1
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Majumder S, Coupe S, Fakhri N, Jain A. Sequence-encoded intermolecular base pairing modulates fluidity in DNA and RNA condensates. Nat Commun 2025; 16:4258. [PMID: 40335475 PMCID: PMC12058984 DOI: 10.1038/s41467-025-59456-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Accepted: 04/22/2025] [Indexed: 05/09/2025] Open
Abstract
Nature uses bottom-up self-assembly to build structures with remarkable complexity and functionality. Understanding how molecular-scale interactions translate to macroscopic properties remains a major challenge and requires systems that effectively bridge these two scales. Here, we generate DNA and RNA-based liquids with exquisite programmability in their macroscopic rheological properties. In the presence of multivalent cations, nucleic acids can condense to a liquid-like state. Within these liquids, DNA and RNA retain sequence-specific hybridization abilities. We show that sequence-specific inter-molecular hybridization in the condensed phase cross-links molecules and slows down chain dynamics. This reduced chain mobility is mirrored in the macroscopic properties of the condensates. Molecular diffusivity and material viscosity scale with the inter-molecular hybridization energy, enabling precise sequence-based modulation of condensate properties over several orders of magnitude. Our work offers a robust platform to create bottom-up programmable fluids and may help advance our understanding of liquid-like compartments in cells.
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Affiliation(s)
- Sumit Majumder
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Sebastian Coupe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nikta Fakhri
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ankur Jain
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Ohno H, Kijima J, Ochi Y, Shoji M, Taira J, Mabuchi T, Sato Y. Oligolysine Enhances and Inhibits DNA Condensate Formation. ACS OMEGA 2025; 10:15781-15789. [PMID: 40290937 PMCID: PMC12019750 DOI: 10.1021/acsomega.5c01928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2025] [Revised: 03/21/2025] [Accepted: 03/28/2025] [Indexed: 04/30/2025]
Abstract
The formation of biomolecular condensates via phase separation relates to various cellular functions. Reconstituting these condensates with designed molecules facilitates the exploration of their mechanisms and potential applications. Sequence-designed DNA nanostructures enable the investigation of how structural design influences condensate formation and the construction of functional artificial condensates. Despite the high designability of DNA-based condensates, free nanostructures that do not assemble into condensates remain a challenge. Combining DNA nanostructures with other molecules, such as peptides, represents a promising approach to overcoming the limitations of DNA condensates and gaining a deeper understanding of molecular condensates. Herein, we report the effects of cationic oligolysines with several residues on DNA condensate formation assembled from Y-shaped DNA nanostructures. DNA condensate formation was enhanced by oligolysines at an appropriate L/P ratio, which refers to the ratio of positively charged amine groups in lysine (L) to negatively charged nucleic acid phosphate groups (P). Oligolysines with five residues enhanced condensate formation while maintaining the sequence-specific interaction of DNA. In contrast, oligolysines inhibited condensate formation depending on the L/P ratio and residue number. This was attributed to nanostructure deformation caused by oligolysines. These results suggest that the amount and length of cationic peptides significantly affect the self-assembly of branched DNA nanostructures. This study offers important insights into biomolecular condensates that can guide further development of DNA/peptide hybrid condensates to enhance the functions of artificial condensates for use in artificial cells and molecular robots.
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Affiliation(s)
- Hiroaki Ohno
- Department
of Intelligent and Control Systems, Kyushu
Institute of Technology 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Junko Kijima
- Institute
of Fluid Science, Tohoku University 2-1-1
Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yosuke Ochi
- Department
of Bioscience and Bioinformatics, Kyushu
Institute of Technology 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Masaaki Shoji
- Department
of Intelligent and Control Systems, Kyushu
Institute of Technology 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Junichi Taira
- Department
of Bioscience and Bioinformatics, Kyushu
Institute of Technology 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Takuya Mabuchi
- Institute
of Fluid Science, Tohoku University 2-1-1
Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yusuke Sato
- Department
of Intelligent and Control Systems, Kyushu
Institute of Technology 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
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3
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Skelly E, Bayard CJ, Jarusek J, Clark B, Rebolledo LP, Radwan Y, Nguyen P, Andrade-Muñoz M, Deaton TA, Lushnikov A, LeBlanc SJ, Krasnoslobodtsev AV, Yingling YG, Afonin KA. Design and Characterization of DNA-Driven Condensates: Regulating Topology, Mechanical Properties, and Immunorecognition. ACS APPLIED MATERIALS & INTERFACES 2025; 17:22322-22336. [PMID: 40168179 PMCID: PMC12012714 DOI: 10.1021/acsami.5c00428] [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: 01/09/2025] [Revised: 03/07/2025] [Accepted: 03/19/2025] [Indexed: 04/03/2025]
Abstract
Cells maintain spatiotemporal control over biochemical processes through the formation and dissolution of biomolecular condensates, dynamic membraneless organelles formed via liquid-liquid phase separation. Composed primarily of proteins and nucleic acids, these condensates regulate key cellular functions, and their properties are influenced by the concentration and type of molecules involved. The structural versatility challenges the de novo design and assembly of condensates with predefined properties. Through feedback between computational and experimental approaches, we introduce a modular system for assembling condensates using nucleic acid nanotechnology. By utilizing programmable oligonucleotides and orthogonal synthesis methods, we control the structural parameters, responsive behavior, and immunorecognition of the products. Dissipative particle dynamics simulations predict some conditions to produce larger, well-defined condensates with compact, globular cores, while others result in smaller, more diffuse analogs. Fluorescence microscopy confirms these findings and microrheology demonstrates the viscoelastic adaptability of tested condensates. Nucleases trigger disruption of structures, and ethidium bromide intercalation protects condensates from digestion. Immunostimulatory assays suggest condensate-specific activation of the IRF pathway via cGAS-STING signaling. This study provides a framework for developing biomolecular condensates with customizable properties and immunorecognition for various biological applications.
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Affiliation(s)
- Elizabeth Skelly
- Chemistry
and Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Christina J. Bayard
- Department
of Materials Science and Engineering, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Joel Jarusek
- Department
of Physics, University of Nebraska Omaha, Omaha, Nebraska 68182, United States
| | - Benjamin Clark
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United
States
| | - Laura P. Rebolledo
- Chemistry
and Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Yasmine Radwan
- Chemistry
and Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Phong Nguyen
- Chemistry
and Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Melanie Andrade-Muñoz
- Chemistry
and Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Thomas A. Deaton
- Department
of Materials Science and Engineering, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Alexander Lushnikov
- Department
of Physics, University of Nebraska Omaha, Omaha, Nebraska 68182, United States
| | - Sharonda J. LeBlanc
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United
States
| | | | - Yaroslava G. Yingling
- Department
of Materials Science and Engineering, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Kirill A. Afonin
- Chemistry
and Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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4
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Boraas LC, Hu M, Martino P, Thornton L, Vejnar CE, Zhen G, Zeng L, Parker DM, Cox AL, Giraldez AJ, Su X, Mayr C, Wang S, Nicoli S. G3BP1 ribonucleoprotein complexes regulate focal adhesion protein mobility and cell migration. Cell Rep 2025; 44:115237. [PMID: 39883578 PMCID: PMC11923778 DOI: 10.1016/j.celrep.2025.115237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 11/05/2024] [Accepted: 01/06/2025] [Indexed: 02/01/2025] Open
Abstract
The subcellular localization of mRNAs plays a pivotal role in biological processes, including cell migration. For instance, β-actin mRNA and its associated RNA-binding protein (RBP), ZBP1/IGF2BP1, are recruited to focal adhesions (FAs) to support localized β-actin synthesis, crucial for cell migration. However, whether other mRNAs and RBPs also localize at FAs remains unclear. Here, we identify hundreds of mRNAs that are enriched at FAs (FA-mRNAs). FA-mRNAs share characteristics with stress granule (SG) mRNAs and are found in ribonucleoprotein (RNP) complexes with the SG RBP. Mechanistically, G3BP1 binds to FA proteins in an RNA-dependent manner, and its RNA-binding and dimerization domains, essential for G3BP1 to form RNPs in SG, are required for FA localization and cell migration. We find that G3BP1 RNPs promote cell speed by enhancing FA protein mobility and FA size. These findings suggest a previously unappreciated role for G3BP1 RNPs in regulating FA function under non-stress conditions.
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Affiliation(s)
- Liana C Boraas
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT 06511, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Mengwei Hu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pieter Martino
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT 06511, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Lauren Thornton
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT 06511, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Charles E Vejnar
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Gang Zhen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Longhui Zeng
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Dylan M Parker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Andy L Cox
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xiaolei Su
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Christine Mayr
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Siyuan Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Stefania Nicoli
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT 06511, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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5
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Bucci J, Malouf L, Tanase DA, Farag N, Lamb JR, Rubio-Sánchez R, Gentile S, Del Grosso E, Kaminski CF, Di Michele L, Ricci F. Enzyme-Responsive DNA Condensates. J Am Chem Soc 2024; 146:31529-31537. [PMID: 39503320 PMCID: PMC11583213 DOI: 10.1021/jacs.4c08919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2024]
Abstract
Membrane-less compartments and organelles are widely acknowledged for their role in regulating cellular processes, and there is an urgent need to harness their full potential as both structural and functional elements of synthetic cells. Despite rapid progress, synthetically recapitulating the nonequilibrium, spatially distributed responses of natural membrane-less organelles remains elusive. Here, we demonstrate that the activity of nucleic-acid cleaving enzymes can be localized within DNA-based membrane-less compartments by sequestering the respective DNA or RNA substrates. Reaction-diffusion processes lead to complex nonequilibrium patterns, dependent on enzyme concentration. By arresting similar dynamic patterns, we spatially organize different substrates in concentric subcompartments, which can be then selectively addressed by different enzymes, demonstrating spatial distribution of enzymatic activity. Besides expanding our ability to engineer advanced biomimetic functions in synthetic membrane-less organelles, our results may facilitate the deployment of DNA-based condensates as microbioreactors or platforms for the detection and quantitation of enzymes and nucleic acids.
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Affiliation(s)
- Juliette Bucci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Layla Malouf
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Diana A Tanase
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Nada Farag
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Jacob R Lamb
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Roger Rubio-Sánchez
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Serena Gentile
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133, Italy
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6
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Kengmana E, Ornelas-Gatdula E, Chen KL, Schulman R. Spatial Control over Reactions via Localized Transcription within Membraneless DNA Nanostar Droplets. J Am Chem Soc 2024. [PMID: 39565729 DOI: 10.1021/jacs.4c07274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2024]
Abstract
Biomolecular condensates control where and how fast many chemical reactions occur in cells by partitioning reactants and catalysts, enabling simultaneous reactions in different spatial locations of a cell. Even without a membrane or physical barrier, the partitioning of the reactants can affect the rates of downstream reaction cascades in ways that depend on reaction location. Such effects can enable systems of biomolecular condensates to spatiotemporally orchestrate chemical reaction networks in cells to facilitate complex behaviors such as ribosome assembly. Here, we develop a system for developing such control in synthetic systems. We localize different transcription templates within different phase-separated, membraneless DNA nanostar (NS) droplets─programmable, in vitro liquid-liquid phase separation systems for partitioning of substrates and localization of reactions to membraneless droplets. When RNA produced within such droplets is also degraded in the bulk, droplet-localized transcription creates RNA concentration gradients. Consistent with the formation of these gradients, toehold-mediated strand displacement reactions involving transcripts are 2-fold slower far from the site of transcription than when nearby. We then demonstrate how multiple such gradients can form and be maintained independently by simultaneous transcription reactions occurring in tandem, each localized to different NS droplet types. Our results provide a means for constructing reaction systems in which different reactions are spatially localized and controlled without the need for physical membranes. This system also provides a means for generally studying how localized reactions and the exchange of reaction products might occur between protocells.
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Affiliation(s)
- Eli Kengmana
- Chemistry-Biology Interface Program, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Elysse Ornelas-Gatdula
- Chemistry-Biology Interface Program, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kuan-Lin Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Rebecca Schulman
- Chemistry-Biology Interface Program, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
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7
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Dizani M, Sorrentino D, Agarwal S, Stewart JM, Franco E. Protein Recruitment to Dynamic DNA-RNA Host Condensates. J Am Chem Soc 2024; 146:29344-29354. [PMID: 39418394 DOI: 10.1021/jacs.4c07555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
We describe the design and characterization of artificial nucleic acid condensates that are engineered to recruit and locally concentrate proteins of interest in vitro. These condensates emerge from the programmed interactions of nanostructured motifs assembling from three DNA strands and one RNA strand that can include an aptamer domain for the recruitment of a target protein. Because condensates are designed to form regardless of the presence of target protein, they function as "host" compartments. As a model protein, we consider Streptavidin (SA) due to its widespread use in binding assays. In addition to demonstrating protein recruitment, we describe two approaches to control the onset of condensation and protein recruitment. The first approach uses UV irradiation, a physical stimulus that bypasses the need for exchanging molecular inputs and is particularly convenient to control condensation in emulsion droplets. The second approach uses RNA transcription, a ubiquitous biochemical reaction that is central to the development of the next generation of living materials. We then show that the combination of RNA transcription and degradation leads to an autonomous dissipative system in which host condensates and protein recruitment occur transiently and that the host condensate size as well as the time scale of the transition can be controlled by the level of RNA-degrading enzyme. We conclude by demonstrating that biotinylated beads can be recruited to SA-host condensates, which may therefore find immediate use for the physical separation of a variety of biotin-tagged components.
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Affiliation(s)
- Mahdi Dizani
- Department of Mechanical & Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Daniela Sorrentino
- Department of Mechanical & Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Siddharth Agarwal
- Department of Mechanical & Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Jaimie Marie Stewart
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095, United States
| | - Elisa Franco
- Department of Mechanical & Aerospace Engineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Department of Bioengineering, University of California at Los Angeles, Los Angeles, California 90095, United States
- Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, United States
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