Structure of Biosystems and Molecular Materials - Radek Marek
CEITEC MU CEITEC MU
Structure of Biosystems and Molecular Materials - Radek Marek

PhD Topics

1. Designing modified DNA fragments

Supervisor: prof. Radek Marek

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

Keywords: modified DNA quadruplexes, NMR spectroscopy, structure and biophysical properties

 

2. Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling

Supervisor: prof. Radek Marek

Consultant: Jan Novotný, Ph.D.

Annotation:
The work will be focused on detailed structural characterisation of short purine oligonucleotides clipped by proper sequential motifs that induce parallel orientation of DNA strands.

For this purpose, NMR experiments combined with MD simulations will be employed. The effect of modifications of selected nucleotides on the structural properties of designed models will be investigated to gain deeper understanding of key noncovalent interactions that contribute to the folding of such systems.

Reference:
William Copp, Alexey Y. Denisov, Jingwei Xie, Anne M. Noronha, Christopher Liczner, Nozhat Safaee, Christopher J. Wilds, Kalle Gehring; Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA. Nucleic Acids Research, 2017, 45(17),10321–1033.

Keywords: oligonucleotides, MD simulations, molecular modelling, NMR spectroscopy