Overview
Doctoral study program: Life Sciences (Faculty of Science, Masaryk University)
Research area: Structural Biology
Supervisor: Radek Marek
Annotation
Novel forms of nucleotides 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) and molecular dynamics. Available candidates of modified nucleobases and sugars will be investigated 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, 2021, 61, 211-222. 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, 2017, 23, 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, 2016, 22, 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, 2015, 21, 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, 2015, 21, 17933-17943. doi:10.1002/chem.201502977.
Funding: RG budget, Czech Science Foundation
Requirements on candidates: Computational and quantum chemistry, structural chemistry or biology
Keywords: DNA, base pairing, molecular modelling, quantum chemistry
Information on the supervisor: Researcher ID: D-6929-2012
Information about the application process: https://www.ceitec.eu/ls-mm-phd/
Application webpage: https://www.ceitec.eu/designing-modified-dna-fragments/t11451
