2023 Fiscal Year Annual Research Report
An integrated approach for mapping RNA protein interactions in the ribosome
| Project/Area Number |
22K19291
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| Research Institution | Kyoto University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
Packwood Daniel 京都大学, 高等研究院, 准教授 (40640884)
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| Project Period (FY) |
2022-06-30 – 2024-03-31
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| Keywords | ナノポアシークエンシング / リボソーム / RNA-たんぱく質相互作用 / ケミカルプローブ / バイオインフォマティクス |
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| Outline of Annual Research Achievements |
During this fiscal year, we accomplished the primary objective of our research: to develop an integrated approach to map RNA modifications and their interaction with proteins. Following the research plan, We have successfully designed, synthesized, and identified the novel bifunctional probe that interacts with an RNA structural modification and their interaction with a peptide sequence of ribosomal proteins. We have advanced an informatic software called Indo-C to distinguish characteristic current signal trace changes due to resulting covalent adducts from the original pattern during nanopore sequencing and achieved a single nucleotide prediction accuracy of 79% using an RNA-targeted CRISPR-CAS13a system. Furthermore, we extended our strategy to map 8-oxo-7,8-dihydroguanine at single-nucleotide resolution in synthesized DNA strands. During our project, we encountered a bottleneck with the compatibility of protein nanopores of smaller sizes with bulkier chemical probes that prompted us to devise a successfully funded proposal for developing a new biomolecular sequencing technology. Our team has already created programmable nanopores using nucleic acids in varied sizes, shapes and constrictions. We plan to demonstrate the sequencing ability of these new nanopores using DNA, RNA, RNA base, structural modifications, and RNA-protein interactions and verify its universal adaptability. Additionally, we summarized the results in a different but closely related theme of nanomaterials, bioinformatic, and selectively reactive chemicals as original articles and reviews.
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