Supervisor: Radek Marek

Annotation: The novel forms of nucleotide moieties will be incorporated in silico in oligomers with sequences relevant for biosystems. The biocompatibility of artificial building blocks will be evaluated using advanced methods of quantum chemistry that provide also analytical tools for investigation of crucial noncovalent interactions. Available candidates of modified nucleobases and sugars will be studied experimentally by using NMR spectroscopy in solution.

Recommended literature:

  • CUYACOT, Ben J.R., Ivo DURNÍK, Cina FOROUTAN-NEJAD and Radek MAREK. Anatomy of Base Pairing in DNA by Interacting Quantum Atoms, Journal of Chemical Information and Modeling, American Chemical Society, 2020, vol. 60, doi:10.1021/acs.jcim.0c00642.
  • YURENKO, Yevgen, Jan NOVOTNÝ and Radek MAREK. Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models. Chemistry – A European Journal, Wiley, 2017, vol. 23, p. 5573-5584. doi:10.1002/chem.201700236.
  • DUREC, Matúš, Francesco ZACCARIA, Célia FONSECA GUERRA and Radek MAREK. Modified guanines as constituents of smart ligands for nucleic acid quadruplexes. Chemistry – A European Journal, Weinheim: Wiley-VCH, 2016, vol. 22, p. 10912-10922. doi:10.1002/chem.201601608.
  • BAZZI, Sophia, Jan NOVOTNÝ, Yevgen YURENKO and Radek MAREK. Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands. Chemistry – A European Journal, Weinheim: Wiley-VCH, 2015, vol. 21, p. 9414-9425. doi:10.1002/chem.201500743.
  • YURENKO, Yevgen, Jan NOVOTNÝ, Vladimír SKLENÁŘ and Radek MAREK. Substituting CF2 for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions. Chemistry – A European Journal, WEINHEIM: Wiley, 2015, vol. 21, p. 17933-17943. doi:10.1002/chem.201502977.

Requirements on candidates:

Structural chemistry or biology, computational and quantum chemistry

More information on CEITEC PhD School website: https://ls-phd.ceitec.cz/ and Research Group website: https://www.ceitec.eu/structure-of-biosystems-and-molecular-materials/rg108.

In case you are interested. ​Please, submit your CV and motivation letter via Registration Form.

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