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Watanabe T, Sato Y, Otaka H, Kawamata I, Murata S, Nomura SIM. DNA Origami "Quick" Refolding Inside of a Micron-Sized Compartment. Molecules 2019; 25:E8. [PMID: 31861399 PMCID: PMC6983259 DOI: 10.3390/molecules25010008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023] Open
Abstract
Investigations into the refolding of DNA origami leads to the creation of reconstructable nanostructures and deepens our understanding of the sustainability of life. Here, we report the refolding of the DNA origami structure inside a micron-sized compartment. In our experiments, conventional DNA origami and truss-type DNA origami were annealed and purified to remove the excess staples in a test tube. The DNA origami was then encapsulated inside of a micron-sized compartment of water-in-oil droplets, composed of neutral surfactants. The re-annealing process was then performed to initiate refolding in the compartment. The resulting 100-nm-sized DNA nanostructures were observed using atomic force microscopy (AFM), and the qualities of their structures were evaluated based on their shape. We found that the refolding of the DNA origami structure was favored inside the droplets compared with refolding in bulk solution. The refolded structures were able to fold even under "quick" one-minute annealing conditions. In addition, the smaller droplets (average diameter: 1.2 µm) appeared to be more advantageous for the refolding of the origamis than larger droplets. These results are expected to contribute to understanding the principles of life phenomena based on multimolecular polymer self-assembly in a micron-sized compartment, and for the production and maintenance of artificially designed molecules.
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Affiliation(s)
- Taiki Watanabe
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Yusuke Sato
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
| | - Hayato Otaka
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Satoshi Murata
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
| | - Shin-Ichiro M. Nomura
- Department of Robotics, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan; (T.W.); (Y.S.); (H.O.); (I.K.); (S.M.)
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Measurement and Numerical Modeling of Cell-Free Protein Synthesis: Combinatorial Block-Variants of the PURE System. DATA 2018. [DOI: 10.3390/data3040041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Protein synthesis is at the core of bottom-up construction of artificial cellular mimics. Intriguingly, several reports have revealed that when a transcription–translation (TX–TL) kit is encapsulated inside lipid vesicles (or water-in-oil droplets), high between-vesicles diversity is observed in terms of protein synthesis rate and yield. Stochastic solute partition can be a major determinant of these observations. In order to verify that the variation of TX–TL components concentration brings about a variation of produced protein rate and yield, here we directly measure the performances of the ‘PURE system’ TX–TL kit variants. We report and share the kinetic traces of the enhanced Green Fluorescent Protein (eGFP) synthesis in bulk aqueous phase, for 27 combinatorial block-variants. The eGFP production is a sensitive function of TX–TL components concentration in the explored concentration range. Providing direct evidence that protein synthesis yield and rate actually mirror the TX–TL composition, this study supports the above-mentioned hypothesis on stochastic solute partition, without excluding, however, the contribution of other factors (e.g., inactivation of components).
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Yoshiyama T, Ichii T, Yomo T, Ichihashi N. Automated in vitro evolution of a translation-coupled RNA replication system in a droplet flow reactor. Sci Rep 2018; 8:11867. [PMID: 30089835 PMCID: PMC6082869 DOI: 10.1038/s41598-018-30374-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 01/23/2023] Open
Abstract
Automation is a useful strategy to make laborious evolutionary experiments faster and easier. To date, several types of continuous flow reactors have been developed for the automated evolutionary experiments of viruses and bacteria. However, the development of a flow reactor applicable to compartmentalized in vitro self-replication systems is still a challenge. In this study, we demonstrate automated in vitro evolution of a translation-coupled RNA system in a droplet flow reactor for the first time. This reactor contains approximately 1010 micro-scale droplets (average diameter is approximately 0.8 μm), which continuously fuse and divide among each other at a controllable rate. In the droplets, an RNA (artificial genomic RNA) replicate through the translation of self-encoded RNA replicase with spontaneously appearing parasitic RNA. We performed two automated replication experiments for more than 400 hours with different mixing intensities. We found that several mutations displayed increased frequencies in the genomic RNA populations and the dominant RNA mutants acquired the ability to replicate faster or acquired resistance to the parasitic RNA, demonstrating that Darwinian evolution occurred during the long-term replication. The droplet flow reactor we developed can be a useful tool to perform in vitro evolutionary experiments of translation-coupled systems.
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Affiliation(s)
- Tomoaki Yoshiyama
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Tetsuo Ichii
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Tetsuya Yomo
- Institute of Biology and Information Science, East China Normal University, 3663 Zhongshan North Rd., Shanghai, 200062, P.R. China
| | - Norikazu Ichihashi
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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Altamura E, Carrara P, D'Angelo F, Mavelli F, Stano P. Extrinsic stochastic factors (solute partition) in gene expression inside lipid vesicles and lipid-stabilized water-in-oil droplets: a review. Synth Biol (Oxf) 2018; 3:ysy011. [PMID: 32995519 PMCID: PMC7445889 DOI: 10.1093/synbio/ysy011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 06/18/2018] [Accepted: 06/21/2018] [Indexed: 11/13/2022] Open
Abstract
The encapsulation of transcription-translation (TX-TL) machinery inside lipid vesicles and water-in-oil droplets leads to the construction of cytomimetic systems (often called 'synthetic cells') for synthetic biology and origins-of-life research. A number of recent reports have shown that protein synthesis inside these microcompartments is highly diverse in terms of rate and amount of synthesized protein. Here, we discuss the role of extrinsic stochastic effects (i.e. solute partition phenomena) as relevant factors contributing to this pattern. We evidence and discuss cases where between-compartment diversity seems to exceed the expected theoretical values. The need of accurate determination of solute content inside individual vesicles or droplets is emphasized, aiming at validating or rejecting the predictions calculated from the standard fluctuations theory. At the same time, we promote the integration of experiments and stochastic modeling to reveal the details of solute encapsulation and intra-compartment reactions.
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Affiliation(s)
- Emiliano Altamura
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70126, Bari, Italy
| | - Paolo Carrara
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146, Rome, Italy
| | - Francesca D'Angelo
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146, Rome, Italy
| | - Fabio Mavelli
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70126, Bari, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Ecotekne, I-73100, Lecce, Italy
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Lee KH, Kwon JH, Kim DM. Direct translational analysis of electrophoretically separated DNA using a cell-free protein synthesis system. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2016.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Sharma B, Takamura Y, Shimoda T, Biyani M. A bulk sub-femtoliter in vitro compartmentalization system using super-fine electrosprays. Sci Rep 2016; 6:26257. [PMID: 27199080 PMCID: PMC4873800 DOI: 10.1038/srep26257] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/28/2016] [Indexed: 12/02/2022] Open
Abstract
The extreme miniaturization of biological and chemical assays in aqueous-droplet compartments enables spatiotemporal control for large-scale parallel experimentation and can thus permit new capabilities for "digitizing" directed molecular evolution methodologies. We report a remarkably facile bulk method to generate mega-scale monodisperse sub-femtoliter aqueous droplets by electrospray, using a prototype head with super-fine inkjet technology. Moreover, the electrostatic inkjet nozzle that injects the aqueous phase when immersed within an immiscible phase (an optimized oil/surfactant mixture) has the advantage of generating cell-like sub-femtoliter compartments for biomolecule encapsulation and successive biological and chemical reactions. Sub-femtoliter droplets of both liquid (water-in-oil, volumes ranging from 0.2 to 6.4 fL) and gel bead (agarose-in-oil, volume ranging from 0.3 to 15.6 fL) compartments with average sizes of 1.3 μm and 1.5 μm, respectively, were successfully generated using an inkjet nozzle at a speed of more than 10(5) droplets per second. We demonstrated the applicability of this system by synthesizing fluorescent proteins using a cell-free expression system inside electrosprayed sub-femtoliter droplets at an accelerated rate, thereby extending the utility of in vitro compartmentalization with improved analytical performance for a top-down artificial cellular system.
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Affiliation(s)
- Bineet Sharma
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Yuzuru Takamura
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Tatsuya Shimoda
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Manish Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
- Biyani BioSolutions Pvt. Ltd., Biyani Research Group, R-4, Sector 3, Vidhyadhar Nagar, Jaipur 302023, India
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