Overview

Doctoral study program: Life Sciences (Faculty of Science, Masaryk University)

Supervisor: Assoc. Prof. Lukas Trantirek, Ph.D.

Annotation

Dynamic transitions between B-DNA and non-canonical DNA conformations, such as G-quadruplexes, i-motifs, and Z-DNA, contribute to the regulatory control of genome integrity and gene expression, playing an essential role in defense against invading pathogens. The function of these structures is linked to their dynamic polymorphism, which allows them to adapt sensitively to changes in the intracellular environment due to cellular stress and physiological oscillations. The project will explore the mechanisms of transferring information from the intracellular environment to the dynamic structural equilibria of DNA as the cell’s physiological state changes.

Recommended literature

  • Víšková et al. In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells. Nat Commun. 2024 Mar 5;15(1):1992.
  • Krafcikova et al. Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy. J Am Chem Soc. 2019 Aug 28;141(34):13281-13285.
  • Gajarsky et al. DNA Quadruplex Structure with a Unique Cation Dependency. Angew Chem Int Ed Engl. 2024 Feb 12;63(7):e202313226.

Research area: Cellular Structural Biology, RNA/nucleic acids research in health and disease

Keywords: Structural Biology; in-cell NMR spectroscopy; DNA; RNA

Funding of the PhD candidate: Czech Science Foundation (24-10605K)

Requirements for candidate

The candidate is expected to have theoretical and practical knowledge of biomolecular NMR spectroscopy and an interest in the biology of nucleic acids.

Information about the supervisor

Publication track record: https://pubmed.ncbi.nlm.nih.gov/?term=trantirek&sort=date

Supervision track record (2005–2023):

  • 8 Postdocs; 3 obtained independent academic positions at the research institutions abroad, 1 acquired job in a biotech company, 2 obtained senior research positions at national research institutions, 2 – currently supervised.
  • 11 Ph.D. students; 8 successfully graduated, 3 – currently supervised; (6 out of 8 graduated PhDs pursued their academic career at research institutions abroad.

Information about the application process: https://www.ceitec.eu/ls-mm-phd/

Application webpage: https://www.ceitec.eu/nucleic-acids-sensing/t11441

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