2017 Fiscal Year Research-status Report
Natural selection driven structure building in a tunable DNA-only system
| Project/Area Number |
17K00399
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| Research Institution | Ochanomizu University |
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Principal Investigator |
オベル加藤 ナタナエル お茶の水女子大学, 基幹研究院, 助教 (10749659)
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| Project Period (FY) |
2017-04-01 – 2020-03-31
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| Keywords | DNA Nanostructures / Molecular Robotics / Evolvability / Origins of Life |
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| Outline of Annual Research Achievements |
The goal of this research project is to observe evolvability in a controlled molecular environment. During this year, in collaboration with Dr. N. Virgo and Dr. A. Baccouche (collaborators), we have made progress on both the experimental and theoretical side.
*Experimental: Set up a proof-of-concept experimental process; performed evolutionary cycles on multiple control systems (DNA origami, non-reactive set of DNA strands, polymerizing DNA strands); checked for correct behavior using fluorescence, gel electrophoresis and dynamic light scattering.
*Theoretical: Designed an abstract model for evolvability in the system (presented at an international conference); designed a molecular-level model for polymerizing DNA molecules; simulated the experimental controls, yielding compatible results.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
We are currently on par with the original schedule: both the experimental setup and models have been done. Experimental results are in concordance with prior expectations.
However, a few difficulties have come to our attention:
- The predictivity of the abstract model is low (it may determine that evolution will happen, but not the kind of structures created)
- The low level model is too computationally expensive to scale it to more complex systems.
- The current experimental setup is hard to automate and can only distinguish structures by size, which makes it hard to compare to the models.
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| Strategy for Future Research Activity |
During the next year, we plan to first solve the issues mentioned in the previous Section:
- Develop a coarse-grain model for the system. Such model would not be able to distinguish structures further than by size, which would make it easier to compare to experiments. It would also be much faster to simulate.
- Update the experimental setup to rely instead on microfluidics, similar to some of our recent work (Baccouche et al. Nature Protocols, 2017). This approach should solve the automation problem.
We also plan to use a "physical" model of the system, using mesoscopic 3D printed structures and magnets, which should be closer in behavior to the abstract model we developed. The 3D printed structures could then be directly implemented in-vitro with DNA origami and sticker strands.
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| Causes of Carryover |
On the first year, when noticing the experimental setup would be difficult to automate, we decided to not hire a technician, contrary to the original plan.
Residual money went instead to buying computer equipment for simulation and international collaboration (with Pr. N. Bredeche from Paris 6 University).
The reminder will be used in part to develop and test a new experimental setup, and to implement the mesoscopic physical model of the system.
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