HomePh.D. Study at IOCBTopics 2019Physical and Computational Chemistry

Physical and Computational Chemistry

Tutor Dr. Vladimír Sychrovský

Petr Bouř

Topic Application of metallo-DNA in nanoelectronics
Faculty MFF UK

Recent advances in chemistry of nucleic acids enabled preparation of chemically modified DNA and RNA molecules including various types of metal-mediated base pairs (M-base pairs) – the M-DNA/RNA molecules. Importantly, the M-base pairs involving regular DNA bases linked by Hg(II) and Ag(I) metals, T-Hg-T and C-Ag-C, perfectly fit in canonical duplex due to very similar spatial occupations as compared to their canonical variants T-A and C-G. Moreover, the metal array aligned along DNA helical axis is shielded from the solvent. Introducing the heavy metals in consecutive M-base pairs illuminated effect of “metallophilic attraction” on stability of M-DNA due to the relativistic effects. The previous studies on chemistry, structure, spectroscopy and thermodynamics of M-nucleic acids highlighted their favorable physicochemical properties with regard to nanoelectronic applications, e.g. in the form of molecular wire as conductance of the normal nucleic acids is known to be small. This Ph.D. project will be focused on theoretical modelling of physicochemical properties, and particularly on charge-transport properties of M-DNAs towards their optimization as functional molecules/nanodevices. Theoretical modelling will be conducted in close collaboration with domestic and Japanese experimental laboratories.

Leading references
1. Tanaka Y., et al. Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs” Chem. Commun., 51, (2015), pp 17343-17360.
2. Dairaku T., Furuita K., Sato H., Sebera J., Nakashima K., Ono A., Sychrovsky V., Kojima C., Tanaka Y., “Hg-II/Ag-I-mediated base pairs and their NMR spectroscopic studies”, Inorg. Chim. Acta, 452, (2016), pp 34-42. 
3. Sebera J., et al. Formation of a Thymine-Hg-II-Thymine Metal-Mediated DNA Base Pair: Proposal and Theoretical Calculation of the Reaction Pathway, Chem.-Eur. J.,19, (2013), pp 9884-9894.
4. Yamaguchi H., et al. The structure of metallo-DNA with consecutive thymine-Hg-II-thymine base pairs explains positive entropy for the metallo base pair formation, Nucleic Acids Res., 42, (2014), pp 4094-4099.
5. Benda L., et al. On the role of mercury in the non-covalent stabilisation of consecutive U-Hg(II)-U metal-mediated nucleic acid base pairs: metallophilic attraction enters the world of nucleic acids, Physical Chemistry Chemical Physics, 13, (2011), pp 100-103.
6. Kratochvilova I., et al. Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns, Journal of Physical Chemistry B, 114, (2010), pp 5196-5205.
7. Kratochvilova I., et al. Theoretical and Experimental Study of Charge Transfer through DNA: Impact of Mercury Mediated T-Hg-T Base Pair, Journal of Physical Chemistry B, 118, (2014), pp 5374-5381.