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Udono H, Nomura SIM, Takinoue M. Remote-controlled mechanical and directional motions of photoswitchable DNA condensates. Nat Commun 2025; 16:4479. [PMID: 40368917 PMCID: PMC12078559 DOI: 10.1038/s41467-025-59100-x] [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: 08/17/2022] [Accepted: 04/10/2025] [Indexed: 05/16/2025] Open
Abstract
Membrane-free synthetic DNA-based condensates enable programmable control of dynamic behaviors as shown by phase-separated condensates in biological cells. We demonstrate remote-controlled microflow using photocontrollable state transitions of DNA condensates, assembled from multi-branched DNA nanostructures via sticky-end (SE) hybridization. Introducing azobenzene into SEs enables their photoswitchable binding affinity, which underlies photoreversible fluidity of the resulting condensates that transition between gel/liquid/dissociated states in a wavelength-dependent manner. Leveraging base-sequence programmability, spatially coupled orthogonal DNA condensates with divergent photoresponsive capabilities perform multi-modal mechanical actions that depend on azobenzene insertion sites in the SE, including switching flows radially expanding and converging under photoswitching. Localizing photoswitching within a DNA liquid condensate generates two distinct directional motions, whose contrasting morphology, direction, and lifetime are determined by switching frequency. Numerical simulations reveal its regulatory role in weight-adjusting energy-exchanging and energy-dissipative interactions between the photoirradiated and unirradiated domains.
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Affiliation(s)
- Hirotake Udono
- Department of Computer Science, School of Computing, Institute of Science Tokyo, Yokohama, Kanagawa, 226-8501, Japan
| | - Shin-Ichiro M Nomura
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Masahiro Takinoue
- Department of Computer Science, School of Computing, Institute of Science Tokyo, Yokohama, Kanagawa, 226-8501, Japan.
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research (IIR), Institute of Science Tokyo, Yokohama, Kanagawa, 226-8501, Japan.
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Pongkulapa T, Yum JH, McLoughlin CD, Conklin B, Kumagai T, Goldston LL, Sugiyama H, Park S, Lee KB. NIR-Induced Photoswitching Hybrid DNA Nanoconstruct-Based Drug Delivery System for Spatiotemporal Control of Stem Cell Fate. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025:e2409530. [PMID: 40007062 DOI: 10.1002/smll.202409530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 01/20/2025] [Indexed: 02/27/2025]
Abstract
Precise spatiotemporal control of drug delivery is extremely valuable for regulating stem cell fate, particularly in stem cell differentiation. A novel near-infrared (NIR)-mediated spatiotemporal delivery system is reported combining photo-switchable arylazopyrazole (AAP)-containing DNA strands and upconversion nanoparticles (UCNPs). This nano-drug delivery system (NDDS) enables precise modulation of DNA duplex structures in response to NIR stimuli, overcoming the limitations of traditional UV-responsive systems. AAP derivatives with enhanced photoswitching efficiency (≈98%) and significantly improved cis-form stability are engineered. The successful delivery of curcumin, a neurogenic compound with an affinity for the minor groove of DNA, to human neural stem cells (NSCs) is achieved using UCNP-DNA-AAP constructs. Upon 980 nm NIR light exposure, UCNPs efficiently up-converted NIR to UV light, triggering AAP photoisomerization and DNA dissociation, thus releasing curcumin. This approach enabled efficient spatiotemporal control over NSC differentiation while facilitating neuroprotection. Immunofluorescence and gene expression analyses demonstrated enhanced neuronal mRNA levels and neurite outgrowth in treated cells. In short, the NIR-mediated photo-switchable NDDS offers a precise and innovative approach to control stem cell fate, enabling spatiotemporal regulation of cellular processes. This technology has significant potential applications in nanomedicine and neuroscience, where precise drug delivery is crucial for targeted neural interventions.
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Affiliation(s)
- Thanapat Pongkulapa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Callan D McLoughlin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Brandon Conklin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Tomotaka Kumagai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Li Ling Goldston
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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Jia L, Gao S, Qiao Y. Optical Control over Liquid–Liquid Phase Separation. SMALL METHODS 2024; 8:e2301724. [PMID: 38530063 DOI: 10.1002/smtd.202301724] [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: 12/12/2023] [Revised: 03/12/2024] [Indexed: 03/27/2024]
Abstract
Liquid-liquid phase separation (LLPS) is responsible for the emergence of intracellular membrane-less organelles and the development of coacervate protocells. Benefitting from the advantages of simplicity, precision, programmability, and noninvasiveness, light has become an effective tool to regulate the assembly dynamics of LLPS, and mediate various biochemical processes associated with LLPS. In this review, recent advances in optically controlling membrane-less organelles within living organisms are summarized, thereby modulating a series of biological processes including irreversible protein aggregation pathologies, transcription activation, metabolic flux, genomic rearrangements, and enzymatic reactions. Among these, the intracellular systems (i.e., optoDroplet, Corelet, PixELL, CasDrop, and other optogenetic systems) that enable the photo-mediated control over biomolecular condensation are highlighted. The design of photoactive complex coacervate protocells in laboratory settings by utilizing photochromic molecules such as azobenzene and diarylethene is further discussed. This review is expected to provide in-depth insights into phase separation-associated biochemical processes, bio-metabolism, and diseases.
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Affiliation(s)
- Liyan Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan Gao
- Department of Orthopedic, Peking University Third Hospital, Beijing, 100191, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Mukherjee A, Seyfried MD, Ravoo BJ. Azoheteroarene and Diazocine Molecular Photoswitches: Self-Assembly, Responsive Materials and Photopharmacology. Angew Chem Int Ed Engl 2023; 62:e202304437. [PMID: 37212536 DOI: 10.1002/anie.202304437] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/23/2023]
Abstract
Aromatic units tethered with an azo (-N=N-) functionality comprise a unique class of compounds, known as molecular photoswitches, exhibiting a reversible transformation between their E- and Z-isomers in response to photo-irradiation. Photoswitches have been explored extensively in the recent past to prepare dynamic self-assembled materials, optoelectronic devices, responsive biomaterials, and more. Most of such materials involve azobenzenes as the molecular photoswitch and to date, SciFinder lists more than 7000 articles and 1000 patents. Subsequently, a great deal of effort has been invested to improve the photo-isomerization efficiency and related mesoscopic properties of azobenzenes. Recently, azoheteroarenes and cyclic azobenzenes, such as arylazopyrazoles, arylazoisoxazoles, arylazopyridines, and diazocines, have emerged as second generation molecular photoswitches beyond conventional azobenzenes. These photoswitches offer distinct photoswitching behavior and responsive properties which make them highly promising candidates for multifaceted applications ranging from photoresponsive materials to photopharmacophores. In this minireview, we introduce the structural refinement and photoresponsive properties of azoheteroarenes and diazocines and summarize the state-of-the-art on utilizing these photoswitches as responsive building blocks in supramolecular assembly, material science and photopharmacology, highlighting their versatile photochemical behavior, enhanced functionality, and latest applications.
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Affiliation(s)
- Anurag Mukherjee
- Organisch-Chemisches Institut and Center for Soft Nanoscience (SoN), Westfälische Wilhelms-Universität Münster Corrensstraße 36, 48149, Münster, Germany
| | - Maximilian D Seyfried
- Organisch-Chemisches Institut and Center for Soft Nanoscience (SoN), Westfälische Wilhelms-Universität Münster Corrensstraße 36, 48149, Münster, Germany
| | - Bart Jan Ravoo
- Organisch-Chemisches Institut and Center for Soft Nanoscience (SoN), Westfälische Wilhelms-Universität Münster Corrensstraße 36, 48149, Münster, Germany
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Fraccia TP, Martin N. Non-enzymatic oligonucleotide ligation in coacervate protocells sustains compartment-content coupling. Nat Commun 2023; 14:2606. [PMID: 37160869 PMCID: PMC10169843 DOI: 10.1038/s41467-023-38163-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/18/2023] [Indexed: 05/11/2023] Open
Abstract
Modern cells are complex chemical compartments tightly regulated by an underlying DNA-encoded program. Achieving a form of coupling between molecular content, chemical reactions, and chassis in synthetic compartments represents a key step to the assembly of evolvable protocells but remains challenging. Here, we design coacervate droplets that promote non-enzymatic oligonucleotide polymerization and that restructure as a result of the reaction dynamics. More specifically, we rationally exploit complexation between end-reactive oligonucleotides able to stack into long physical polymers and a cationic azobenzene photoswitch to produce three different phases-soft solids, liquid crystalline or isotropic coacervates droplets-each of them having a different impact on the reaction efficiency. Dynamical modulation of coacervate assembly and dissolution via trans-cis azobenzene photo-isomerization is used to demonstrate cycles of light-actuated oligonucleotide ligation. Remarkably, changes in the population of polynucleotides during polymerization induce phase transitions due to length-based DNA self-sorting to produce multiphase coacervates. Overall, by combining a tight reaction-structure coupling and environmental responsiveness, our reactive coacervates provide a general route to the non-enzymatic synthesis of polynucleotides and pave the way to the emergence of a primitive compartment-content coupling in membrane-free protocells.
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Affiliation(s)
- Tommaso P Fraccia
- Institut Pierre-Gilles de Gennes, Chimie Biologie et Innovation, UMR 8231, ESPCI Paris, PSL University, CNRS, 6 rue Jean Calvin, 75005, Paris, France.
- Department of Pharmacological and Biomolecular Sciences, University of Milano, 20133, Milano, Italy.
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France.
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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: 18] [Impact Index Per Article: 9.0] [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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