2021 Fiscal Year Annual Research Report
Natural selection driven structure building in a tunable DNA-only system
| Project/Area Number |
17K00399
|
|---|
| Research Institution | Ochanomizu University |
|---|
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, 講師 (10749659)
|
|---|
| Project Period (FY) |
2017-04-01 – 2022-03-31
|
| Keywords | DNA Nanostructures / Molecular Robotics / Quality-Diversity / Robustness to failure / Stochastic Simulations / CRN |
|---|
| Outline of Annual Research Achievements |
Over the course of the year, we used the framework developed during the previous fiscal year to explore in a more in-depth fashions libraries of DNA strands. As a reminder, the framework consists three parts: (1) a quality-diversity exploration, (2) a sequence design optimization, and (3) a chemical reaction network and structure analysis module. The quality-diversity algorithm selects sets of strands from the library based on the potential nanostructures that could be formed from the set. The design optimization uses an off-the-shelf structure prediction algorithm to find DNA sequences that are most likely to actually generate the structures of interest. The last part analyzes how robust the creation of those structures is, in terms of reaction paths.
Since the past year, additional network analysis have been performed, yielding insights with respect to the types of structure that can be easily created from given libraries. Specifically, low number of independent domains favored linear polymer structures, while a larger number of domain types favored branching structures, although both types of structures can be theoretically obtained in all libraries explored. We expect those insights to help researcher designing libraries for the creation of DNA nano-structures.
|
