• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Development of an efficient method combining quantum chemistry and machine learning to evolve PCR technology and gene mutation analysis

Research Project

Project/Area Number 22KJ2450
Project/Area Number (Other) 22J13006 (2022)
Research Category

Grant-in-Aid for JSPS Fellows

Allocation TypeMulti-year Fund (2023)
Single-year Grants (2022)
Section国内
Review Section Basic Section 61030:Intelligent informatics-related
Research InstitutionKyushu University

Principal Investigator

IVONINA Mariia  九州大学, 総合理工学府, 特別研究員(PD)

Project Period (FY) 2023-03-08 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥1,700,000 (Direct Cost: ¥1,700,000)
Fiscal Year 2023: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2022: ¥900,000 (Direct Cost: ¥900,000)
KeywordsSARS-CoV-2 / Methylated DNA / TS/TB / Molecular Dynamics / Binding energy / DNA mutations / O6-methylguanine / Quantum chemistry / TS/TB analysis / Orbital interactions
Outline of Research at the Start

I will create a computer model of DNA containing mutations and special ligands that can bind to mutations. Then I will collect data on the DNA-ligand interaction and analyze it using quantum chemistry and machine learning. Finally, I will design drug molecules that can recognize dangerous mutations.

Outline of Annual Research Achievements

In FY2023, we optimized the TS/TB algorithm and developed TS/TB-based binding energy decomposition analysis (TS/TB-EDA). This approach was successfully used to identify the primary cause of mutations in methylated DNA. The results will be published as soon as ELG-TS/TB combined technique is patented. Another research target, SARS-CoV-2 RNA, was studied while visiting Stockholm University from December 2023 to February 2024 and receiving guidance from a local research group on how to analyze large-scale biomolecules by MD calculations. As a result, the shape of SARS-CoV-2 RNA pseudoknot was obtained using MD. The interaction of pseudoknots with drug molecules was also studied. Next, the TS/TB-EDA will be applied to reveal driving force of interaction between pseudoknot and drug molecules.

Report

(2 results)
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • Research Products

    (4 results)

All 2023 2022

All Presentation (4 results)

  • [Presentation] "Mutagenesis in methylated DNA: a quantum chemical insight via Through-space/bond orbital interaction analysis"2023

    • Author(s)
      IVONINA Mariia, 折本 裕一, 青木 百 合子
    • Organizer
      第17回分子科学討論会
    • Related Report
      2023 Annual Research Report
  • [Presentation] "Through-space/Through-bond method for analyzing molecular orbital interactions and its application to DNA mutations"2023

    • Author(s)
      M. Ivonina, Y. Orimoto, Y. Aoki.
    • Organizer
      10th Asia Pacific Association of Theoretical and Computational Chemistry (APATCC-10)
    • Related Report
      2022 Annual Research Report
  • [Presentation] "Exploring the mutagenesis mechanism in DNA damaged by O6-methylguanine via through-space/bond orbital interaction analysis"2022

    • Author(s)
      M. Ivonina, Y. Orimoto, Y. Aoki.
    • Organizer
      第17回分子科学討論会 9月2022横浜
    • Related Report
      2022 Annual Research Report
  • [Presentation] "Analyzing chemical bonds via “Through-space/Through-bond” method: application to DNA mutations"2022

    • Author(s)
      M. Ivonina, Y. Orimoto, Y. Aoki.
    • Organizer
      High Performance Computing Summer School (HPCSS)
    • Related Report
      2022 Annual Research Report

URL: 

Published: 2022-04-28   Modified: 2024-12-25  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi