.128203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative similarities between liquid-liquid phase separation in these systems, the extent to which the phase-separation kinetics differ remains unclear. Here we show that inhomogeneous chemical reactions can alter the nucleation kinetics of liquid-liquid phase separation in a manner that is consistent with classical nucleation theory, but can only be rationalized by introducing a nonequilibrium interfacial tension. We identify conditions under which nucleation can be accelerated without changing the energetics or supersaturation, thus breaking the correlation between fast nucleation and strong driving forces that is typical of phase separation and self-assembly at thermal equilibrium.
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Affiliation(s)
- Yongick Cho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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17
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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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18
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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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19
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Chew PY, Joseph JA, Collepardo-Guevara R, Reinhardt A. Thermodynamic origins of two-component multiphase condensates of proteins. Chem Sci 2023; 14:1820-1836. [PMID: 36819870 PMCID: PMC9931050 DOI: 10.1039/d2sc05873a] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
Intracellular condensates are highly multi-component systems in which complex phase behaviour can ensue, including the formation of architectures comprising multiple immiscible condensed phases. Relying solely on physical intuition to manipulate such condensates is difficult because of the complexity of their composition, and systematically learning the underlying rules experimentally would be extremely costly. We address this challenge by developing a computational approach to design pairs of protein sequences that result in well-separated multilayered condensates and elucidate the molecular origins of these compartments. Our method couples a genetic algorithm to a residue-resolution coarse-grained protein model. We demonstrate that we can design protein partners to form multiphase condensates containing naturally occurring proteins, such as the low-complexity domain of hnRNPA1 and its mutants, and show how homo- and heterotypic interactions must differ between proteins to result in multiphasicity. We also show that in some cases the specific pattern of amino-acid residues plays an important role. Our findings have wide-ranging implications for understanding and controlling the organisation, functions and material properties of biomolecular condensates.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Jerelle A. Joseph
- Yusuf Hamied Department of Chemistry, University of CambridgeCambridgeCB2 1EWUK,Department of Physics, University of CambridgeCambridgeCB3 0HEUK,Department of Genetics, University of CambridgeCambridgeCB2 3EHUK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK .,Department of Physics, University of Cambridge Cambridge CB3 0HE UK.,Department of Genetics, University of Cambridge Cambridge CB2 3EH UK
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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20
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Hydrogel-based thermosensor using peptide nucleic acid and PEGylated graphene oxide. Anal Chim Acta 2023; 1239:340708. [PMID: 36628715 DOI: 10.1016/j.aca.2022.340708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Developing a ready-to-use miniaturized thermosensor is a great challenge due to its individual use on a large scale for daily business such as food industry and healthcare. Herein, a polyethylene glycol (PEG)-modified graphene oxide (GO)-based hydrogel thermosensor was established with a fluorescent dye-labeled peptide nucleic acid (F-PNA). The size-tunable hydrogel with high water content and sufficient solidity allowed free movement of the oligonucleotides through the pores and improved usability for handling the sensor. In the PEG-GO hydrogel, the DNA/F-PNA duplex could be denatured by increasing the temperature, followed by selective PNA capture on the PEG-GO. Using this principle, the PEG-GO hydrogel exhibited a change in the fluorescence signal of F-PNA in a temperature-dependent manner, allowing real-time visualization of temperature on a large scale. The temperature detection range of this system can be adjusted by designing the PNA strands based on the melting temperature of the DNAzyme/PNA duplex. Its sensing specificity and detection range could be increased and broadened by observing multi-color detection using PNA probes labeled with different fluorescent dyes of different lengths in a single hydrogel. In addition, the hydrogel platform is easy to store for long time periods via dehydration and can be restored with the addition of water, allowing easy transport, storage, and use of the thermosensor in everyday life.
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21
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Tekin E, Salditt A, Schwintek P, Wunnava S, Langlais J, Saenz J, Tang D, Schwille P, Mast C, Braun D. Prebiotic Foam Environments to Oligomerize and Accumulate RNA. Chembiochem 2022; 23:e202200423. [PMID: 36354762 PMCID: PMC10100173 DOI: 10.1002/cbic.202200423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/24/2022] [Indexed: 11/12/2022]
Abstract
When water interacts with porous rocks, its wetting and surface tension properties create air bubbles in large number. To probe their relevance as a setting for the emergence of life, we microfluidically created foams that were stabilized with lipids. A persistent non-equilibrium setting was provided by a thermal gradient. The foam's large surface area triggers capillary flows and wet-dry reactions that accumulate, aggregate and oligomerize RNA, offering a compelling habitat for RNA-based early life as it offers both wet and dry conditions in direct neighborhood. Lipids were screened to stabilize the foams. The prebiotically more probable myristic acid stabilized foams over many hours. The capillary flow created by the evaporation at the water-air interface provided an attractive force for molecule localization and selection for molecule size. For example, self-binding oligonucleotide sequences accumulated and formed micrometer-sized aggregates which were shuttled between gas bubbles. The wet-dry cycles at the foam bubble interfaces triggered a non-enzymatic RNA oligomerization from 2',3'-cyclic CMP and GMP which despite the small dry reaction volume was superior to the corresponding dry reaction. The found characteristics make heated foams an interesting, localized setting for early molecular evolution.
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Affiliation(s)
- Emre Tekin
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Annalena Salditt
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Philipp Schwintek
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Sreekar Wunnava
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Juliette Langlais
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - James Saenz
- Center for Molecular BioengineeringTechnische Universität DresdenHelmholtzstrasse 1001069DresdenGermany
| | - Dora Tang
- Dynamic Protocellular SystemsMax-Planck Institute for Molecular Cell Biology and GeneticsPfotenhauerstrasse 10801307DresdenGermany
| | - Petra Schwille
- Cellular and Molecular BiophysicsMax-Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Christof Mast
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
| | - Dieter Braun
- Systems BiophysicsCenter for Nano-Science and Origins Cluster Initiative Department of PhysicsLudwig-Maximilians-Universität MünchenAmalienstrasse 5480799MünchenGermany
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22
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Donau C, Späth F, Stasi M, Bergmann AM, Boekhoven J. Phase Transitions in Chemically Fueled, Multiphase Complex Coacervate Droplets. Angew Chem Int Ed Engl 2022; 61:e202211905. [PMID: 36067054 PMCID: PMC9828839 DOI: 10.1002/anie.202211905] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 01/12/2023]
Abstract
Membraneless organelles are droplets in the cytosol that are regulated by chemical reactions. Increasing studies suggest that they are internally organized. However, how these subcompartments are regulated remains elusive. Herein, we describe a complex coacervate-based model composed of two polyanions and a short peptide. With a chemical reaction cycle, we control the affinity of the peptide for the polyelectrolytes leading to distinct regimes inside the phase diagram. We study the transitions from one regime to another and identify new transitions that can only occur under kinetic control. Finally, we show that the chemical reaction cycle controls the liquidity of the droplets offering insights into how active processes inside cells play an important role in tuning the liquid state of membraneless organelles. Our work demonstrates that not only thermodynamic properties but also kinetics should be considered in the organization of multiple phases in droplets.
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Affiliation(s)
- Carsten Donau
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Fabian Späth
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Michele Stasi
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Alexander M. Bergmann
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Job Boekhoven
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
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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 AP, Appel EA, Ashby PD, Baker BM, Franco E, Gu L, Haynes K, Joshi NS, Kloxin AM, Kouwer PHJ, Mittal J, Morsut L, Noireaux V, Parekh S, Schulman R, Tang SKY, Valentine MT, Vega SL, Weber W, Stephanopoulos N, Chaudhuri O. The living interface between synthetic biology and biomaterial design. NATURE MATERIALS 2022; 21:390-397. [PMID: 35361951 PMCID: PMC10265650 DOI: 10.1038/s41563-022-01231-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Recent far-reaching advances in synthetic biology have yielded exciting tools for the creation of new materials. Conversely, advances in the fundamental understanding of soft-condensed matter, polymers and biomaterials offer new avenues to extend the reach of synthetic biology. The broad and exciting range of possible applications have substantial implications to address grand challenges in health, biotechnology and sustainability. Despite the potentially transformative impact that lies at the interface of synthetic biology and biomaterials, the two fields have, so far, progressed mostly separately. This Perspective provides a review of recent key advances in these two fields, and a roadmap for collaboration at the interface between the two communities. We highlight the near-term applications of this interface to the development of hierarchically structured biomaterials, from bioinspired building blocks to 'living' materials that sense and respond based on the reciprocal interactions between materials and embedded cells.
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Affiliation(s)
- Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Eric A Appel
- Department of Materials Science & Engineering, Stanford University, Stanford, CA, USA
| | - Paul D Ashby
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brendon M Baker
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Luo Gu
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Karmella Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
| | - Neel S Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - April M Kloxin
- Department of Chemical and Biomolecular Engineering and Materials Science and Engineering, University of Delaware, Newark, DE, USA
| | - Paul H J Kouwer
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Leonardo Morsut
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, USA
| | - Sapun Parekh
- Department of Biomedical Engineering, University of Texas, Austin, Austin, TX, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Megan T Valentine
- Department of Mechanical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ, USA
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | | | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA.
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26
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Zhao QH, Cao FH, Luo ZH, Huck WTS, Deng NN. Photoswitchable Molecular Communication between Programmable DNA-Based Artificial Membraneless Organelles. Angew Chem Int Ed Engl 2022; 61:e202117500. [PMID: 35090078 DOI: 10.1002/anie.202117500] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 01/26/2023]
Abstract
Spatiotemporal organization of distinct biological processes in cytomimetic compartments is a crucial step towards engineering functional artificial cells. Mimicking controlled bi-directional molecular communication inside artificial cells remains a considerable challenge. Here we present photoswitchable molecular transport between programmable membraneless organelle-like DNA coacervates in a synthetic microcompartment. We use droplet microfluidics to fabricate membraneless non-fusing DNA coacervates by liquid-liquid phase separation in a water-in-oil droplet, and employ the interior DNA coacervates as artificial organelles to imitate intracellular communication via photo-regulated uni- and bi-directional transfer of biomolecules. Our results highlight a promising new route to assembly of multicompartment artificial cells with functional networks.
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Affiliation(s)
- Qi-Hong Zhao
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fang-Hao Cao
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhen-Hong Luo
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, 800 Dongchuan Road, Shanghai, 200240, China
| | - Wilhelm T S Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Nan-Nan Deng
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, 800 Dongchuan Road, Shanghai, 200240, China
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27
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Zhao QH, Cao FH, Luo ZH, Huck WTS, Deng NN. Photoswitchable Molecular Communication between Programmable DNA‐based Artificial Membraneless Organelles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qi-Hong Zhao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Fang-Hao Cao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Zhen-Hong Luo
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Wilhelm T. S. Huck
- Radboud University Institute for Molecules and Materials: Radboud Universiteit Institute for Molecules and Materials Institue for Molecules and Materials NETHERLANDS
| | - Nan-Nan Deng
- Shanghai Jiao Tong University Chemistry and Chemical Engineering 800 Dongchuan RD. Minhang District 200240 Shanghai CHINA
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28
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Tom JK, Deniz AA. Complex dynamics of multicomponent biological coacervates. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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29
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Ma L, Xiong W, Yu K, Wang X, Cao Y, Lu X, Cai Y. Liquid-Phase Condensation via Macromolecular Crowding in Polymerization-Induced Electrostatic Self-Assembly. ACS Macro Lett 2021; 10:1410-1415. [PMID: 35549018 DOI: 10.1021/acsmacrolett.1c00557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Macromolecular crowding plays a key role in liquid-phase condensation of proteins and membraneless organelles yet is largely unexplored for artificial liquid materials. Herein, we present a strategy for direct access to multiphase liquid condensates with individual charged/neutral subdomains, by introducing macromolecular crowding to our previous protocol of liquid-liquid phase-separation-driven polymerization-induced electrostatic self-assembly (LLPS-PIESA). We show that reversible addition fragmentation chain transfer (RAFT) aqueous dispersion photo-copolymerization of a charged monomer with a specific neutral monomer, in the presence of a polar macrochain transfer agent (CTA) and an oppositely charged polyion, can induce self-sorting and macromolecular crowding. LLPS-PIESA proceeds via liquid-phase condensation of as-assembled nascent clusters up to biologically important nanostructured multiphase condensates with individual charged/neutral subdomains.
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Affiliation(s)
- Lei Ma
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Weixing Xiong
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Kaiwen Yu
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xiyu Wang
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Ying Cao
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xinhua Lu
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yuanli Cai
- State-Local Joint Engineering Laboratory for Novel Functional Polymer Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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30
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Lichtinger SM, Garaizar A, Collepardo-Guevara R, Reinhardt A. Targeted modulation of protein liquid-liquid phase separation by evolution of amino-acid sequence. PLoS Comput Biol 2021; 17:e1009328. [PMID: 34428231 PMCID: PMC8415608 DOI: 10.1371/journal.pcbi.1009328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/03/2021] [Accepted: 08/07/2021] [Indexed: 12/27/2022] Open
Abstract
Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid-liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose a computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We validate the predicted critical solution temperatures of the mutated sequences with ABSINTH, a more accurate all-atom model. We apply the algorithm to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction, and we find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the make-up of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.
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Affiliation(s)
- Simon M. Lichtinger
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Adiran Garaizar
- Department of Physics, Cavendish Laboratory, Maxwell Centre, University of Cambridge, Cambridge, United Kingdom
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Physics, Cavendish Laboratory, Maxwell Centre, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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31
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Masukawa MK, Okuda Y, Takinoue M. Aqueous Triple-Phase System in Microwell Array for Generating Uniform-Sized DNA Hydrogel Particles. Front Genet 2021; 12:705022. [PMID: 34367260 PMCID: PMC8343185 DOI: 10.3389/fgene.2021.705022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/03/2021] [Indexed: 11/19/2022] Open
Abstract
DNA hydrogels are notable for their biocompatibility and ability to incorporate DNA information and computing properties into self-assembled micrometric structures. These hydrogels are assembled by the thermal gelation of DNA motifs, a process which requires a high salt concentration and yields polydisperse hydrogel particles, thereby limiting their application and physicochemical characterization. In this study, we demonstrate that single, uniform DNA hydrogel particles can form inside aqueous/aqueous two-phase systems (ATPSs) assembled in a microwell array. In this process, uniform dextran droplets are formed in a microwell array inside a microfluidic device. The dextran droplets, which contain DNA motifs, are isolated from each other by an immiscible PEG solution containing magnesium ions and spermine, which enables the DNA hydrogel to undergo gelation. Upon thermal annealing of the device, we observed the formation of an aqueous triple-phase system in which uniform DNA hydrogel particles (the innermost aqueous phase) resided at the interface of the aqueous two-phase system of dextran and PEG. We expect ATPS microdroplet arrays to be used to manufacture other hydrogel microparticles and DNA/dextran/PEG aqueous triple-phase systems to serve as a highly parallel model for artificial cells and membraneless organelles.
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Affiliation(s)
| | | | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Yokohama, Japan
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32
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Kato S, Garenne D, Noireaux V, Maeda YT. Phase Separation and Protein Partitioning in Compartmentalized Cell-Free Expression Reactions. Biomacromolecules 2021; 22:3451-3459. [PMID: 34258998 DOI: 10.1021/acs.biomac.1c00546] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) is important to control a wide range of reactions from gene expression to protein degradation in a cell-sized space. To bring a better understanding of the compatibility of such phase-separated structures with protein synthesis, we study emergent LLPS in a cell-free transcription-translation (TXTL) reaction. When the TXTL reaction composed of many proteins is concentrated, the uniformly mixed state becomes unstable, and membrane-less phases form spontaneously. This LLPS droplet formation is induced when the TXTL reaction is enclosed in water-in-oil emulsion droplets, in which water evaporates from the surface. As the emulsion droplets shrink, smaller LLPS droplets appear inside the emulsion droplets and coalesce into large phase-separated domains that partition the localization of synthesized reporter proteins. The presence of PEG in the TXTL reaction is important not only for versatile cell-free protein synthesis but also for the formation of two large domains capable of protein partitioning. Our results may shed light on the dynamic interplay of LLPS formation and cell-free protein synthesis toward the construction of synthetic organelles.
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Affiliation(s)
- Shuzo Kato
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - David Garenne
- School of Physics and Astronomy, University of Minnesota, 115 Union Street Se, Minneapolis, Minnesota 55455, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 115 Union Street Se, Minneapolis, Minnesota 55455, United States
| | - Yusuke T Maeda
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
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33
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Spoelstra WK, Jacques JM, Gonzalez-Linares R, Nobrega FL, Haagsma AC, Dogterom M, Meijer DH, Idema T, Brouns SJJ, Reese L. CRISPR-based DNA and RNA detection with liquid-liquid phase separation. Biophys J 2021; 120:1198-1209. [PMID: 33617832 PMCID: PMC8059199 DOI: 10.1016/j.bpj.2021.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/01/2021] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
The ability to detect specific nucleic acid sequences allows for a wide range of applications such as the identification of pathogens, clinical diagnostics, and genotyping. CRISPR-Cas proteins Cas12a and Cas13a are RNA-guided endonucleases that bind and cleave specific DNA and RNA sequences, respectively. After recognition of a target sequence, both enzymes activate indiscriminate nucleic acid cleavage, which has been exploited for sequence-specific molecular diagnostics of nucleic acids. Here, we present a label-free detection approach that uses a readout based on solution turbidity caused by liquid-liquid phase separation (LLPS). Our approach relies on the fact that the LLPS of oppositely charged polymers requires polymers to be longer than a critical length. This length dependence is predicted by the Voorn-Overbeek model, which we describe in detail and validate experimentally in mixtures of polynucleotides and polycations. We show that the turbidity resulting from LLPS can be used to detect the presence of specific nucleic acid sequences by employing the programmable CRISPR-nucleases Cas12a and Cas13a. Because LLPS of polynucleotides and polycations causes solutions to become turbid, the detection of specific nucleic acid sequences can be observed with the naked eye. We furthermore demonstrate that there is an optimal polynucleotide concentration for detection. Finally, we provide a theoretical prediction that hints towards possible improvements of an LLPS-based detection assay. The deployment of LLPS complements CRISPR-based molecular diagnostic applications and facilitates easy and low-cost nucleotide sequence detection.
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Affiliation(s)
- Willem Kasper Spoelstra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Jeroen M Jacques
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Rodrigo Gonzalez-Linares
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Franklin L Nobrega
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Anna C Haagsma
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Dimphna H Meijer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Timon Idema
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Louis Reese
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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34
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O'Flynn BG, Mittag T. The role of liquid-liquid phase separation in regulating enzyme activity. Curr Opin Cell Biol 2021; 69:70-79. [PMID: 33503539 PMCID: PMC8058252 DOI: 10.1016/j.ceb.2020.12.012] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022]
Abstract
Liquid-liquid phase separation (LLPS) is now recognized as a common mechanism underlying regulation of enzyme activity in cells. Insights from studies in cells are complemented by in vitro studies aimed at developing a better understanding of mechanisms underlying such control. These mechanisms are often based on the influence of LLPS on the physicochemical properties of the enzyme's environment. Biochemical mechanisms underlying such regulation include the potential for concentrating reactants together, tuning reaction rates, and controlling competing metabolic pathways. LLPS is thus a powerful tool with extensive utilities at the cell's disposal, e.g. for consolidating cell survival under stress or rerouting metabolic pathways in response to the energy state of the cell. Here, we examin the evidence for how LLPS affects enzyme catalysis and begin to understand emerging concepts and expand our understanding of enzyme catalysis in living cells.
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Affiliation(s)
- Brian G O'Flynn
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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35
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Schuster BS, Regy RM, Dolan EM, Kanchi Ranganath A, Jovic N, Khare SD, Shi Z, Mittal J. Biomolecular Condensates: Sequence Determinants of Phase Separation, Microstructural Organization, Enzymatic Activity, and Material Properties. J Phys Chem B 2021; 125:3441-3451. [PMID: 33661634 DOI: 10.1021/acs.jpcb.0c11606] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This perspective article highlights recent progress and emerging challenges in understanding the formation and function of membraneless organelles (MLOs). A long-term goal in the MLO field is to identify the sequence-encoded rules that dictate the formation of compositionally controlled biomolecular condensates, which cells utilize to perform a wide variety of functions. The molecular organization of the different components within a condensate can vary significantly, ranging from a homogeneous mixture to core-shell droplet structures. We provide many examples to highlight the richness of the observed behavior and potential research directions for improving our mechanistic understanding. The tunable environment within condensates can, in principle, alter enzymatic activity significantly. We examine recent examples where this was demonstrated, including applications in synthetic biology. An important question about MLOs is the role of liquid-like material properties in biological function. We discuss the need for improved quantitative characterization tools and the development of sequence-structure-dynamics relationships.
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Affiliation(s)
- Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Elliott M Dolan
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Aishwarya Kanchi Ranganath
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Nina Jovic
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Zheng Shi
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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36
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Muzzopappa F, Hertzog M, Erdel F. DNA length tunes the fluidity of DNA-based condensates. Biophys J 2021; 120:1288-1300. [PMID: 33640380 PMCID: PMC8059207 DOI: 10.1016/j.bpj.2021.02.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/31/2021] [Accepted: 02/15/2021] [Indexed: 02/09/2023] Open
Abstract
Living organisms typically store their genomic DNA in a condensed form. Mechanistically, DNA condensation can be driven by macromolecular crowding, multivalent cations, or positively charged proteins. At low DNA concentration, condensation triggers the conformational change of individual DNA molecules into a compacted state, with distinct morphologies. Above a critical DNA concentration, condensation goes along with phase separation into a DNA-dilute and a DNA-dense phase. The latter DNA-dense phase can have different material properties and has been reported to be rather liquid-like or solid-like depending on the characteristics of the DNA and the solvent composition. Here, we systematically assess the influence of DNA length on the properties of the resulting condensates. We show that short DNA molecules with sizes below 1 kb can form dynamic liquid-like assemblies when condensation is triggered by polyethylene glycol and magnesium ions, binding of linker histone H1, or nucleosome reconstitution in combination with linker histone H1. With increasing DNA length, molecules preferentially condense into less dynamic more solid-like assemblies, with phage λ-DNA with 48.5 kb forming mostly solid-like assemblies under the conditions assessed here. The transition from liquid-like to solid-like condensates appears to be gradual, with DNA molecules of roughly 1–10 kb forming condensates with intermediate properties. Titration experiments with linker histone H1 suggest that the fluidity of condensates depends on the net number of attractive interactions established by each DNA molecule. We conclude that DNA molecules that are much shorter than a typical human gene are able to undergo liquid-liquid phase separation, whereas longer DNA molecules phase separate by default into rather solid-like condensates. We speculate that the local distribution of condensing factors can modulate the effective length of chromosomal domains in the cell. We anticipate that the link between DNA length and fluidity established here will improve our understanding of biomolecular condensates involving DNA.
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Affiliation(s)
- Fernando Muzzopappa
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Maud Hertzog
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Fabian Erdel
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France.
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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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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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